Mercurial > repos > hogart > unafold
changeset 4:bda10049b902 draft
Uploaded correct files instead of GitHub fetched
| author | hogart |
|---|---|
| date | Tue, 10 Mar 2015 05:54:18 -0400 |
| parents | 188b9cec6b79 |
| children | 5f95a9afe2ee |
| files | LICENSE README.md unafold.sh unafold.xml |
| diffstat | 4 files changed, 423 insertions(+), 3978 deletions(-) [+] |
line wrap: on
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--- a/LICENSE Tue Mar 10 05:45:34 2015 -0400 +++ b/LICENSE Tue Mar 10 05:54:18 2015 -0400 @@ -1,1943 +1,340 @@ - - - -<!DOCTYPE html> -<html lang="en" class=""> - <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#"> - <meta charset='utf-8'> - <meta http-equiv="X-UA-Compatible" content="IE=edge"> - <meta http-equiv="Content-Language" content="en"> - - - <title>galaxy-tools-unafold/LICENSE at master · DrHogart/galaxy-tools-unafold · GitHub</title> - <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> - <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> - <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png"> - <link rel="apple-touch-icon" sizes="144x144" href="/apple-touch-icon-144.png"> - 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You can apply it to</td> - </tr> - <tr> - <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> - <td id="LC19" class="blob-code js-file-line">your programs, too.</td> - </tr> - <tr> - <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> - <td id="LC20" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> - <td id="LC21" class="blob-code js-file-line"> When we speak of free software, we are referring to freedom, not</td> - </tr> - <tr> - <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> - <td id="LC22" class="blob-code js-file-line">price. 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(Hereinafter, translation is included without limitation in</td> - </tr> - <tr> - <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> - <td id="LC70" class="blob-code js-file-line">the term "modification".) Each licensee is addressed as "you".</td> - </tr> - <tr> - <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> - <td id="LC71" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> - <td id="LC72" class="blob-code js-file-line">Activities other than copying, distribution and modification are not</td> - </tr> - <tr> - <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> - <td id="LC73" class="blob-code js-file-line">covered by this License; they are outside its scope. The act of</td> - </tr> - <tr> - <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> - <td id="LC74" class="blob-code js-file-line">running the Program is not restricted, and the output from the Program</td> - </tr> - <tr> - <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> - <td id="LC75" class="blob-code js-file-line">is covered only if its contents constitute a work based on the</td> - </tr> - <tr> - <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> - <td id="LC76" class="blob-code js-file-line">Program (independent of having been made by running the Program).</td> - </tr> - <tr> - <td id="L77" class="blob-num js-line-number" data-line-number="77"></td> - <td id="LC77" class="blob-code js-file-line">Whether that is true depends on what the Program does.</td> - </tr> - <tr> - <td id="L78" class="blob-num js-line-number" data-line-number="78"></td> - <td id="LC78" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L79" class="blob-num js-line-number" data-line-number="79"></td> - <td id="LC79" class="blob-code js-file-line"> 1. You may copy and distribute verbatim copies of the Program's</td> - </tr> - <tr> - <td id="L80" class="blob-num js-line-number" data-line-number="80"></td> - <td id="LC80" class="blob-code js-file-line">source code as you receive it, in any medium, provided that you</td> - </tr> - <tr> - <td id="L81" class="blob-num js-line-number" data-line-number="81"></td> - <td id="LC81" class="blob-code js-file-line">conspicuously and appropriately publish on each copy an appropriate</td> - </tr> - <tr> - <td id="L82" class="blob-num js-line-number" data-line-number="82"></td> - <td id="LC82" class="blob-code js-file-line">copyright notice and disclaimer of warranty; keep intact all the</td> - </tr> - <tr> - <td id="L83" class="blob-num js-line-number" data-line-number="83"></td> - <td id="LC83" class="blob-code js-file-line">notices that refer to this License and to the absence of any warranty;</td> - </tr> - <tr> - <td id="L84" class="blob-num js-line-number" data-line-number="84"></td> - <td id="LC84" class="blob-code js-file-line">and give any other recipients of the Program a copy of this License</td> - </tr> - <tr> - <td id="L85" class="blob-num js-line-number" data-line-number="85"></td> - <td id="LC85" class="blob-code js-file-line">along with the Program.</td> - </tr> - <tr> - <td id="L86" class="blob-num js-line-number" data-line-number="86"></td> - <td id="LC86" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L87" class="blob-num js-line-number" data-line-number="87"></td> - <td id="LC87" class="blob-code js-file-line">You may charge a fee for the physical act of transferring a copy, and</td> - </tr> - <tr> - <td id="L88" class="blob-num js-line-number" data-line-number="88"></td> - <td id="LC88" class="blob-code js-file-line">you may at your option offer warranty protection in exchange for a fee.</td> - </tr> - <tr> - <td id="L89" class="blob-num js-line-number" data-line-number="89"></td> - <td id="LC89" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L90" class="blob-num js-line-number" data-line-number="90"></td> - <td id="LC90" class="blob-code js-file-line"> 2. You may modify your copy or copies of the Program or any portion</td> - </tr> - <tr> - <td id="L91" class="blob-num js-line-number" data-line-number="91"></td> - <td id="LC91" class="blob-code js-file-line">of it, thus forming a work based on the Program, and copy and</td> - </tr> - <tr> - <td id="L92" class="blob-num js-line-number" data-line-number="92"></td> - <td id="LC92" class="blob-code js-file-line">distribute such modifications or work under the terms of Section 1</td> - </tr> - <tr> - <td id="L93" class="blob-num js-line-number" data-line-number="93"></td> - <td id="LC93" class="blob-code js-file-line">above, provided that you also meet all of these conditions:</td> - </tr> - <tr> - <td id="L94" class="blob-num js-line-number" data-line-number="94"></td> - <td id="LC94" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L95" class="blob-num js-line-number" data-line-number="95"></td> - <td id="LC95" class="blob-code js-file-line"> a) You must cause the modified files to carry prominent notices</td> - </tr> - <tr> - <td id="L96" class="blob-num js-line-number" data-line-number="96"></td> - <td id="LC96" class="blob-code js-file-line"> stating that you changed the files and the date of any change.</td> - </tr> - <tr> - <td id="L97" class="blob-num js-line-number" data-line-number="97"></td> - <td id="LC97" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L98" class="blob-num js-line-number" data-line-number="98"></td> - <td id="LC98" class="blob-code js-file-line"> b) You must cause any work that you distribute or publish, that in</td> - </tr> - <tr> - <td id="L99" class="blob-num js-line-number" data-line-number="99"></td> - <td id="LC99" class="blob-code js-file-line"> whole or in part contains or is derived from the Program or any</td> - </tr> - <tr> - <td id="L100" class="blob-num js-line-number" data-line-number="100"></td> - <td id="LC100" class="blob-code js-file-line"> part thereof, to be licensed as a whole at no charge to all third</td> - </tr> - <tr> - <td id="L101" class="blob-num js-line-number" data-line-number="101"></td> - <td id="LC101" class="blob-code js-file-line"> parties under the terms of this License.</td> - </tr> - <tr> - <td id="L102" class="blob-num js-line-number" data-line-number="102"></td> - <td id="LC102" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L103" class="blob-num js-line-number" data-line-number="103"></td> - <td id="LC103" class="blob-code js-file-line"> c) If the modified program normally reads commands interactively</td> - </tr> - <tr> - <td id="L104" class="blob-num js-line-number" data-line-number="104"></td> - <td id="LC104" class="blob-code js-file-line"> when run, you must cause it, when started running for such</td> - </tr> - <tr> - <td id="L105" class="blob-num js-line-number" data-line-number="105"></td> - <td id="LC105" class="blob-code js-file-line"> interactive use in the most ordinary way, to print or display an</td> - </tr> - <tr> - <td id="L106" class="blob-num js-line-number" data-line-number="106"></td> - <td id="LC106" class="blob-code js-file-line"> announcement including an appropriate copyright notice and a</td> - </tr> - <tr> - <td id="L107" class="blob-num js-line-number" data-line-number="107"></td> - <td id="LC107" class="blob-code js-file-line"> notice that there is no warranty (or else, saying that you provide</td> - </tr> - <tr> - <td id="L108" class="blob-num js-line-number" data-line-number="108"></td> - <td id="LC108" class="blob-code js-file-line"> a warranty) and that users may redistribute the program under</td> - </tr> - <tr> - <td id="L109" class="blob-num js-line-number" data-line-number="109"></td> - <td id="LC109" class="blob-code js-file-line"> these conditions, and telling the user how to view a copy of this</td> - </tr> - <tr> - <td id="L110" class="blob-num js-line-number" data-line-number="110"></td> - <td id="LC110" class="blob-code js-file-line"> License. (Exception: if the Program itself is interactive but</td> - </tr> - <tr> - <td id="L111" class="blob-num js-line-number" data-line-number="111"></td> - <td id="LC111" class="blob-code js-file-line"> does not normally print such an announcement, your work based on</td> - </tr> - <tr> - <td id="L112" class="blob-num js-line-number" data-line-number="112"></td> - <td id="LC112" class="blob-code js-file-line"> the Program is not required to print an announcement.)</td> - </tr> - <tr> - <td id="L113" class="blob-num js-line-number" data-line-number="113"></td> - <td id="LC113" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L114" class="blob-num js-line-number" data-line-number="114"></td> - <td id="LC114" class="blob-code js-file-line">These requirements apply to the modified work as a whole. If</td> - </tr> - <tr> - <td id="L115" class="blob-num js-line-number" data-line-number="115"></td> - <td id="LC115" class="blob-code js-file-line">identifiable sections of that work are not derived from the Program,</td> - </tr> - <tr> - <td id="L116" class="blob-num js-line-number" data-line-number="116"></td> - <td id="LC116" class="blob-code js-file-line">and can be reasonably considered independent and separate works in</td> - </tr> - <tr> - <td id="L117" class="blob-num js-line-number" data-line-number="117"></td> - <td id="LC117" class="blob-code js-file-line">themselves, then this License, and its terms, do not apply to those</td> - </tr> - <tr> - <td id="L118" class="blob-num js-line-number" data-line-number="118"></td> - <td id="LC118" class="blob-code js-file-line">sections when you distribute them as separate works. But when you</td> - </tr> - <tr> - <td id="L119" class="blob-num js-line-number" data-line-number="119"></td> - <td id="LC119" class="blob-code js-file-line">distribute the same sections as part of a whole which is a work based</td> - </tr> - <tr> - <td id="L120" class="blob-num js-line-number" data-line-number="120"></td> - <td id="LC120" class="blob-code js-file-line">on the Program, the distribution of the whole must be on the terms of</td> - </tr> - <tr> - <td id="L121" class="blob-num js-line-number" data-line-number="121"></td> - <td id="LC121" class="blob-code js-file-line">this License, whose permissions for other licensees extend to the</td> - </tr> - <tr> - <td id="L122" class="blob-num js-line-number" data-line-number="122"></td> - <td id="LC122" class="blob-code js-file-line">entire whole, and thus to each and every part regardless of who wrote it.</td> - </tr> - <tr> - <td id="L123" class="blob-num js-line-number" data-line-number="123"></td> - <td id="LC123" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L124" class="blob-num js-line-number" data-line-number="124"></td> - <td id="LC124" class="blob-code js-file-line">Thus, it is not the intent of this section to claim rights or contest</td> - </tr> - <tr> - <td id="L125" class="blob-num js-line-number" data-line-number="125"></td> - <td id="LC125" class="blob-code js-file-line">your rights to work written entirely by you; rather, the intent is to</td> - </tr> - <tr> - <td id="L126" class="blob-num js-line-number" data-line-number="126"></td> - <td id="LC126" class="blob-code js-file-line">exercise the right to control the distribution of derivative or</td> - </tr> - <tr> - <td id="L127" class="blob-num js-line-number" data-line-number="127"></td> - <td id="LC127" class="blob-code js-file-line">collective works based on the Program.</td> - </tr> - <tr> - <td id="L128" class="blob-num js-line-number" data-line-number="128"></td> - <td id="LC128" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L129" class="blob-num js-line-number" data-line-number="129"></td> - <td id="LC129" class="blob-code js-file-line">In addition, mere aggregation of another work not based on the Program</td> - </tr> - <tr> - <td id="L130" class="blob-num js-line-number" data-line-number="130"></td> - <td id="LC130" class="blob-code js-file-line">with the Program (or with a work based on the Program) on a volume of</td> - </tr> - <tr> - <td id="L131" class="blob-num js-line-number" data-line-number="131"></td> - <td id="LC131" class="blob-code js-file-line">a storage or distribution medium does not bring the other work under</td> - </tr> - <tr> - <td id="L132" class="blob-num js-line-number" data-line-number="132"></td> - <td id="LC132" class="blob-code js-file-line">the scope of this License.