Mercurial > repos > vipints > fml_gff3togtf
changeset 7:ee541c1852da
Uploaded version 2.1.0
| author | vipints |
|---|---|
| date | Thu, 23 Apr 2015 17:43:11 -0400 |
| parents | 154887a3d92f |
| children | d4f9b7beb52f |
| files | GFFtools-GX |
| diffstat | 1 files changed, 959 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/GFFtools-GX Thu Apr 23 17:43:11 2015 -0400 @@ -0,0 +1,959 @@ + + + +<!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>vipints/GFFtools-GX · 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" 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href="/vipints/GFFtools-GX/commit/46e670f9d93f3797740d21a100428fe195b6c83f" class="message" data-pjax="true" title="functional test perfomed after the change">functional test perfomed after the change</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-21T22:42:01Z" is="time-ago">Apr 21, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/.gitignore" class="js-directory-link" id="a084b794bc0759e7a6b77810e01874f2-0334fc9da4d9b7a262012ae6cae37002259af5b2" title=".gitignore">.gitignore</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/c5b661defaf94700cf290651669846c8258e220d" class="message" data-pjax="true" title="ignored pyc and swap files">ignored pyc and swap files</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2014-07-18T22:28:50Z" is="time-ago">Jul 18, 2014</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/GFFParser.py" class="js-directory-link" id="4a9c2f3a2b51d00c039e9951aa5df3fd-505eece57e21af803c93cdb06d9d569c81d1d811" title="GFFParser.py">GFFParser.py</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/cb38052d271326df1d0577bfe0f6a877458da8a6" class="message" data-pjax="true" title="added a new field to carryover the isoform level score from the GFF file- has to sync with main gfftools">added a new field to carryover the isoform level score from the GFF f…</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/README.md" class="js-directory-link" id="04c6e90faac2675aa89e2176d2eec7d8-17e766c0f2926d94933cb7320afd6c1f5db293fb" title="README.md">README.md</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/0ea921f8d7cc65bb044616b14dfdae59b54e2073" class="message" data-pjax="true" title="fixed">fixed</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-23T21:27:17Z" is="time-ago">Apr 23, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.py" class="js-directory-link" id="4fd14b034003e6ed6b3c1243f3f285ed-461ae7292d229b40fb98dec1d28a67aebfde7c96" title="bed_to_gff.py">bed_to_gff.py</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/b882fc8c206c3203792da6c4c856005eb06934c4" class="message" data-pjax="true" title="removing print statement from the code">removing print statement from the code</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-14T23:41:11Z" is="time-ago">Apr 14, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/bed_to_gff.xml" class="js-directory-link" id="fd45df94f6d642a741c0c8d038949b37-2b5908455dd6730bd4bbd634f56316dfd70eca03" title="bed_to_gff.xml">bed_to_gff.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/34fdf81381a56ffc7e3a57736a49d516f20c120b" class="message" data-pjax="true" title="updated the gbk_to_gff wrapper and fixed typo">updated the gbk_to_gff wrapper and fixed typo</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:14:52Z" is="time-ago">Apr 17, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.py" class="js-directory-link" id="8cedf4409efd74682d25ee79bb3574dc-6638d994bf8d1a8aaa231c70bf44b6021f9ccf1b" title="gbk_to_gff.py">gbk_to_gff.py</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/84a145c7ee9efa171dbe1d64223e20ceb1930de6" class="message" data-pjax="true" title="gbk parsing and correctly assigning feature type">gbk parsing and correctly assigning feature type</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:04:25Z" is="time-ago">Apr 17, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gbk_to_gff.xml" class="js-directory-link" id="5e708155a06e4244e26c978ed02c6fd2-c90e390761eb5390bda2e245b7eb7456d5e9c665" title="gbk_to_gff.xml">gbk_to_gff.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/34fdf81381a56ffc7e3a57736a49d516f20c120b" class="message" data-pjax="true" title="updated the gbk_to_gff wrapper and fixed typo">updated the gbk_to_gff wrapper and fixed typo</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-17T21:14:52Z" is="time-ago">Apr 17, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.py" class="js-directory-link" id="95b17a03c0948b20d1264fcd269b60fa-457e6d44dbc1f4531de174641f74f9e6ec689982" title="gff_to_bed.py">gff_to_bed.py</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/f84e0d96db79436b685066c088bf1555a3bf29e1" class="message" data-pjax="true" title="changing the float behaviour to int">changing the float behaviour to int</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-22T16:25:13Z" is="time-ago">Apr 22, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_bed.xml" class="js-directory-link" id="8c7d5ae4b79728262acfc56888f2444e-10754bece6a7a5a7c5dc9d533d92ddfa046e6b6b" title="gff_to_bed.xml">gff_to_bed.