</td> - </tr> - <tr> - <td id="L133" class="blob-num js-line-number" data-line-number="133"></td> - <td id="LC133" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L134" class="blob-num js-line-number" data-line-number="134"></td> - <td id="LC134" class="blob-code js-file-line"> 3. You may copy and distribute the Program (or a work based on it,</td> - </tr> - <tr> - <td id="L135" class="blob-num js-line-number" data-line-number="135"></td> - <td id="LC135" class="blob-code js-file-line">under Section 2) in object code or executable form under the terms of</td> - </tr> - <tr> - <td id="L136" class="blob-num js-line-number" data-line-number="136"></td> - <td id="LC136" class="blob-code js-file-line">Sections 1 and 2 above provided that you also do one of the following:</td> - </tr> - <tr> - <td id="L137" class="blob-num js-line-number" data-line-number="137"></td> - <td id="LC137" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L138" class="blob-num js-line-number" data-line-number="138"></td> - <td id="LC138" class="blob-code js-file-line"> a) Accompany it with the complete corresponding machine-readable</td> - </tr> - <tr> - <td id="L139" class="blob-num js-line-number" data-line-number="139"></td> - <td id="LC139" class="blob-code js-file-line"> source code, which must be distributed under the terms of Sections</td> - </tr> - <tr> - <td id="L140" class="blob-num js-line-number" data-line-number="140"></td> - <td id="LC140" class="blob-code js-file-line"> 1 and 2 above on a medium customarily used for software interchange; or,</td> - </tr> - <tr> - <td id="L141" class="blob-num js-line-number" data-line-number="141"></td> - <td id="LC141" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L142" class="blob-num js-line-number" data-line-number="142"></td> - <td id="LC142" class="blob-code js-file-line"> b) Accompany it with a written offer, valid for at least three</td> - </tr> - <tr> - <td id="L143" class="blob-num js-line-number" data-line-number="143"></td> - <td id="LC143" class="blob-code js-file-line"> years, to give any third party, for a charge no more than your</td> - </tr> - <tr> - <td id="L144" class="blob-num js-line-number" data-line-number="144"></td> - <td id="LC144" class="blob-code js-file-line"> cost of physically performing source distribution, a complete</td> - </tr> - <tr> - <td id="L145" class="blob-num js-line-number" data-line-number="145"></td> - <td id="LC145" class="blob-code js-file-line"> machine-readable copy of the corresponding source code, to be</td> - </tr> - <tr> - <td id="L146" class="blob-num js-line-number" data-line-number="146"></td> - <td id="LC146" class="blob-code js-file-line"> distributed under the terms of Sections 1 and 2 above on a medium</td> - </tr> - <tr> - <td id="L147" class="blob-num js-line-number" data-line-number="147"></td> - <td id="LC147" class="blob-code js-file-line"> customarily used for software interchange; or,</td> - </tr> - <tr> - <td id="L148" class="blob-num js-line-number" data-line-number="148"></td> - <td id="LC148" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L149" class="blob-num js-line-number" data-line-number="149"></td> - <td id="LC149" class="blob-code js-file-line"> c) Accompany it with the information you received as to the offer</td> - </tr> - <tr> - <td id="L150" class="blob-num js-line-number" data-line-number="150"></td> - <td id="LC150" class="blob-code js-file-line"> to distribute corresponding source code. (This alternative is</td> - </tr> - <tr> - <td id="L151" class="blob-num js-line-number" data-line-number="151"></td> - <td id="LC151" class="blob-code js-file-line"> allowed only for noncommercial distribution and only if you</td> - </tr> - <tr> - <td id="L152" class="blob-num js-line-number" data-line-number="152"></td> - <td id="LC152" class="blob-code js-file-line"> received the program in object code or executable form with such</td> - </tr> - <tr> - <td id="L153" class="blob-num js-line-number" data-line-number="153"></td> - <td id="LC153" class="blob-code js-file-line"> an offer, in accord with Subsection b above.)</td> - </tr> - <tr> - <td id="L154" class="blob-num js-line-number" data-line-number="154"></td> - <td id="LC154" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L155" class="blob-num js-line-number" data-line-number="155"></td> - <td id="LC155" class="blob-code js-file-line">The source code for a work means the preferred form of the work for</td> - </tr> - <tr> - <td id="L156" class="blob-num js-line-number" data-line-number="156"></td> - <td id="LC156" class="blob-code js-file-line">making modifications to it. For an executable work, complete source</td> - </tr> - <tr> - <td id="L157" class="blob-num js-line-number" data-line-number="157"></td> - <td id="LC157" class="blob-code js-file-line">code means all the source code for all modules it contains, plus any</td> - </tr> - <tr> - <td id="L158" class="blob-num js-line-number" data-line-number="158"></td> - <td id="LC158" class="blob-code js-file-line">associated interface definition files, plus the scripts used to</td> - </tr> - <tr> - <td id="L159" class="blob-num js-line-number" data-line-number="159"></td> - <td id="LC159" class="blob-code js-file-line">control compilation and installation of the executable. However, as a</td> - </tr> - <tr> - <td id="L160" class="blob-num js-line-number" data-line-number="160"></td> - <td id="LC160" class="blob-code js-file-line">special exception, the source code distributed need not include</td> - </tr> - <tr> - <td id="L161" class="blob-num js-line-number" data-line-number="161"></td> - <td id="LC161" class="blob-code js-file-line">anything that is normally distributed (in either source or binary</td> - </tr> - <tr> - <td id="L162" class="blob-num js-line-number" data-line-number="162"></td> - <td id="LC162" class="blob-code js-file-line">form) with the major components (compiler, kernel, and so on) of the</td> - </tr> - <tr> - <td id="L163" class="blob-num js-line-number" data-line-number="163"></td> - <td id="LC163" class="blob-code js-file-line">operating system on which the executable runs, unless that component</td> - </tr> - <tr> - <td id="L164" class="blob-num js-line-number" data-line-number="164"></td> - <td id="LC164" class="blob-code js-file-line">itself accompanies the executable.</td> - </tr> - <tr> - <td id="L165" class="blob-num js-line-number" data-line-number="165"></td> - <td id="LC165" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L166" class="blob-num js-line-number" data-line-number="166"></td> - <td id="LC166" class="blob-code js-file-line">If distribution of executable or object code is made by offering</td> - </tr> - <tr> - <td id="L167" class="blob-num js-line-number" data-line-number="167"></td> - <td id="LC167" class="blob-code js-file-line">access to copy from a designated place, then offering equivalent</td> - </tr> - <tr> - <td id="L168" class="blob-num js-line-number" data-line-number="168"></td> - <td id="LC168" class="blob-code js-file-line">access to copy the source code from the same place counts as</td> - </tr> - <tr> - <td id="L169" class="blob-num js-line-number" data-line-number="169"></td> - <td id="LC169" class="blob-code js-file-line">distribution of the source code, even though third parties are not</td> - </tr> - <tr> - <td id="L170" class="blob-num js-line-number" data-line-number="170"></td> - <td id="LC170" class="blob-code js-file-line">compelled to copy the source along with the object code.</td> - </tr> - <tr> - <td id="L171" class="blob-num js-line-number" data-line-number="171"></td> - <td id="LC171" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L172" class="blob-num js-line-number" data-line-number="172"></td> - <td id="LC172" class="blob-code js-file-line"> 4. You may not copy, modify, sublicense, or distribute the Program</td> - </tr> - <tr> - <td id="L173" class="blob-num js-line-number" data-line-number="173"></td> - <td id="LC173" class="blob-code js-file-line">except as expressly provided under this License. Any attempt</td> - </tr> - <tr> - <td id="L174" class="blob-num js-line-number" data-line-number="174"></td> - <td id="LC174" class="blob-code js-file-line">otherwise to copy, modify, sublicense or distribute the Program is</td> - </tr> - <tr> - <td id="L175" class="blob-num js-line-number" data-line-number="175"></td> - <td id="LC175" class="blob-code js-file-line">void, and will automatically terminate your rights under this License.</td> - </tr> - <tr> - <td id="L176" class="blob-num js-line-number" data-line-number="176"></td> - <td id="LC176" class="blob-code js-file-line">However, parties who have received copies, or rights, from you under</td> - </tr> - <tr> - <td id="L177" class="blob-num js-line-number" data-line-number="177"></td> - <td id="LC177" class="blob-code js-file-line">this License will not have their licenses terminated so long as such</td> - </tr> - <tr> - <td id="L178" class="blob-num js-line-number" data-line-number="178"></td> - <td id="LC178" class="blob-code js-file-line">parties remain in full compliance.</td> - </tr> - <tr> - <td id="L179" class="blob-num js-line-number" data-line-number="179"></td> - <td id="LC179" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L180" class="blob-num js-line-number" data-line-number="180"></td> - <td id="LC180" class="blob-code js-file-line"> 5. You are not required to accept this License, since you have not</td> - </tr> - <tr> - <td id="L181" class="blob-num js-line-number" data-line-number="181"></td> - <td id="LC181" class="blob-code js-file-line">signed it. However, nothing else grants you permission to modify or</td> - </tr> - <tr> - <td id="L182" class="blob-num js-line-number" data-line-number="182"></td> - <td id="LC182" class="blob-code js-file-line">distribute the Program or its derivative works. These actions are</td> - </tr> - <tr> - <td id="L183" class="blob-num js-line-number" data-line-number="183"></td> - <td id="LC183" class="blob-code js-file-line">prohibited by law if you do not accept this License. Therefore, by</td> - </tr> - <tr> - <td id="L184" class="blob-num js-line-number" data-line-number="184"></td> - <td id="LC184" class="blob-code js-file-line">modifying or distributing the Program (or any work based on the</td> - </tr> - <tr> - <td id="L185" class="blob-num js-line-number" data-line-number="185"></td> - <td id="LC185" class="blob-code js-file-line">Program), you indicate your acceptance of this License to do so, and</td> - </tr> - <tr> - <td id="L186" class="blob-num js-line-number" data-line-number="186"></td> - <td id="LC186" class="blob-code js-file-line">all its terms and conditions for copying, distributing or modifying</td> - </tr> - <tr> - <td id="L187" class="blob-num js-line-number" data-line-number="187"></td> - <td id="LC187" class="blob-code js-file-line">the Program or works based on it.</td> - </tr> - <tr> - <td id="L188" class="blob-num js-line-number" data-line-number="188"></td> - <td id="LC188" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L189" class="blob-num js-line-number" data-line-number="189"></td> - <td id="LC189" class="blob-code js-file-line"> 6. Each time you redistribute the Program (or any work based on the</td> - </tr> - <tr> - <td id="L190" class="blob-num js-line-number" data-line-number="190"></td> - <td id="LC190" class="blob-code js-file-line">Program), the recipient automatically receives a license from the</td> - </tr> - <tr> - <td id="L191" class="blob-num js-line-number" data-line-number="191"></td> - <td id="LC191" class="blob-code js-file-line">original licensor to copy, distribute or modify the Program subject to</td> - </tr> - <tr> - <td id="L192" class="blob-num js-line-number" data-line-number="192"></td> - <td id="LC192" class="blob-code js-file-line">these terms and conditions. You may not impose any further</td> - </tr> - <tr> - <td id="L193" class="blob-num js-line-number" data-line-number="193"></td> - <td id="LC193" class="blob-code js-file-line">restrictions on the recipients' exercise of the rights granted herein.</td> - </tr> - <tr> - <td id="L194" class="blob-num js-line-number" data-line-number="194"></td> - <td id="LC194" class="blob-code js-file-line">You are not responsible for enforcing compliance by third parties to</td> - </tr> - <tr> - <td id="L195" class="blob-num js-line-number" data-line-number="195"></td> - <td id="LC195" class="blob-code js-file-line">this License.</td> - </tr> - <tr> - <td id="L196" class="blob-num js-line-number" data-line-number="196"></td> - <td id="LC196" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L197" class="blob-num js-line-number" data-line-number="197"></td> - <td id="LC197" class="blob-code js-file-line"> 7. If, as a consequence of a court judgment or allegation of patent</td> - </tr> - <tr> - <td id="L198" class="blob-num js-line-number" data-line-number="198"></td> - <td id="LC198" class="blob-code js-file-line">infringement or for any other reason (not limited to patent issues),</td> - </tr> - <tr> - <td id="L199" class="blob-num js-line-number" data-line-number="199"></td> - <td id="LC199" class="blob-code js-file-line">conditions are imposed on you (whether by court order, agreement or</td> - </tr> - <tr> - <td id="L200" class="blob-num js-line-number" data-line-number="200"></td> - <td id="LC200" class="blob-code js-file-line">otherwise) that contradict the conditions of this License, they do not</td> - </tr> - <tr> - <td id="L201" class="blob-num js-line-number" data-line-number="201"></td> - <td id="LC201" class="blob-code js-file-line">excuse you from the conditions of this License. If you cannot</td> - </tr> - <tr> - <td id="L202" class="blob-num js-line-number" data-line-number="202"></td> - <td id="LC202" class="blob-code js-file-line">distribute so as to satisfy simultaneously your obligations under this</td> - </tr> - <tr> - <td id="L203" class="blob-num js-line-number" data-line-number="203"></td> - <td id="LC203" class="blob-code js-file-line">License and any other pertinent obligations, then as a consequence you</td> - </tr> - <tr> - <td id="L204" class="blob-num js-line-number" data-line-number="204"></td> - <td id="LC204" class="blob-code js-file-line">may not distribute the Program at all. For example, if a patent</td> - </tr> - <tr> - <td id="L205" class="blob-num js-line-number" data-line-number="205"></td> - <td id="LC205" class="blob-code js-file-line">license would not permit royalty-free redistribution of the Program by</td> - </tr> - <tr> - <td id="L206" class="blob-num js-line-number" data-line-number="206"></td> - <td id="LC206" class="blob-code js-file-line">all those who receive copies directly or indirectly through you, then</td> - </tr> - <tr> - <td id="L207" class="blob-num js-line-number" data-line-number="207"></td> - <td id="LC207" class="blob-code js-file-line">the only way you could satisfy both it and this License would be to</td> - </tr> - <tr> - <td id="L208" class="blob-num js-line-number" data-line-number="208"></td> - <td id="LC208" class="blob-code js-file-line">refrain entirely from distribution of the Program.</td> - </tr> - <tr> - <td id="L209" class="blob-num js-line-number" data-line-number="209"></td> - <td id="LC209" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L210" class="blob-num js-line-number" data-line-number="210"></td> - <td id="LC210" class="blob-code js-file-line">If any portion of this section is held invalid or unenforceable under</td> - </tr> - <tr> - <td id="L211" class="blob-num js-line-number" data-line-number="211"></td> - <td id="LC211" class="blob-code js-file-line">any particular circumstance, the balance of the section is intended to</td> - </tr> - <tr> - <td id="L212" class="blob-num js-line-number" data-line-number="212"></td> - <td id="LC212" class="blob-code js-file-line">apply and the section as a whole is intended to apply in other</td> - </tr> - <tr> - <td id="L213" class="blob-num js-line-number" data-line-number="213"></td> - <td id="LC213" class="blob-code js-file-line">circumstances.</td> - </tr> - <tr> - <td id="L214" class="blob-num js-line-number" data-line-number="214"></td> - <td id="LC214" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L215" class="blob-num js-line-number" data-line-number="215"></td> - <td id="LC215" class="blob-code js-file-line">It is not the purpose of this section to induce you to infringe any</td> - </tr> - <tr> - <td id="L216" class="blob-num js-line-number" data-line-number="216"></td> - <td id="LC216" class="blob-code js-file-line">patents or other property right claims or to contest validity of any</td> - </tr> - <tr> - <td id="L217" class="blob-num js-line-number" data-line-number="217"></td> - <td id="LC217" class="blob-code js-file-line">such claims; this section has the sole purpose of protecting the</td> - </tr> - <tr> - <td id="L218" class="blob-num js-line-number" data-line-number="218"></td> - <td id="LC218" class="blob-code js-file-line">integrity of the free software distribution system, which is</td> - </tr> - <tr> - <td id="L219" class="blob-num js-line-number" data-line-number="219"></td> - <td id="LC219" class="blob-code js-file-line">implemented by public license practices. Many people have made</td> - </tr> - <tr> - <td id="L220" class="blob-num js-line-number" data-line-number="220"></td> - <td id="LC220" class="blob-code js-file-line">generous contributions to the wide range of software distributed</td> - </tr> - <tr> - <td id="L221" class="blob-num js-line-number" data-line-number="221"></td> - <td id="LC221" class="blob-code js-file-line">through that system in reliance on consistent application of that</td> - </tr> - <tr> - <td id="L222" class="blob-num js-line-number" data-line-number="222"></td> - <td id="LC222" class="blob-code js-file-line">system; it is up to the author/donor to decide if he or she is willing</td> - </tr> - <tr> - <td id="L223" class="blob-num js-line-number" data-line-number="223"></td> - <td id="LC223" class="blob-code js-file-line">to distribute software through any other system and a licensee cannot</td> - </tr> - <tr> - <td id="L224" class="blob-num js-line-number" data-line-number="224"></td> - <td id="LC224" class="blob-code js-file-line">impose that choice.</td> - </tr> - <tr> - <td id="L225" class="blob-num js-line-number" data-line-number="225"></td> - <td id="LC225" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L226" class="blob-num js-line-number" data-line-number="226"></td> - <td id="LC226" class="blob-code js-file-line">This section is intended to make thoroughly clear what is believed to</td> - </tr> - <tr> - <td id="L227" class="blob-num js-line-number" data-line-number="227"></td> - <td id="LC227" class="blob-code js-file-line">be a consequence of the rest of this License.</td> - </tr> - <tr> - <td id="L228" class="blob-num js-line-number" data-line-number="228"></td> - <td id="LC228" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L229" class="blob-num js-line-number" data-line-number="229"></td> - <td id="LC229" class="blob-code js-file-line"> 8. If the distribution and/or use of the Program is restricted in</td> - </tr> - <tr> - <td id="L230" class="blob-num js-line-number" data-line-number="230"></td> - <td id="LC230" class="blob-code js-file-line">certain countries either by patents or by copyrighted interfaces, the</td> - </tr> - <tr> - <td id="L231" class="blob-num js-line-number" data-line-number="231"></td> - <td id="LC231" class="blob-code js-file-line">original copyright holder who places the Program under this License</td> - </tr> - <tr> - <td id="L232" class="blob-num js-line-number" data-line-number="232"></td> - <td id="LC232" class="blob-code js-file-line">may add an explicit geographical distribution limitation excluding</td> - </tr> - <tr> - <td id="L233" class="blob-num js-line-number" data-line-number="233"></td> - <td id="LC233" class="blob-code js-file-line">those countries, so that distribution is permitted only in or among</td> - </tr> - <tr> - <td id="L234" class="blob-num js-line-number" data-line-number="234"></td> - <td id="LC234" class="blob-code js-file-line">countries not thus excluded. In such case, this License incorporates</td> - </tr> - <tr> - <td id="L235" class="blob-num js-line-number" data-line-number="235"></td> - <td id="LC235" class="blob-code js-file-line">the limitation as if written in the body of this License.</td> - </tr> - <tr> - <td id="L236" class="blob-num js-line-number" data-line-number="236"></td> - <td id="LC236" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L237" class="blob-num js-line-number" data-line-number="237"></td> - <td id="LC237" class="blob-code js-file-line"> 9. The Free Software Foundation may publish revised and/or new versions</td> - </tr> - <tr> - <td id="L238" class="blob-num js-line-number" data-line-number="238"></td> - <td id="LC238" class="blob-code js-file-line">of the General Public License from time to time. Such new versions will</td> - </tr> - <tr> - <td id="L239" class="blob-num js-line-number" data-line-number="239"></td> - <td id="LC239" class="blob-code js-file-line">be similar in spirit to the present version, but may differ in detail to</td> - </tr> - <tr> - <td id="L240" class="blob-num js-line-number" data-line-number="240"></td> - <td id="LC240" class="blob-code js-file-line">address new problems or concerns.</td> - </tr> - <tr> - <td id="L241" class="blob-num js-line-number" data-line-number="241"></td> - <td id="LC241" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L242" class="blob-num js-line-number" data-line-number="242"></td> - <td id="LC242" class="blob-code js-file-line">Each version is given a distinguishing version number. If the Program</td> - </tr> - <tr> - <td id="L243" class="blob-num js-line-number" data-line-number="243"></td> - <td id="LC243" class="blob-code js-file-line">specifies a version number of this License which applies to it and "any</td> - </tr> - <tr> - <td id="L244" class="blob-num js-line-number" data-line-number="244"></td> - <td id="LC244" class="blob-code js-file-line">later version", you have the option of following the terms and conditions</td> - </tr> - <tr> - <td id="L245" class="blob-num js-line-number" data-line-number="245"></td> - <td id="LC245" class="blob-code js-file-line">either of that version or of any later version published by the Free</td> - </tr> - <tr> - <td id="L246" class="blob-num js-line-number" data-line-number="246"></td> - <td id="LC246" class="blob-code js-file-line">Software Foundation. If the Program does not specify a version number of</td> - </tr> - <tr> - <td id="L247" class="blob-num js-line-number" data-line-number="247"></td> - <td id="LC247" class="blob-code js-file-line">this License, you may choose any version ever published by the Free Software</td> - </tr> - <tr> - <td id="L248" class="blob-num js-line-number" data-line-number="248"></td> - <td id="LC248" class="blob-code js-file-line">Foundation.</td> - </tr> - <tr> - <td id="L249" class="blob-num js-line-number" data-line-number="249"></td> - <td id="LC249" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L250" class="blob-num js-line-number" data-line-number="250"></td> - <td id="LC250" class="blob-code js-file-line"> 10. If you wish to incorporate parts of the Program into other free</td> - </tr> - <tr> - <td id="L251" class="blob-num js-line-number" data-line-number="251"></td> - <td id="LC251" class="blob-code js-file-line">programs whose distribution conditions are different, write to the author</td> - </tr> - <tr> - <td id="L252" class="blob-num js-line-number" data-line-number="252"></td> - <td id="LC252" class="blob-code js-file-line">to ask for permission. For software which is copyrighted by the Free</td> - </tr> - <tr> - <td id="L253" class="blob-num js-line-number" data-line-number="253"></td> - <td id="LC253" class="blob-code js-file-line">Software Foundation, write to the Free Software Foundation; we sometimes</td> - </tr> - <tr> - <td id="L254" class="blob-num js-line-number" data-line-number="254"></td> - <td id="LC254" class="blob-code js-file-line">make exceptions for this. Our decision will be guided by the two goals</td> - </tr> - <tr> - <td id="L255" class="blob-num js-line-number" data-line-number="255"></td> - <td id="LC255" class="blob-code js-file-line">of preserving the free status of all derivatives of our free software and</td> - </tr> - <tr> - <td id="L256" class="blob-num js-line-number" data-line-number="256"></td> - <td id="LC256" class="blob-code js-file-line">of promoting the sharing and reuse of software generally.</td> - </tr> - <tr> - <td id="L257" class="blob-num js-line-number" data-line-number="257"></td> - <td id="LC257" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L258" class="blob-num js-line-number" data-line-number="258"></td> - <td id="LC258" class="blob-code js-file-line"> NO WARRANTY</td> - </tr> - <tr> - <td id="L259" class="blob-num js-line-number" data-line-number="259"></td> - <td id="LC259" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L260" class="blob-num js-line-number" data-line-number="260"></td> - <td id="LC260" class="blob-code js-file-line"> 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY</td> - </tr> - <tr> - <td id="L261" class="blob-num js-line-number" data-line-number="261"></td> - <td id="LC261" class="blob-code js-file-line">FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN</td> - </tr> - <tr> - <td id="L262" class="blob-num js-line-number" data-line-number="262"></td> - <td id="LC262" class="blob-code js-file-line">OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES</td> - </tr> - <tr> - <td id="L263" class="blob-num js-line-number" data-line-number="263"></td> - <td id="LC263" class="blob-code js-file-line">PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED</td> - </tr> - <tr> - <td id="L264" class="blob-num js-line-number" data-line-number="264"></td> - <td id="LC264" class="blob-code js-file-line">OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF</td> - </tr> - <tr> - <td id="L265" class="blob-num js-line-number" data-line-number="265"></td> - <td id="LC265" class="blob-code js-file-line">MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS</td> - </tr> - <tr> - <td id="L266" class="blob-num js-line-number" data-line-number="266"></td> - <td id="LC266" class="blob-code js-file-line">TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE</td> - </tr> - <tr> - <td id="L267" class="blob-num js-line-number" data-line-number="267"></td> - <td id="LC267" class="blob-code js-file-line">PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING,</td> - </tr> - <tr> - <td id="L268" class="blob-num js-line-number" data-line-number="268"></td> - <td id="LC268" class="blob-code js-file-line">REPAIR OR CORRECTION.</td> - </tr> - <tr> - <td id="L269" class="blob-num js-line-number" data-line-number="269"></td> - <td id="LC269" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L270" class="blob-num js-line-number" data-line-number="270"></td> - <td id="LC270" class="blob-code js-file-line"> 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING</td> - </tr> - <tr> - <td id="L271" class="blob-num js-line-number" data-line-number="271"></td> - <td id="LC271" class="blob-code js-file-line">WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR</td> - </tr> - <tr> - <td id="L272" class="blob-num js-line-number" data-line-number="272"></td> - <td id="LC272" class="blob-code js-file-line">REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES,</td> - </tr> - <tr> - <td id="L273" class="blob-num js-line-number" data-line-number="273"></td> - <td id="LC273" class="blob-code js-file-line">INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING</td> - </tr> - <tr> - <td id="L274" class="blob-num js-line-number" data-line-number="274"></td> - <td id="LC274" class="blob-code js-file-line">OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED</td> - </tr> - <tr> - <td id="L275" class="blob-num js-line-number" data-line-number="275"></td> - <td id="LC275" class="blob-code js-file-line">TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY</td> - </tr> - <tr> - <td id="L276" class="blob-num js-line-number" data-line-number="276"></td> - <td id="LC276" class="blob-code js-file-line">YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER</td> - </tr> - <tr> - <td id="L277" class="blob-num js-line-number" data-line-number="277"></td> - <td id="LC277" class="blob-code js-file-line">PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE</td> - </tr> - <tr> - <td id="L278" class="blob-num js-line-number" data-line-number="278"></td> - <td id="LC278" class="blob-code js-file-line">POSSIBILITY OF SUCH DAMAGES.