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/2c96e399526d372a61df5b4068bc91e08af49092" class="message" data-pjax="true" title="updated the wrapper version">updated the wrapper version</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T02:59:32Z" is="time-ago">Apr 18, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.py" class="js-directory-link" id="88b7a441373dfec1e07cd28bb1eb8c3e-9ff53c56125edfa286255f489e61cda154a21693" title="gff_to_gtf.py">gff_to_gtf.py</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/f76a6c972d5e4200f182bb25493a675ca3fe09ae" class="message" data-pjax="true" title="functional test performed and changed version to 0.6">functional test performed and changed version to 0.6</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:14:25Z" is="time-ago">Apr 20, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gff_to_gtf.xml" class="js-directory-link" id="f4676750a1f71b9fbf35b537b0546842-a2b41ec7924d6609f219bdf8c0372af59ea747d2" title="gff_to_gtf.xml">gff_to_gtf.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/f76a6c972d5e4200f182bb25493a675ca3fe09ae" class="message" data-pjax="true" title="functional test performed and changed version to 0.6">functional test performed and changed version to 0.6</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:14:25Z" is="time-ago">Apr 20, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.py" class="js-directory-link" id="6989ac39182645599caeb47b4e0e8ef6-6d786691f74f0c00db3da883f4e6e7e1d009d2c2" title="gtf_to_gff.py">gtf_to_gff.py</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/1ee80e9b0a4b7a05094f42fd8836ec248af85d0e" class="message" data-pjax="true" title="updated the version 0.6 gtftogff">updated the version 0.6 gtftogff</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T23:08:52Z" is="time-ago">Apr 20, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/gtf_to_gff.xml" class="js-directory-link" id="a8bd25db400514c2556192045eacd820-dc2031de1c3daa1cf8644a5c62c9d4afce97ad39" title="gtf_to_gff.xml">gtf_to_gff.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/1ee80e9b0a4b7a05094f42fd8836ec248af85d0e" class="message" data-pjax="true" title="updated the version 0.6 gtftogff">updated the version 0.6 gtftogff</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T23:08:52Z" is="time-ago">Apr 20, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/helper.py" class="js-directory-link" id="702b6abf015bfdb4e41308ddd3b297a9-a711ed60defe1bd9ef579fada75e32da2313935c" title="helper.py">helper.py</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/cb38052d271326df1d0577bfe0f6a877458da8a6" class="message" data-pjax="true" title="added a new field to carryover the isoform level score from the GFF file- has to sync with main gfftools">added a new field to carryover the isoform level score from the GFF f…</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-19T21:50:45Z" is="time-ago">Apr 19, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/tool_conf.xml.sample" class="js-directory-link" id="76a06ab03a6f35bfb6ff2be40e654b7e-e26478f762dbc5e03f339bc5598086009e4f8be0" title="tool_conf.xml.sample">tool_conf.xml.sample</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/04ccdc96c4bf8d6b8420a05c9afa8c8540345e32" class="message" data-pjax="true" title="updated the toolpanel list">updated the toolpanel list</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-20T22:15:28Z" is="time-ago">Apr 20, 2015</time></span> + </td> + </tr> + <tr> + <td class="icon"> + <span class="octicon octicon-file-text"></span> + <img alt="" class="spinner" height="16" src="https://assets-cdn.github.com/assets/spinners/octocat-spinner-32-e513294efa576953719e4e2de888dd9cf929b7d62ed8d05f25e731d02452ab6c.gif" width="16" /> + </td> + <td class="content"> + <span class="css-truncate css-truncate-target"><a href="/vipints/GFFtools-GX/blob/master/tool_dependencies.xml" class="js-directory-link" id="1f1e2fcbf1ddc07a88bc59ca246c9a90-a0a1a7f1bb7e1a6a8b79f30629c8968f8b4c8d36" title="tool_dependencies.xml">tool_dependencies.xml</a></span> + </td> + <td class="message"> + <span class="css-truncate css-truncate-target"> + <a href="/vipints/GFFtools-GX/commit/c75c2be2f54ca59449e999346de2427584789ec9" class="message" data-pjax="true" title="biopython