</td> - </tr> - <tr> - <td id="L279" class="blob-num js-line-number" data-line-number="279"></td> - <td id="LC279" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L280" class="blob-num js-line-number" data-line-number="280"></td> - <td id="LC280" class="blob-code js-file-line"> END OF TERMS AND CONDITIONS</td> - </tr> - <tr> - <td id="L281" class="blob-num js-line-number" data-line-number="281"></td> - <td id="LC281" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L282" class="blob-num js-line-number" data-line-number="282"></td> - <td id="LC282" class="blob-code js-file-line"> How to Apply These Terms to Your New Programs</td> - </tr> - <tr> - <td id="L283" class="blob-num js-line-number" data-line-number="283"></td> - <td id="LC283" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L284" class="blob-num js-line-number" data-line-number="284"></td> - <td id="LC284" class="blob-code js-file-line"> If you develop a new program, and you want it to be of the greatest</td> - </tr> - <tr> - <td id="L285" class="blob-num js-line-number" data-line-number="285"></td> - <td id="LC285" class="blob-code js-file-line">possible use to the public, the best way to achieve this is to make it</td> - </tr> - <tr> - <td id="L286" class="blob-num js-line-number" data-line-number="286"></td> - <td id="LC286" class="blob-code js-file-line">free software which everyone can redistribute and change under these terms.</td> - </tr> - <tr> - <td id="L287" class="blob-num js-line-number" data-line-number="287"></td> - <td id="LC287" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L288" class="blob-num js-line-number" data-line-number="288"></td> - <td id="LC288" class="blob-code js-file-line"> To do so, attach the following notices to the program. It is safest</td> - </tr> - <tr> - <td id="L289" class="blob-num js-line-number" data-line-number="289"></td> - <td id="LC289" class="blob-code js-file-line">to attach them to the start of each source file to most effectively</td> - </tr> - <tr> - <td id="L290" class="blob-num js-line-number" data-line-number="290"></td> - <td id="LC290" class="blob-code js-file-line">convey the exclusion of warranty; and each file should have at least</td> - </tr> - <tr> - <td id="L291" class="blob-num js-line-number" data-line-number="291"></td> - <td id="LC291" class="blob-code js-file-line">the "copyright" line and a pointer to where the full notice is found.</td> - </tr> - <tr> - <td id="L292" class="blob-num js-line-number" data-line-number="292"></td> - <td id="LC292" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L293" class="blob-num js-line-number" data-line-number="293"></td> - <td id="LC293" class="blob-code js-file-line"> {description}</td> - </tr> - <tr> - <td id="L294" class="blob-num js-line-number" data-line-number="294"></td> - <td id="LC294" class="blob-code js-file-line"> Copyright (C) {year} {fullname}</td> - </tr> - <tr> - <td id="L295" class="blob-num js-line-number" data-line-number="295"></td> - <td id="LC295" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L296" class="blob-num js-line-number" data-line-number="296"></td> - <td id="LC296" class="blob-code js-file-line"> This program is free software; you can redistribute it and/or modify</td> - </tr> - <tr> - <td id="L297" class="blob-num js-line-number" data-line-number="297"></td> - <td id="LC297" class="blob-code js-file-line"> it under the terms of the GNU General Public License as published by</td> - </tr> - <tr> - <td id="L298" class="blob-num js-line-number" data-line-number="298"></td> - <td id="LC298" class="blob-code js-file-line"> the Free Software Foundation; either version 2 of the License, or</td> - </tr> - <tr> - <td id="L299" class="blob-num js-line-number" data-line-number="299"></td> - <td id="LC299" class="blob-code js-file-line"> (at your option) any later version.</td> - </tr> - <tr> - <td id="L300" class="blob-num js-line-number" data-line-number="300"></td> - <td id="LC300" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L301" class="blob-num js-line-number" data-line-number="301"></td> - <td id="LC301" class="blob-code js-file-line"> This program is distributed in the hope that it will be useful,</td> - </tr> - <tr> - <td id="L302" class="blob-num js-line-number" data-line-number="302"></td> - <td id="LC302" class="blob-code js-file-line"> but WITHOUT ANY WARRANTY; without even the implied warranty of</td> - </tr> - <tr> - <td id="L303" class="blob-num js-line-number" data-line-number="303"></td> - <td id="LC303" class="blob-code js-file-line"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</td> - </tr> - <tr> - <td id="L304" class="blob-num js-line-number" data-line-number="304"></td> - <td id="LC304" class="blob-code js-file-line"> GNU General Public License for more details.</td> - </tr> - <tr> - <td id="L305" class="blob-num js-line-number" data-line-number="305"></td> - <td id="LC305" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L306" class="blob-num js-line-number" data-line-number="306"></td> - <td id="LC306" class="blob-code js-file-line"> You should have received a copy of the GNU General Public License along</td> - </tr> - <tr> - <td id="L307" class="blob-num js-line-number" data-line-number="307"></td> - <td id="LC307" class="blob-code js-file-line"> with this program; if not, write to the Free Software Foundation, Inc.,</td> - </tr> - <tr> - <td id="L308" class="blob-num js-line-number" data-line-number="308"></td> - <td id="LC308" class="blob-code js-file-line"> 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</td> - </tr> - <tr> - <td id="L309" class="blob-num js-line-number" data-line-number="309"></td> - <td id="LC309" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L310" class="blob-num js-line-number" data-line-number="310"></td> - <td id="LC310" class="blob-code js-file-line">Also add information on how to contact you by electronic and paper mail.</td> - </tr> - <tr> - <td id="L311" class="blob-num js-line-number" data-line-number="311"></td> - <td id="LC311" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L312" class="blob-num js-line-number" data-line-number="312"></td> - <td id="LC312" class="blob-code js-file-line">If the program is interactive, make it output a short notice like this</td> - </tr> - <tr> - <td id="L313" class="blob-num js-line-number" data-line-number="313"></td> - <td id="LC313" class="blob-code js-file-line">when it starts in an interactive mode:</td> - </tr> - <tr> - <td id="L314" class="blob-num js-line-number" data-line-number="314"></td> - <td id="LC314" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L315" class="blob-num js-line-number" data-line-number="315"></td> - <td id="LC315" class="blob-code js-file-line"> Gnomovision version 69, Copyright (C) year name of author</td> - </tr> - <tr> - <td id="L316" class="blob-num js-line-number" data-line-number="316"></td> - <td id="LC316" class="blob-code js-file-line"> Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.</td> - </tr> - <tr> - <td id="L317" class="blob-num js-line-number" data-line-number="317"></td> - <td id="LC317" class="blob-code js-file-line"> This is free software, and you are welcome to redistribute it</td> - </tr> - <tr> - <td id="L318" class="blob-num js-line-number" data-line-number="318"></td> - <td id="LC318" class="blob-code js-file-line"> under certain conditions; type `show c' for details.</td> - </tr> - <tr> - <td id="L319" class="blob-num js-line-number" data-line-number="319"></td> - <td id="LC319" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L320" class="blob-num js-line-number" data-line-number="320"></td> - <td id="LC320" class="blob-code js-file-line">The hypothetical commands `show w' and `show c' should show the appropriate</td> - </tr> - <tr> - <td id="L321" class="blob-num js-line-number" data-line-number="321"></td> - <td id="LC321" class="blob-code js-file-line">parts of the General Public License. Of course, the commands you use may</td> - </tr> - <tr> - <td id="L322" class="blob-num js-line-number" data-line-number="322"></td> - <td id="LC322" class="blob-code js-file-line">be called something other than `show w' and `show c'; they could even be</td> - </tr> - <tr> - <td id="L323" class="blob-num js-line-number" data-line-number="323"></td> - <td id="LC323" class="blob-code js-file-line">mouse-clicks or menu items--whatever suits your program.</td> - </tr> - <tr> - <td id="L324" class="blob-num js-line-number" data-line-number="324"></td> - <td id="LC324" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L325" class="blob-num js-line-number" data-line-number="325"></td> - <td id="LC325" class="blob-code js-file-line">You should also get your employer (if you work as a programmer) or your</td> - </tr> - <tr> - <td id="L326" class="blob-num js-line-number" data-line-number="326"></td> - <td id="LC326" class="blob-code js-file-line">school, if any, to sign a "copyright disclaimer" for the program, if</td> - </tr> - <tr> - <td id="L327" class="blob-num js-line-number" data-line-number="327"></td> - <td id="LC327" class="blob-code js-file-line">necessary. Here is a sample; alter the names:</td> - </tr> - <tr> - <td id="L328" class="blob-num js-line-number" data-line-number="328"></td> - <td id="LC328" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L329" class="blob-num js-line-number" data-line-number="329"></td> - <td id="LC329" class="blob-code js-file-line"> Yoyodyne, Inc., hereby disclaims all copyright interest in the program</td> - </tr> - <tr> - <td id="L330" class="blob-num js-line-number" data-line-number="330"></td> - <td id="LC330" class="blob-code js-file-line"> `Gnomovision' (which makes passes at compilers) written by James Hacker.</td> - </tr> - <tr> - <td id="L331" class="blob-num js-line-number" data-line-number="331"></td> - <td id="LC331" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L332" class="blob-num js-line-number" data-line-number="332"></td> - <td id="LC332" class="blob-code js-file-line"> {signature of Ty Coon}, 1 April 1989</td> - </tr> - <tr> - <td id="L333" class="blob-num js-line-number" data-line-number="333"></td> - <td id="LC333" class="blob-code js-file-line"> Ty Coon, President of Vice</td> - </tr> - <tr> - <td id="L334" class="blob-num js-line-number" data-line-number="334"></td> - <td id="LC334" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L335" class="blob-num js-line-number" data-line-number="335"></td> - <td id="LC335" class="blob-code js-file-line">This General Public License does not permit incorporating your program into</td> - </tr> - <tr> - <td id="L336" class="blob-num js-line-number" data-line-number="336"></td> - <td id="LC336" class="blob-code js-file-line">proprietary programs. If your program is a subroutine library, you may</td> - </tr> - <tr> - <td id="L337" class="blob-num js-line-number" data-line-number="337"></td> - <td id="LC337" class="blob-code js-file-line">consider it more useful to permit linking proprietary applications with the</td> - </tr> - <tr> - <td id="L338" class="blob-num js-line-number" data-line-number="338"></td> - <td id="LC338" class="blob-code js-file-line">library. If this is what you want to do, use the GNU Lesser General</td> - </tr> - <tr> - <td id="L339" class="blob-num js-line-number" data-line-number="339"></td> - <td id="LC339" class="blob-code js-file-line">Public License instead of this License.</td> - </tr> - <tr> - <td id="L340" class="blob-num js-line-number" data-line-number="340"></td> - <td id="LC340" class="blob-code js-file-line"> -</td> - </tr> -</table> +If distribution of executable or object code is made by offering +access to copy from a designated place, then offering equivalent +access to copy the source code from the same place counts as +distribution of the source code, even though third parties are not +compelled to copy the source along with the object code. + + 4. You may not copy, modify, sublicense, or distribute the Program +except as expressly provided under this License. Any attempt +otherwise to copy, modify, sublicense or distribute the Program is +void, and will automatically terminate your rights under this License. +However, parties who have received copies, or rights, from you under +this License will not have their licenses terminated so long as such +parties remain in full compliance. + + 5. You are not required to accept this License, since you have not +signed it. However, nothing else grants you permission to modify or +distribute the Program or its derivative works. These actions are +prohibited by law if you do not accept this License. Therefore, by +modifying or distributing the Program (or any work based on the +Program), you indicate your acceptance of this License to do so, and +all its terms and conditions for copying, distributing or modifying +the Program or works based on it. + + 6. Each time you redistribute the Program (or any work based on the +Program), the recipient automatically receives a license from the +original licensor to copy, distribute or modify the Program subject to +these terms and conditions. You may not impose any further +restrictions on the recipients' exercise of the rights granted herein. +You are not responsible for enforcing compliance by third parties to +this License. + + 7. If, as a consequence of a court judgment or allegation of patent +infringement or for any other reason (not limited to patent issues), +conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot +distribute so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you +may not distribute the Program at all. For example, if a patent +license would not permit royalty-free redistribution of the Program by +all those who receive copies directly or indirectly through you, then +the only way you could satisfy both it and this License would be to +refrain entirely from distribution of the Program. + +If any portion of this section is held invalid or unenforceable under +any particular circumstance, the balance of the section is intended to +apply and the section as a whole is intended to apply in other +circumstances. + +It is not the purpose of this section to induce you to infringe any +patents or other property right claims or to contest validity of any +such claims; this section has the sole purpose of protecting the +integrity of the free software distribution system, which is +implemented by public license practices. Many people have made +generous contributions to the wide range of software distributed +through that system in reliance on consistent application of that +system; it is up to the author/donor to decide if he or she is willing +to distribute software through any other system and a licensee cannot +impose that choice. + +This section is intended to make thoroughly clear what is believed to +be a consequence of the rest of this License. + + 8. If the distribution and/or use of the Program is restricted in +certain countries either by patents or by copyrighted interfaces, the +original copyright holder who places the Program under this License +may add an explicit geographical distribution limitation excluding +those countries, so that distribution is permitted only in or among +countries not thus excluded. In such case, this License incorporates +the limitation as if written in the body of this License. + + 9. The Free Software Foundation may publish revised and/or new versions +of the General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies a version number of this License which applies to it and "any +later version", you have the option of following the terms and conditions +either of that version or of any later version published by the Free +Software Foundation. If the Program does not specify a version number of +this License, you may choose any version ever published by the Free Software +Foundation. - </div> + 10. If you wish to incorporate parts of the Program into other free +programs whose distribution conditions are different, write to the author +to ask for permission. For software which is copyrighted by the Free +Software Foundation, write to the Free Software Foundation; we sometimes +make exceptions for this. Our decision will be guided by the two goals +of preserving the free status of all derivatives of our free software and +of promoting the sharing and reuse of software generally. -</div> + NO WARRANTY -<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> -<div id="jump-to-line" style="display:none"> - <form accept-charset="UTF-8" class="js-jump-to-line-form"> - <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> - <button type="submit" class="button">Go</button> - </form> -</div> - - </div> + 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY +FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN +OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED +OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS +TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE +PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, +REPAIR OR CORRECTION. - </div><!-- /.repo-container --> - <div class="modal-backdrop"></div> - </div><!-- /.container --> - </div><!-- /.site --> + 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR +REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED +TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. - - </div><!-- /.wrapper --> + END OF TERMS AND CONDITIONS - <div class="container"> - <div class="site-footer" role="contentinfo"> - <ul class="site-footer-links right"> - <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li><a href="http://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li><a href="http://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> - <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li> + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. - </ul> + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +convey the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + {description} + Copyright (C) {year} {fullname} - <a href="https://github.com" aria-label="Homepage"> - <span class="mega-octicon octicon-mark-github" title="GitHub"></span> -</a> - <ul class="site-footer-links"> - <li>© 2015 <span title="0.07870s from github-fe125-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> - <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li> - <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li> - <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li> - <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li> - </ul> - </div> -</div> + This program is free software; you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation; either version 2 of the License, or + (at your option) any later version. + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License along + with this program; if not, write to the Free Software Foundation, Inc., + 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. + +Also add information on how to contact you by electronic and paper mail. + +If the program is interactive, make it output a short notice like this +when it starts in an interactive mode: - <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay"> - <div class="fullscreen-container js-suggester-container"> - <div class="textarea-wrap"> - <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea> - <div class="suggester-container"> - <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div> - </div> - </div> - </div> - <div class="fullscreen-sidebar"> - <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode"> - <span class="mega-octicon octicon-screen-normal"></span> - </a> - <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w" - aria-label="Switch themes"> - <span class="octicon octicon-color-mode"></span> - </a> - </div> -</div> + Gnomovision version 69, Copyright (C) year name of author + Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, the commands you use may +be called something other than `show w' and `show c'; they could even be +mouse-clicks or menu items--whatever suits your program. - - - +You should also get your employer (if you work as a programmer) or your +school, if any, to sign a "copyright disclaimer" for the program, if +necessary. Here is a sample; alter the names: - <div id="ajax-error-message" class="flash flash-error"> - <span class="octicon octicon-alert"></span> - <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a> - Something went wrong with that request. 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</li> - <li class="header-nav-item"> - <a class="header-nav-link" href="https://enterprise.github.com/" data-ga-click="(Logged out) Header, go to enterprise, text:enterprise">Enterprise</a> - </li> - <li class="header-nav-item"> - <a class="header-nav-link" href="/blog" data-ga-click="(Logged out) Header, go to blog, text:blog">Blog</a> - </li> - </ul> - - </div> -</div> - - - - <div id="start-of-content" class="accessibility-aid"></div> - <div class="site" itemscope itemtype="http://schema.org/WebPage"> - <div id="js-flash-container"> - - </div> - <div class="pagehead repohead instapaper_ignore readability-menu"> - <div class="container"> - -<ul class="pagehead-actions"> +This is the [Galaxy](http://usegalaxy.org) wrapper for the [UNAFold](http://mfold.rna.albany.edu/?q=DINAMelt/software). UNAFold software was developed for nucleic acid folding and hybridization prediction ([doi: 10.1007/978-1-60327-429-6_1](http://dx.doi.org/10.1007/978-1-60327-429-6_1), [doi: 10.1093/nar/gki591](http://dx.doi.org/10.1093/nar/gki591)). 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<div class="file-history-tease-header"> - Fetching contributors… - </div> +* Create the directory `unafold` in `$GALAXY_DIR/tools/` and copy `unafold.xml` and `unafold.sh` files into it. +* Add the Galaxy tool definition to the `tools_conf.xml`: +```html + <section id="unafold_tool" name="UNAFold"> + <tool file="unafold/unafold.xml" /> + </section>` +``` - <div class="participation"> - <p class="loader-loading"><img alt="" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-EAF2F5-0bdc57d34b85c4a4de9d0d1db10cd70e8a95f33ff4f46c5a8c48b4bf4e5a9abe.gif" width="16" /></p> - <p class="loader-error">Cannot retrieve contributors at this time</p> - </div> -</include-fragment> -<div class="file"> - <div class="file-header"> - <div class="file-actions"> - <div class="button-group"> - <a href="/DrHogart/galaxy-tools-unafold/raw/master/README.md" class="minibutton " id="raw-url">Raw</a> - <a href="/DrHogart/galaxy-tools-unafold/blame/master/README.md" class="minibutton js-update-url-with-hash">Blame</a> - <a href="/DrHogart/galaxy-tools-unafold/commits/master/README.md" class="minibutton " rel="nofollow">History</a> - </div><!-- /.button-group --> - - - <a class="octicon-button disabled tooltipped tooltipped-w" href="#" - aria-label="You must be signed in to make or propose changes"><span class="octicon octicon-pencil"></span></a> - - <a class="octicon-button danger disabled tooltipped tooltipped-w" href="#" - aria-label="You must be signed in to make or propose changes"> - </a> - </div><!-- /.actions --> - <div class="file-info"> - 23 lines (16 sloc) - <span class="file-info-divider"></span> - 1.239 kb - </div> - </div> - <div id="readme" class="blob instapaper_body"> - <article class="markdown-body entry-content" itemprop="mainContentOfPage"><h1> -<a id="user-content-galaxy-tool-wrapper-for-unafold" class="anchor" href="#galaxy-tool-wrapper-for-unafold" aria-hidden="true"><span class="octicon octicon-link"></span></a>Galaxy Tool wrapper for UNAFold</h1> - -<p>This is the <a href="http://usegalaxy.org">Galaxy</a> wrapper for the <a href="http://mfold.rna.albany.edu/?q=DINAMelt/software">UNAFold</a>. UNAFold software was developed for nucleic acid folding and hybridization prediction (<a href="http://dx.doi.org/10.1007/978-1-60327-429-6_1">doi: 10.1007/978-1-60327-429-6_1</a>, <a href="http://dx.doi.org/10.1093/nar/gki591">doi: 10.1093/nar/gki591</a>). This wrapper is not yet deposited in the Tool-Shed repository, so this is the single place where it can downloaded.</p> - -<h2> -<a id="user-content-installation" class="anchor" href="#installation" aria-hidden="true"><span class="octicon octicon-link"></span></a>Installation</h2> - -<ul class="task-list"> -<li><p>Save <a href="http://mfold.rna.albany.edu/?q=DINAMelt/software">UNAFold.pl</a> in your $PATH, that is accesable to the Galaxy.</p></li> -<li><p>Create the directory <code>unafold</code> in <code>$GALAXY_DIR/tools/</code> and copy <code>unafold.xml</code> and <code>unafold.sh</code> files into it.</p></li> -<li>Add the Galaxy tool definition to the <code>tools_conf.xml</code>:</li> -</ul> - -<div class="highlight highlight-html"><pre> <<span class="pl-ent">section</span> <span class="pl-e">id</span>=<span class="pl-s1"><span class="pl-pds">"</span>unafold_tool<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>UNAFold<span class="pl-pds">"</span></span>> - <<span class="pl-ent">tool</span> <span class="pl-e">file</span>=<span class="pl-s1"><span class="pl-pds">"</span>unafold/unafold.xml<span class="pl-pds">"</span></span> /> - </<span class="pl-ent">section</span>>`</pre></div> - -<ul class="task-list"> -<li>Please, be sure that <code>zip</code> datatype is registered in your Galaxy instance. If not, add the following string to the <code>datatypes_conf.xml</code> file:</li> -</ul> - -<div class="highlight highlight-html"><pre> <<span class="pl-ent">datatype</span> <span class="pl-e">extension</span>=<span class="pl-s1"><span class="pl-pds">"</span>zip<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>galaxy.datatypes.binary:Binary<span class="pl-pds">"</span></span> <span class="pl-e">mimetype</span>=<span class="pl-s1"><span class="pl-pds">"</span>application/zip<span class="pl-pds">"</span></span> <span class="pl-e">subclass</span>=<span class="pl-s1"><span class="pl-pds">"</span>True<span class="pl-pds">"</span></span> /></pre></div> - -<ul class="task-list"> -<li>Reload the Galaxy instance.</li> -</ul> -</article> - </div> - -</div> - -<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> -<div id="jump-to-line" style="display:none"> - <form accept-charset="UTF-8" class="js-jump-to-line-form"> - <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> - <button type="submit" class="button">Go</button> - </form> -</div> - - </div> +* Please, be sure that `zip` datatype is registered in your Galaxy instance. If not, add the following string to the `datatypes_conf.xml` file: +```html + <datatype extension="zip" type="galaxy.datatypes.binary:Binary" mimetype="application/zip" subclass="True" /> +``` - </div><!-- /.repo-container --> - <div class="modal-backdrop"></div> - </div><!-- /.container --> - </div><!-- /.site --> - - - </div><!-- /.wrapper --> - - <div class="container"> - <div class="site-footer" role="contentinfo"> - <ul class="site-footer-links right"> - <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li><a href="http://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li><a href="http://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> - <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li> - - </ul> - - <a href="https://github.com" aria-label="Homepage"> - <span class="mega-octicon octicon-mark-github" title="GitHub"></span> -</a> - <ul class="site-footer-links"> - <li>© 2015 <span title="0.04783s from github-fe143-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> - <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li> - <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li> - <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li> - <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li> - </ul> - </div> -</div> - - - <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay"> - <div class="fullscreen-container js-suggester-container"> - <div class="textarea-wrap"> - <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea> - <div class="suggester-container"> - <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div> - </div> - </div> - </div> - <div class="fullscreen-sidebar"> - <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode"> - <span class="mega-octicon octicon-screen-normal"></span> - </a> - <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w" - aria-label="Switch themes"> - <span class="octicon octicon-color-mode"></span> - </a> - </div> -</div> - - - - - - <div id="ajax-error-message" class="flash flash-error"> - <span class="octicon octicon-alert"></span> - <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a> - Something went wrong with that request. Please try again. - </div> - - - <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-4bf9533935259bb898a8d60e1958f4d047968c430eae889800a187e279faf38f.js"></script> - <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-9d83860b0798bdd794d00b491fc7cb4ab9ea416cc8c511f719e253faa86e635b.js"></script> - - - - </body> -</html> - +* Reload the Galaxy instance.