required">biopython required</a> + </span> + </td> + <td class="age"> + <span class="css-truncate css-truncate-target"><time datetime="2015-04-21T22:54:33Z" is="time-ago">Apr 21, 2015</time></span> + </td> + </tr> + </tbody> + </table> + +</div> + + + <div id="readme" class="boxed-group flush clearfix announce instapaper_body md"> + <h3> + <span class="octicon octicon-book"></span> + README.md + </h3> + + <article class="markdown-body entry-content" itemprop="mainContentOfPage"><h1> +<a id="user-content-gfftools-gx-" class="anchor" href="#gfftools-gx-" aria-hidden="true"><span class="octicon octicon-link"></span></a>GFFtools-GX </h1> + +<p>A collection of tools for converting genome annotation between <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format4">GTF</a>, <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format1">BED</a>, <a href="http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html">GenBank</a> and <a href="https://genome.ucsc.edu/FAQ/FAQformat.html#format3">GFF</a>.</p> + +<h5> +<a id="user-content-introduction" class="anchor" href="#introduction" aria-hidden="true"><span class="octicon octicon-link"></span></a>INTRODUCTION</h5> + +<p>Several genome annotation centers provide their data in GTF, BED, GFF and GenBank format. I have few programs, they mainly deals with converting between GTF, BED GenBank and GFF formats. They are extensively tested with files from different centers like <a href="http://www.ensembl.org">ENSEMBL</a>, <a href="https://genome.ucsc.edu/">UCSC</a>, <a href="http://genome.jgi.doe.gov/">JGI</a> and <a href="http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/HelpJan.html">NCBI AceView</a>. These programs can be easily integrated into your galaxy instance.</p> + +<h5> +<a id="user-content-contents" class="anchor" href="#contents" aria-hidden="true"><span class="octicon octicon-link"></span></a>CONTENTS</h5> + +<p>Included utilities are: </p> + +<pre><code>BED-to-GFF: convert data from a 12 column UCSC wiggle BED format to GFF +GBK-to-GFF: convert data from genbank format to GFF +GFF-to-BED: convert data from GFF to 12 column BED format +GFF-to-GTF: convert data from GFF to GTF +GTF-to-GFF: convert data from GTF to valid GFF +</code></pre> + +<p>test-data: Test data set. (move to your galaxy-root-folder/test-data/)</p> + +<pre><code>You may need to move the test files into your test-data directory so galaxy can find them. +If you want to run the functional tests eg as: + +exmaple: +sh run_functional_tests.sh -id fml_gtf2gff +</code></pre> + +<h5> +<a id="user-content-requirements" class="anchor" href="#requirements" aria-hidden="true"><span class="octicon octicon-link"></span></a>REQUIREMENTS</h5> + +<pre><code>python2.6 or 2.7 and biopython + +Galaxy should be able to automatically install biopython via Galaxy toolshed. +</code></pre> + +<h5> +<a id="user-content-commentsquestions" class="anchor" href="#commentsquestions" aria-hidden="true"><span class="octicon octicon-link"></span></a>COMMENTS/QUESTIONS</h5> + +<p>I can be reached at vipin [at] cbio.mskcc.org </p> + +<h5> +<a id="user-content-license" class="anchor" href="#license" aria-hidden="true"><span class="octicon octicon-link"></span></a>LICENSE</h5> + +<p>Copyright (c) 2009-2012, Friedrich Miescher Laboratory of the Max Planck Society</p> + +<pre><code> 2013-2015, Memorial Sloan Kettering Cancer Center + Vipin T Sreedharan <vipin@cbio.mskcc.org> +</code></pre> + +<p>All rights reserved.</p> + +<p>Licensed under the BSD 2-Clause License: <a href="http://opensource.org/licenses/BSD-2-Clause">http://opensource.org/licenses/BSD-2-Clause</a></p> + +<pre><code>Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + + * Redistributions of source code must retain the above copyright notice, + this list of conditions and the following disclaimer. + + * Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND +ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED +WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. +</code></pre> + +<h5> +<a id="user-content-courtesy" class="anchor" href="#courtesy" aria-hidden="true"><span class="octicon octicon-link"></span></a>COURTESY</h5> + +<p>To the Galaxy Team.</p> +</article> + </div> + + + </div> + + </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="https://training.github.com" data-ga-click="Footer, go to training, text:training">Training</a></li> + <li><a href="https://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="0.04621s from github-fe120-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. 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