--- a/unafold.sh Tue Mar 10 05:45:34 2015 -0400 +++ b/unafold.sh Tue Mar 10 05:54:18 2015 -0400 @@ -1,833 +1,76 @@ - - - -<!DOCTYPE html> -<html lang="en" class=""> - <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#"> - <meta charset='utf-8'> - <meta http-equiv="X-UA-Compatible" content="IE=edge"> - <meta http-equiv="Content-Language" content="en"> - - - <title>galaxy-tools-unafold/unafold.sh at master · DrHogart/galaxy-tools-unafold · GitHub</title> - <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> - <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> - <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png"> - <link rel="apple-touch-icon" sizes="144x144" href="/apple-touch-icon-144.png"> - 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<a class="octicon-button disabled tooltipped tooltipped-w" href="#" - aria-label="You must be signed in to make or propose changes"><span class="octicon octicon-pencil"></span></a> +NA=RNA +TM=37 +NAT=1 +MG=0 - <a class="octicon-button danger disabled tooltipped tooltipped-w" href="#" - aria-label="You must be signed in to make or propose changes"> - </a> - </div><!-- /.actions --> - <div class="file-info"> - 77 lines (66 sloc) - <span class="file-info-divider"></span> - 1.912 kb - </div> - </div> - - <div class="blob-wrapper data type-shell"> - <table class="highlight tab-size-8 js-file-line-container"> - <tr> - <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> - <td id="LC1" class="blob-code js-file-line"><span class="pl-c">#!/bin/bash</span></td> - </tr> - <tr> - <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> - <td id="LC2" class="blob-code js-file-line"><span class="pl-s3">set</span> -e</td> - </tr> - <tr> - <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> - <td id="LC3" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> - <td id="LC4" class="blob-code js-file-line"><span class="pl-c">#arguments are -i input sequence file in fasta </span></td> - </tr> - <tr> - <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> - <td id="LC5" class="blob-code js-file-line"><span class="pl-c"># -o output zip arhive </span></td> - </tr> - <tr> - <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> - <td id="LC6" class="blob-code js-file-line"><span class="pl-c"># -t temp directory with results</span></td> - </tr> - <tr> - <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> - <td id="LC7" class="blob-code js-file-line"><span class="pl-c"># -a DNA|RNA</span></td> - </tr> - <tr> - <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> - <td id="LC8" class="blob-code js-file-line"><span class="pl-c"># -c tempreature (C)</span></td> - </tr> - <tr> - <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> - <td id="LC9" class="blob-code js-file-line"><span class="pl-c"># -s [Na+] in M</span></td> - </tr> - <tr> - <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> - <td id="LC10" class="blob-code js-file-line"><span class="pl-c"># -m [Mg++] in M</span></td> - </tr> - <tr> - <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> - <td id="LC11" class="blob-code js-file-line"><span class="pl-c"># -b maxbp</span></td> - </tr> - <tr> - <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> - <td id="LC12" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> - <td id="LC13" class="blob-code js-file-line"><span class="pl-c">#-n, --NA=(RNA | DNA) (defaults to RNA)</span></td> - </tr> - <tr> - <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> - <td id="LC14" class="blob-code js-file-line"><span class="pl-c">#-t, --temp=<temperature> (defaults to 37)</span></td> - </tr> - <tr> - <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> - <td id="LC15" class="blob-code js-file-line"><span class="pl-c">#-N, --sodium=<[Na+] in M> (defaults to 1)</span></td> - </tr> - <tr> - <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> - <td id="LC16" class="blob-code js-file-line"><span class="pl-c">#-M, --magnesium=<[Mg++] in M> (defaults to 0)</span></td> - </tr> - <tr> - <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> - <td id="LC17" class="blob-code js-file-line"><span class="pl-c">#-p, --polymer</span></td> - </tr> - <tr> - <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> - <td id="LC18" class="blob-code js-file-line"><span class="pl-c">#-C, --Ct=<total strand concentration></span></td> - </tr> - <tr> - <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> - <td id="LC19" class="blob-code js-file-line"><span class="pl-c">#-I, --noisolate</span></td> - </tr> - <tr> - <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> - <td id="LC20" class="blob-code js-file-line"><span class="pl-c">#-m, --maxbp=<maximum basepair distance></span></td> - </tr> - <tr> - <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> - <td id="LC21" class="blob-code js-file-line"><span class="pl-c">#-c, --constraints=<name of constraints file> (defaults to prefix.aux)</span></td> - </tr> - <tr> - <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> - <td id="LC22" class="blob-code js-file-line"><span class="pl-c">#-P, --percent=<energy increment percent> (defaults to 5)</span></td> - </tr> - <tr> - <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> - <td id="LC23" class="blob-code js-file-line"><span class="pl-c">#-W, --window=<window size> (default set by sequence length)</span></td> - </tr> - <tr> - <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> - <td id="LC24" class="blob-code js-file-line"><span class="pl-c">#-X, --max=<maximum number of foldings> (defaults to 100)</span></td> - </tr> - <tr> - <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> - <td id="LC25" class="blob-code js-file-line"><span class="pl-c"># --ann=(none | p-num | ss-count) (defaults to none)</span></td> - </tr> - <tr> - <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> - <td id="LC26" class="blob-code js-file-line"><span class="pl-c"># --mode=(auto | bases | lines) (defaults to auto)</span></td> - </tr> - <tr> - <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> - <td id="LC27" class="blob-code js-file-line"><span class="pl-c"># --label=<base numbering frequency></span></td> - </tr> - <tr> - <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> - <td id="LC28" class="blob-code js-file-line"><span class="pl-c"># --rotate=<structure rotation angle></span></td> - </tr> - <tr> - <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> - <td id="LC29" class="blob-code js-file-line"><span class="pl-c"># --run-type=(text | html) (defaults to text)</span></td> - </tr> - <tr> - <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> - <td id="LC30" class="blob-code js-file-line"><span class="pl-c"># --model=(EM | PF) (defaults to EM)</span></td> - </tr> - <tr> - <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> - <td id="LC31" class="blob-code js-file-line"><span class="pl-c"># --circular</span></td> - </tr> - <tr> - <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> - <td id="LC32" class="blob-code js-file-line"><span class="pl-c">#Obscure options:</span></td> - </tr> - <tr> - <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> - <td id="LC33" class="blob-code js-file-line"><span class="pl-c"># --allpairs</span></td> - </tr> - <tr> - <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> - <td id="LC34" class="blob-code js-file-line"><span class="pl-c"># --maxloop=<maximum bulge/interior loop size> (defaults to 30)</span></td> - </tr> - <tr> - <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> - <td id="LC35" class="blob-code js-file-line"><span class="pl-c"># --nodangle</span></td> - </tr> - <tr> - <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> - <td id="LC36" class="blob-code js-file-line"><span class="pl-c"># --simple</span></td> - </tr> - <tr> - <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> - <td id="LC37" class="blob-code js-file-line"><span class="pl-c"># --prefilter=<filter value></span></td> - </tr> - <tr> - <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> - <td id="LC38" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> - <td id="LC39" class="blob-code js-file-line">NA=RNA</td> - </tr> - <tr> - <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> - <td id="LC40" class="blob-code js-file-line">TM=37</td> - </tr> - <tr> - <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> - <td id="LC41" class="blob-code js-file-line">NAT=1</td> - </tr> - <tr> - <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> - <td id="LC42" class="blob-code js-file-line">MG=0</td> - </tr> - <tr> - <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> - <td id="LC43" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> - <td id="LC44" class="blob-code js-file-line"><span class="pl-k">while</span> <span class="pl-s3">getopts</span> <span class="pl-s1"><span class="pl-pds">"</span>:i:o:t:a:c:s:m:<span class="pl-pds">"</span></span> OPTION<span class="pl-k">;</span></td> - </tr> - <tr> - <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> - <td id="LC45" class="blob-code js-file-line"><span class="pl-k">do</span></td> - </tr> - <tr> - <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> - <td id="LC46" class="blob-code js-file-line"> <span class="pl-k">case</span> <span class="pl-vo">$OPTION</span> in</td> - </tr> - <tr> - <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> - <td id="LC47" class="blob-code js-file-line"> i) INPUT=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> - </tr> - <tr> - <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> - <td id="LC48" class="blob-code js-file-line"> o) ZIP_ARHIVE=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> - </tr> - <tr> - <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> - <td id="LC49" class="blob-code js-file-line"> t) TEMP_DIR=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> - </tr> - <tr> - <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> - <td id="LC50" class="blob-code js-file-line"> a) NA=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> - </tr> - <tr> - <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> - <td id="LC51" class="blob-code js-file-line"> c) TM=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> - </tr> - <tr> - <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> - <td id="LC52" class="blob-code js-file-line"> s) NAT=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> - </tr> - <tr> - <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> - <td id="LC53" class="blob-code js-file-line"> m) MG=<span class="pl-s1"><span class="pl-pds">"</span><span class="pl-vo">$OPTARG</span><span class="pl-pds">"</span></span>;;</td> - </tr> - <tr> - <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> - <td id="LC54" class="blob-code js-file-line"> <span class="pl-k">esac</span></td> - </tr> - <tr> - <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> - <td id="LC55" class="blob-code js-file-line"><span class="pl-k">done</span></td> - </tr> - <tr> - <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> - <td id="LC56" class="blob-code js-file-line"> </td> - </tr> - <tr> - <td id="L57" class="blob-num js-line-number" data-line-number="57"></td> - <td id="LC57" class="blob-code js-file-line">mkdir -p <span class="pl-vo">${TEMP_DIR}</span>/unafold</td> - </tr> - <tr> - <td id="L58" class="blob-num js-line-number" data-line-number="58"></td> - <td id="LC58" class="blob-code js-file-line"><span class="pl-s3">cd</span> <span class="pl-vo">${TEMP_DIR}</span>/unafold</td> - </tr> - <tr> - <td id="L59" class="blob-num js-line-number" data-line-number="59"></td> - <td id="LC59" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L60" class="blob-num js-line-number" data-line-number="60"></td> - <td id="LC60" class="blob-code js-file-line">NA=<span class="pl-s1"><span class="pl-pds">$(</span><span class="pl-s3">echo</span> <span class="pl-vo">$NA</span> <span class="pl-k">|</span> tr <span class="pl-s1"><span class="pl-pds">'</span>[:lower:]<span class="pl-pds">'</span></span> <span class="pl-s1"><span class="pl-pds">'</span>[:upper:]<span class="pl-pds">'</span></span><span class="pl-pds">)</span></span></td> - </tr> - <tr> - <td id="L61" class="blob-num js-line-number" data-line-number="61"></td> - <td id="LC61" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L62" class="blob-num js-line-number" data-line-number="62"></td> - <td id="LC62" class="blob-code js-file-line"><span class="pl-c"># calucalation of RNA don't need the concentraion of salts</span></td> - </tr> - <tr> - <td id="L63" class="blob-num js-line-number" data-line-number="63"></td> - <td id="LC63" class="blob-code js-file-line"><span class="pl-k">if</span> [[ <span class="pl-vo">${NA}</span> <span class="pl-k">==</span> <span class="pl-s1"><span class="pl-pds">'</span>DNA<span class="pl-pds">'</span></span> ]]<span class="pl-k">;</span> <span class="pl-k">then</span></td> - </tr> - <tr> - <td id="L64" class="blob-num js-line-number" data-line-number="64"></td> - <td id="LC64" class="blob-code js-file-line"> UNAFold.pl -n <span class="pl-vo">${NA}</span> -t <span class="pl-vo">${TM}</span> -N <span class="pl-vo">${NAT}</span> -M <span class="pl-vo">${MG}</span> <span class="pl-vo">${INPUT}</span></td> - </tr> - <tr> - <td id="L65" class="blob-num js-line-number" data-line-number="65"></td> - <td id="LC65" class="blob-code js-file-line"><span class="pl-k">else</span></td> - </tr> - <tr> - <td id="L66" class="blob-num js-line-number" data-line-number="66"></td> - <td id="LC66" class="blob-code js-file-line"> UNAFold.pl -n <span class="pl-vo">${NA}</span> -t <span class="pl-vo">${TM}</span> <span class="pl-vo">${INPUT}</span></td> - </tr> - <tr> - <td id="L67" class="blob-num js-line-number" data-line-number="67"></td> - <td id="LC67" class="blob-code js-file-line"><span class="pl-k">fi</span></td> - </tr> - <tr> - <td id="L68" class="blob-num js-line-number" data-line-number="68"></td> - <td id="LC68" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L69" class="blob-num js-line-number" data-line-number="69"></td> - <td id="LC69" class="blob-code js-file-line"><span class="pl-s3">echo</span> <span class="pl-s1"><span class="pl-pds">"</span><span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L70" class="blob-num js-line-number" data-line-number="70"></td> - <td id="LC70" class="blob-code js-file-line"><span class="pl-s3">echo</span> <span class="pl-s1"><span class="pl-pds">"</span>Parametres of UNAFold run:<span class="pl-pds">"</span></span></td> - </tr> - <tr> - <td id="L71" class="blob-num js-line-number" data-line-number="71"></td> - <td id="LC71" class="blob-code js-file-line">cat <span class="pl-k">*</span>run</td> - </tr> - <tr> - <td id="L72" class="blob-num js-line-number" data-line-number="72"></td> - <td id="LC72" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L73" class="blob-num js-line-number" data-line-number="73"></td> - <td id="LC73" class="blob-code js-file-line"><span class="pl-s3">cd</span> ../</td> - </tr> - <tr> - <td id="L74" class="blob-num js-line-number" data-line-number="74"></td> - <td id="LC74" class="blob-code js-file-line">zip -r -q unafold.zip unafold</td> - </tr> - <tr> - <td id="L75" class="blob-num js-line-number" data-line-number="75"></td> - <td id="LC75" class="blob-code js-file-line">mv unafold.zip <span class="pl-vo">${ZIP_ARHIVE}</span></td> - </tr> - <tr> - <td id="L76" class="blob-num js-line-number" data-line-number="76"></td> - <td id="LC76" class="blob-code js-file-line"> -</td> - </tr> -</table> +while getopts ":i:o:t:a:c:s:m:" OPTION; +do + case $OPTION in + i) INPUT="$OPTARG";; + o) ZIP_ARHIVE="$OPTARG";; + t) TEMP_DIR="$OPTARG";; + a) NA="$OPTARG";; + c) TM="$OPTARG";; + s) NAT="$OPTARG";; + m) MG="$OPTARG";; + esac +done + +mkdir -p ${TEMP_DIR}/unafold +cd ${TEMP_DIR}/unafold - </div> - -</div> - -<a href="#jump-to-line" rel="facebox[.linejump]" data-hotkey="l" style="display:none">Jump to Line</a> -<div id="jump-to-line" style="display:none"> - <form accept-charset="UTF-8" class="js-jump-to-line-form"> - <input class="linejump-input js-jump-to-line-field" type="text" placeholder="Jump to line…" autofocus> - <button type="submit" class="button">Go</button> - </form> -</div> - - </div> +NA=$(echo $NA | tr '[:lower:]' '[:upper:]') - </div><!-- /.repo-container --> - <div class="modal-backdrop"></div> - </div><!-- /.container --> - </div><!-- /.site --> - - - </div><!-- /.wrapper --> - - <div class="container"> - <div class="site-footer" role="contentinfo"> - <ul class="site-footer-links right"> - <li><a href="https://status.github.com/" data-ga-click="Footer, go to status, text:status">Status</a></li> - <li><a href="https://developer.github.com" data-ga-click="Footer, go to api, text:api">API</a></li> - <li><a href="http://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> - <li><a href="http://shop.github.com" data-ga-click="Footer, go to shop, text:shop">Shop</a></li> - <li><a href="https://github.com/blog" data-ga-click="Footer, go to blog, text:blog">Blog</a></li> - <li><a href="https://github.com/about" data-ga-click="Footer, go to about, text:about">About</a></li> - - </ul> +# calucalation of RNA don't need the concentraion of salts +if [[ ${NA} == 'DNA' ]]; then + UNAFold.pl -n ${NA} -t ${TM} -N ${NAT} -M ${MG} ${INPUT} +else + UNAFold.pl -n ${NA} -t ${TM} ${INPUT} +fi - <a href="https://github.com" aria-label="Homepage"> - <span class="mega-octicon octicon-mark-github" title="GitHub"></span> -</a> - <ul class="site-footer-links"> - <li>© 2015 <span title="0.03449s from github-fe124-cp1-prd.iad.github.net">GitHub</span>, Inc.</li> - <li><a href="https://github.com/site/terms" data-ga-click="Footer, go to terms, text:terms">Terms</a></li> - <li><a href="https://github.com/site/privacy" data-ga-click="Footer, go to privacy, text:privacy">Privacy</a></li> - <li><a href="https://github.com/security" data-ga-click="Footer, go to security, text:security">Security</a></li> - <li><a href="https://github.com/contact" data-ga-click="Footer, go to contact, text:contact">Contact</a></li> - </ul> - </div> -</div> - +echo "" +echo "Parametres of UNAFold run:" +cat *run - <div class="fullscreen-overlay js-fullscreen-overlay" id="fullscreen_overlay"> - <div class="fullscreen-container js-suggester-container"> - <div class="textarea-wrap"> - <textarea name="fullscreen-contents" id="fullscreen-contents" class="fullscreen-contents js-fullscreen-contents" placeholder=""></textarea> - <div class="suggester-container"> - <div class="suggester fullscreen-suggester js-suggester js-navigation-container"></div> - </div> - </div> - </div> - <div class="fullscreen-sidebar"> - <a href="#" class="exit-fullscreen js-exit-fullscreen tooltipped tooltipped-w" aria-label="Exit Zen Mode"> - <span class="mega-octicon octicon-screen-normal"></span> - </a> - <a href="#" class="theme-switcher js-theme-switcher tooltipped tooltipped-w" - aria-label="Switch themes"> - <span class="octicon octicon-color-mode"></span> - </a> - </div> -</div> +cd ../ +zip -r -q unafold.zip unafold +mv unafold.zip ${ZIP_ARHIVE} - - - - - <div id="ajax-error-message" class="flash flash-error"> - <span class="octicon octicon-alert"></span> - <a href="#" class="octicon octicon-x flash-close js-ajax-error-dismiss" aria-label="Dismiss error"></a> - Something went wrong with that request. Please try again. - </div> - - - <script crossorigin="anonymous" src="https://assets-cdn.github.com/assets/frameworks-4bf9533935259bb898a8d60e1958f4d047968c430eae889800a187e279faf38f.js"></script> - <script async="async" crossorigin="anonymous" src="https://assets-cdn.github.com/assets/github-9d83860b0798bdd794d00b491fc7cb4ab9ea416cc8c511f719e253faa86e635b.js"></script> - - - - </body> -</html> -
--- a/unafold.xml Tue Mar 10 05:45:34 2015 -0400 +++ b/unafold.xml Tue Mar 10 05:54:18 2015 -0400 @@ -1,747 +1,57 @@ - - - -<!DOCTYPE html> -<html lang="en" class=""> - <head prefix="og: http://ogp.me/ns# fb: http://ogp.me/ns/fb# object: http://ogp.me/ns/object# article: http://ogp.me/ns/article# profile: http://ogp.me/ns/profile#"> - <meta charset='utf-8'> - <meta http-equiv="X-UA-Compatible" content="IE=edge"> - <meta http-equiv="Content-Language" content="en"> - - - <title>galaxy-tools-unafold/unafold.xml at master · DrHogart/galaxy-tools-unafold · GitHub</title> - <link rel="search" type="application/opensearchdescription+xml" href="/opensearch.xml" title="GitHub"> - <link rel="fluid-icon" href="https://github.com/fluidicon.png" title="GitHub"> - <link rel="apple-touch-icon" sizes="57x57" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="114x114" href="/apple-touch-icon-114.png"> - <link rel="apple-touch-icon" sizes="72x72" href="/apple-touch-icon-144.png"> - 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</div> +<?xml version="1.0"?> +<tool id="unafold_1" name="unafold" version="0.0.1"> + <description>Folding of RNA sequences using UNAFold</description> + <command interpreter="bash"> +unafold.sh -i $inputFastaFile -o $outputArhive -t '$outputArhive.extra_files_path' -a ${ na_type.nucacid } -c $tmp +#if str($na_type.nucacid) == 'dna': + -s ${ na_type.sodium } -m ${ na_type.magnesium } +#end if + > $outputLog + </command> - <div class="site-search repo-scope js-site-search" role="search"> - <form accept-charset="UTF-8" action="/DrHogart/galaxy-tools-unafold/search" class="js-site-search-form" data-global-search-url="/search" data-repo-search-url="/DrHogart/galaxy-tools-unafold/search" method="get"><div style="margin:0;padding:0;display:inline"><input name="utf8" type="hidden" value="✓" /></div> - <input type="text" - class="js-site-search-field is-clearable" - data-hotkey="s" - name="q" - placeholder="Search" - data-global-scope-placeholder="Search GitHub" - data-repo-scope-placeholder="Search" - 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rel="nofollow"> - <span class="octicon octicon-cloud-download"></span> - Download ZIP - </a> - </div> - </div><!-- /.repository-sidebar --> + <outputs> + <data format="zip" name="outputArhive" label="Arhive: UNAFold on $on_string"/> + <data format="txt" name="outputLog" label="Log: UNAFold on $on_string"/> + </outputs> - <div id="js-repo-pjax-container" class="repository-content context-loader-container" data-pjax-container> - - -<a href="/DrHogart/galaxy-tools-unafold/blob/4d192467d646410e4d9552bbcdfc23690e425596/unafold.xml" class="hidden js-permalink-shortcut" data-hotkey="y">Permalink</a> - -<!-- blob contrib key: blob_contributors:v21:026caa4b1440c0ca74f5157b497718b9 --> +<help> -<div class="file-navigation js-zeroclipboard-container"> - -<div class="select-menu js-menu-container js-select-menu left"> - <span class="minibutton select-menu-button js-menu-target css-truncate" data-hotkey="w" - data-master-branch="master" - data-ref="master" - title="master" - role="button" aria-label="Switch branches or tags" tabindex="0" aria-haspopup="true"> - <span class="octicon octicon-git-branch"></span> - <i>branch:</i> - <span class="js-select-button css-truncate-target">master</span> - </span> - - <div class="select-menu-modal-holder js-menu-content js-navigation-container" data-pjax aria-hidden="true"> +This tool computes the fold of RNA/DNA using UNAFold v.3.8. - <div class="select-menu-modal"> - <div class="select-menu-header"> - <span class="select-menu-title">Switch branches/tags</span> - <span class="octicon octicon-x js-menu-close" role="button" aria-label="Close"></span> - </div> +UNAFold (http://mfold.rna.albany.edu/?q=unafold-man-pages) is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from "Unified Nucleic Acid Folding". Folding of single-stranded RNA or DNA, or hybridization between two single-strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous mfold software. - <div class="select-menu-filters"> - <div class="select-menu-text-filter"> - <input type="text" aria-label="Filter branches/tags" id="context-commitish-filter-field" class="js-filterable-field js-navigation-enable" placeholder="Filter branches/tags"> - </div> - <div class="select-menu-tabs"> - <ul> - <li class="select-menu-tab"> - <a href="#" data-tab-filter="branches" data-filter-placeholder="Filter branches/tags" class="js-select-menu-tab">Branches</a> - </li> - <li class="select-menu-tab"> - <a href="#" data-tab-filter="tags" data-filter-placeholder="Find a tag…" class="js-select-menu-tab">Tags</a> - </li> - </ul> - </div> - </div> +For melting simulations, the package computes not just melting temperatures, but entire melting profiles. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. ITC (Isothermal Titration Calorimetry) and van't Hoff plots are also simulated. + +UNAFold v.3.8 (http://mfold.rna.albany.edu/?q=unafold-man-pages) - <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="branches"> - - <div data-filterable-for="context-commitish-filter-field" data-filterable-type="substring"> - +Galaxy wrapper for UNAFold v. 0.0.1 - <a class="select-menu-item js-navigation-item js-navigation-open selected" - href="/DrHogart/galaxy-tools-unafold/blob/master/unafold.xml" - data-name="master" - data-skip-pjax="true" - rel="nofollow"> - <span class="select-menu-item-icon octicon octicon-check"></span> - <span class="select-menu-item-text css-truncate-target" title="master"> - master - </span> - </a> - </div> +Author: Sergei Ryazansky, s.ryazansky@gmail.com - <div class="select-menu-no-results">Nothing to show</div> - </div> - - <div class="select-menu-list select-menu-tab-bucket js-select-menu-tab-bucket" data-tab-filter="tags"> - 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</div><!-- /.button-group --> - - - <a class="octicon-button disabled tooltipped tooltipped-w" href="#" - aria-label="You must be signed in to make or propose changes"><span class="octicon octicon-pencil"></span></a> +</help> +</tool> - <a class="octicon-button danger disabled tooltipped tooltipped-w" href="#" - aria-label="You must be signed in to make or propose changes"> - </a> - </div><!-- /.actions --> - <div class="file-info"> - 58 lines (41 sloc) - <span class="file-info-divider"></span> - 2.602 kb - </div> - </div> - - <div class="blob-wrapper data type-xml"> - <table class="highlight tab-size-8 js-file-line-container"> - <tr> - <td id="L1" class="blob-num js-line-number" data-line-number="1"></td> - <td id="LC1" class="blob-code js-file-line"><?<span class="pl-ent">xml</span><span class="pl-e"> version</span>=<span class="pl-s1"><span class="pl-pds">"</span>1.0<span class="pl-pds">"</span></span>?></td> - </tr> - <tr> - <td id="L2" class="blob-num js-line-number" data-line-number="2"></td> - <td id="LC2" class="blob-code js-file-line"><<span class="pl-ent">tool</span> <span class="pl-e">id</span>=<span class="pl-s1"><span class="pl-pds">"</span>unafold_1<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>unafold<span class="pl-pds">"</span></span> <span class="pl-e">version</span>=<span class="pl-s1"><span class="pl-pds">"</span>0.0.1<span class="pl-pds">"</span></span>></td> - </tr> - <tr> - <td id="L3" class="blob-num js-line-number" data-line-number="3"></td> - <td id="LC3" class="blob-code js-file-line"> <<span class="pl-ent">description</span>>Folding of RNA sequences using UNAFold</<span class="pl-ent">description</span>></td> - </tr> - <tr> - <td id="L4" class="blob-num js-line-number" data-line-number="4"></td> - <td id="LC4" class="blob-code js-file-line"> <<span class="pl-ent">command</span> <span class="pl-e">interpreter</span>=<span class="pl-s1"><span class="pl-pds">"</span>bash<span class="pl-pds">"</span></span>></td> - </tr> - <tr> - <td id="L5" class="blob-num js-line-number" data-line-number="5"></td> - <td id="LC5" class="blob-code js-file-line">unafold.sh -i $inputFastaFile -o $outputArhive -t '$outputArhive.extra_files_path' -a ${ na_type.nucacid } -c $tmp</td> - </tr> - <tr> - <td id="L6" class="blob-num js-line-number" data-line-number="6"></td> - <td id="LC6" class="blob-code js-file-line">#if str($na_type.nucacid) == 'dna':</td> - </tr> - <tr> - <td id="L7" class="blob-num js-line-number" data-line-number="7"></td> - <td id="LC7" class="blob-code js-file-line"> -s ${ na_type.sodium } -m ${ na_type.magnesium }</td> - </tr> - <tr> - <td id="L8" class="blob-num js-line-number" data-line-number="8"></td> - <td id="LC8" class="blob-code js-file-line">#end if</td> - </tr> - <tr> - <td id="L9" class="blob-num js-line-number" data-line-number="9"></td> - <td id="LC9" class="blob-code js-file-line"> > $outputLog</td> - </tr> - <tr> - <td id="L10" class="blob-num js-line-number" data-line-number="10"></td> - <td id="LC10" class="blob-code js-file-line"> </<span class="pl-ent">command</span>></td> - </tr> - <tr> - <td id="L11" class="blob-num js-line-number" data-line-number="11"></td> - <td id="LC11" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L12" class="blob-num js-line-number" data-line-number="12"></td> - <td id="LC12" class="blob-code js-file-line"> <<span class="pl-ent">inputs</span>></td> - </tr> - <tr> - <td id="L13" class="blob-num js-line-number" data-line-number="13"></td> - <td id="LC13" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">format</span>=<span class="pl-s1"><span class="pl-pds">"</span>fasta<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>inputFastaFile<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>data<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Fasta input file<span class="pl-pds">"</span></span>/></td> - </tr> - <tr> - <td id="L14" class="blob-num js-line-number" data-line-number="14"></td> - <td id="LC14" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L15" class="blob-num js-line-number" data-line-number="15"></td> - <td id="LC15" class="blob-code js-file-line"> <<span class="pl-ent">conditional</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>na_type<span class="pl-pds">"</span></span>></td> - </tr> - <tr> - <td id="L16" class="blob-num js-line-number" data-line-number="16"></td> - <td id="LC16" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>nucacid<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>select<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Nucleic Acid Type<span class="pl-pds">"</span></span>></td> - </tr> - <tr> - <td id="L17" class="blob-num js-line-number" data-line-number="17"></td> - <td id="LC17" class="blob-code js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>rna<span class="pl-pds">"</span></span> <span class="pl-e">selected</span>=<span class="pl-s1"><span class="pl-pds">"</span>true<span class="pl-pds">"</span></span>>RNA</<span class="pl-ent">option</span>></td> - </tr> - <tr> - <td id="L18" class="blob-num js-line-number" data-line-number="18"></td> - <td id="LC18" class="blob-code js-file-line"> <<span class="pl-ent">option</span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>dna<span class="pl-pds">"</span></span>>DNA</<span class="pl-ent">option</span>></td> - </tr> - <tr> - <td id="L19" class="blob-num js-line-number" data-line-number="19"></td> - <td id="LC19" class="blob-code js-file-line"> </<span class="pl-ent">param</span>></td> - </tr> - <tr> - <td id="L20" class="blob-num js-line-number" data-line-number="20"></td> - <td id="LC20" class="blob-code js-file-line"> <<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>dna<span class="pl-pds">"</span></span>></td> - </tr> - <tr> - <td id="L21" class="blob-num js-line-number" data-line-number="21"></td> - <td id="LC21" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>sodium<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>float<span class="pl-pds">"</span></span> <span class="pl-e">size</span>=<span class="pl-s1"><span class="pl-pds">"</span>6<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>1.0<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s1"><span class="pl-pds">"</span>0<span class="pl-pds">"</span></span> <span class="pl-e">max</span>=<span class="pl-s1"><span class="pl-pds">"</span>100<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>[Na+] in M<span class="pl-pds">"</span></span>/></td> - </tr> - <tr> - <td id="L22" class="blob-num js-line-number" data-line-number="22"></td> - <td id="LC22" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>magnesium<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>float<span class="pl-pds">"</span></span> <span class="pl-e">size</span>=<span class="pl-s1"><span class="pl-pds">"</span>6<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>0.0<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s1"><span class="pl-pds">"</span>0<span class="pl-pds">"</span></span> <span class="pl-e">max</span>=<span class="pl-s1"><span class="pl-pds">"</span>100<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>[Mg++] in M<span class="pl-pds">"</span></span>/></td> - </tr> - <tr> - <td id="L23" class="blob-num js-line-number" data-line-number="23"></td> - <td id="LC23" class="blob-code js-file-line"> </<span class="pl-ent">when</span>></td> - </tr> - <tr> - <td id="L24" class="blob-num js-line-number" data-line-number="24"></td> - <td id="LC24" class="blob-code js-file-line"> <<span class="pl-ent">when</span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>rna<span class="pl-pds">"</span></span>></td> - </tr> - <tr> - <td id="L25" class="blob-num js-line-number" data-line-number="25"></td> - <td id="LC25" class="blob-code js-file-line"> <span class="pl-c"><!-- do nothing here --></span></td> - </tr> - <tr> - <td id="L26" class="blob-num js-line-number" data-line-number="26"></td> - <td id="LC26" class="blob-code js-file-line"> </<span class="pl-ent">when</span>></td> - </tr> - <tr> - <td id="L27" class="blob-num js-line-number" data-line-number="27"></td> - <td id="LC27" class="blob-code js-file-line"> </<span class="pl-ent">conditional</span>></td> - </tr> - <tr> - <td id="L28" class="blob-num js-line-number" data-line-number="28"></td> - <td id="LC28" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L29" class="blob-num js-line-number" data-line-number="29"></td> - <td id="LC29" class="blob-code js-file-line"> <<span class="pl-ent">param</span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>tmp<span class="pl-pds">"</span></span> <span class="pl-e">type</span>=<span class="pl-s1"><span class="pl-pds">"</span>integer<span class="pl-pds">"</span></span> <span class="pl-e">size</span>=<span class="pl-s1"><span class="pl-pds">"</span>3<span class="pl-pds">"</span></span> <span class="pl-e">value</span>=<span class="pl-s1"><span class="pl-pds">"</span>37<span class="pl-pds">"</span></span> <span class="pl-e">min</span>=<span class="pl-s1"><span class="pl-pds">"</span>0<span class="pl-pds">"</span></span> <span class="pl-e">max</span>=<span class="pl-s1"><span class="pl-pds">"</span>100<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Temperature (C)<span class="pl-pds">"</span></span>/></td> - </tr> - <tr> - <td id="L30" class="blob-num js-line-number" data-line-number="30"></td> - <td id="LC30" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L31" class="blob-num js-line-number" data-line-number="31"></td> - <td id="LC31" class="blob-code js-file-line"> </<span class="pl-ent">inputs</span>></td> - </tr> - <tr> - <td id="L32" class="blob-num js-line-number" data-line-number="32"></td> - <td id="LC32" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L33" class="blob-num js-line-number" data-line-number="33"></td> - <td id="LC33" class="blob-code js-file-line"> <<span class="pl-ent">outputs</span>></td> - </tr> - <tr> - <td id="L34" class="blob-num js-line-number" data-line-number="34"></td> - <td id="LC34" class="blob-code js-file-line"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s1"><span class="pl-pds">"</span>zip<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>outputArhive<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Arhive: UNAFold on $on_string<span class="pl-pds">"</span></span>/></td> - </tr> - <tr> - <td id="L35" class="blob-num js-line-number" data-line-number="35"></td> - <td id="LC35" class="blob-code js-file-line"> <<span class="pl-ent">data</span> <span class="pl-e">format</span>=<span class="pl-s1"><span class="pl-pds">"</span>txt<span class="pl-pds">"</span></span> <span class="pl-e">name</span>=<span class="pl-s1"><span class="pl-pds">"</span>outputLog<span class="pl-pds">"</span></span> <span class="pl-e">label</span>=<span class="pl-s1"><span class="pl-pds">"</span>Log: UNAFold on $on_string<span class="pl-pds">"</span></span>/></td> - </tr> - <tr> - <td id="L36" class="blob-num js-line-number" data-line-number="36"></td> - <td id="LC36" class="blob-code js-file-line"> </<span class="pl-ent">outputs</span>></td> - </tr> - <tr> - <td id="L37" class="blob-num js-line-number" data-line-number="37"></td> - <td id="LC37" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L38" class="blob-num js-line-number" data-line-number="38"></td> - <td id="LC38" class="blob-code js-file-line"><<span class="pl-ent">help</span>></td> - </tr> - <tr> - <td id="L39" class="blob-num js-line-number" data-line-number="39"></td> - <td id="LC39" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L40" class="blob-num js-line-number" data-line-number="40"></td> - <td id="LC40" class="blob-code js-file-line">This tool computes the fold of RNA/DNA using UNAFold v.3.8.</td> - </tr> - <tr> - <td id="L41" class="blob-num js-line-number" data-line-number="41"></td> - <td id="LC41" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L42" class="blob-num js-line-number" data-line-number="42"></td> - <td id="LC42" class="blob-code js-file-line">UNAFold (http://mfold.rna.albany.edu/?q=unafold-man-pages) is a comprehensive software package for nucleic acid folding and hybridization prediction. The name is derived from "Unified Nucleic Acid Folding". Folding of single-stranded RNA or DNA, or hybridization between two single-strands, is accomplished in a variety of ways. Partition functions can be computed to derive base pair probabilities and stochastic samples of foldings or hybridizations. Energy minimization methods compute minimum free energy foldings or hybridizations, and can also compute suboptimal foldings that mimic the performance of the famous mfold software.</td> - </tr> - <tr> - <td id="L43" class="blob-num js-line-number" data-line-number="43"></td> - <td id="LC43" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L44" class="blob-num js-line-number" data-line-number="44"></td> - <td id="LC44" class="blob-code js-file-line">For melting simulations, the package computes not just melting temperatures, but entire melting profiles. UV absorbance at 260 nm, heat capacity change (Cp), and mole fractions of different molecular species are computed as a function of temperature. ITC (Isothermal Titration Calorimetry) and van't Hoff plots are also simulated.</td> - </tr> - <tr> - <td id="L45" class="blob-num js-line-number" data-line-number="45"></td> - <td id="LC45" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L46" class="blob-num js-line-number" data-line-number="46"></td> - <td id="LC46" class="blob-code js-file-line">UNAFold v.3.8 (http://mfold.rna.albany.edu/?q=unafold-man-pages)</td> - </tr> - <tr> - <td id="L47" class="blob-num js-line-number" data-line-number="47"></td> - <td id="LC47" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L48" class="blob-num js-line-number" data-line-number="48"></td> - <td id="LC48" class="blob-code js-file-line">Galaxy wrapper for UNAFold v. 0.0.1</td> - </tr> - <tr> - <td id="L49" class="blob-num js-line-number" data-line-number="49"></td> - <td id="LC49" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L50" class="blob-num js-line-number" data-line-number="50"></td> - <td id="LC50" class="blob-code js-file-line">Author: Sergei Ryazansky, s.ryazansky@gmail.com</td> - </tr> - <tr> - <td id="L51" class="blob-num js-line-number" data-line-number="51"></td> - <td id="LC51" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L52" class="blob-num js-line-number" data-line-number="52"></td> - <td id="LC52" class="blob-code js-file-line">Web-site: https://github.com/DrHogart/galaxy-tools-unafold)</td> - </tr> - <tr> - <td id="L53" class="blob-num js-line-number" data-line-number="53"></td> - <td id="LC53" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L54" class="blob-num js-line-number" data-line-number="54"></td> - <td id="LC54" class="blob-code js-file-line"> -</td> - </tr> - <tr> - <td id="L55" class="blob-num js-line-number" data-line-number="55"></td> - <td id="LC55" class="blob-code js-file-line"></<span class="pl-ent">help</span>></td> - </tr> - <tr> - <td id="L56" class="blob-num js-line-number" data-line-number="56"></td> - <td id="LC56" class="blob-code js-file-line"></<span class="pl-ent">tool</span>></td> - </tr> - 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