diff tool_dependencies.xml @ 0:75d83e0939c5 draft default tip

planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5

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+++ b/tool_dependencies.xml	Mon Oct 24 13:14:45 2016 -0400
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+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="stringmlst" version="2.1">
+        <install version="1.0">
+          <actions>
+            <action type="download_by_url" sha256sum="164f1ea5f486036dbb77481d0cc560315f40ce7aecffbb0f28521431be188de0">https://github.com/anujg1991/stringMLST/archive/v0.2.1.tar.gz</action>
+            <action type="move_file">
+		<source>stringMLST.py</source>
+		<destination>$INSTALL_DIR</destination>
+	    </action>
+            <action type="set_environment">
+              <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/</environment_variable>
+            </action>
+   	    <action type="setup_virtualenv">biopython==1.68</action>
+            </actions>
+        </install>
+        <readme>
+
+stringMLST
+
+Fast k-mer based tool for multi locus sequence typing (MLST) stringMLST is a tool for detecting the MLST of an isolate directly from the genome sequencing reads. stringMLST predicts the ST of an isolate in a completely assembly and alignment free manner. The tool is designed in a light-weight, platform-independent fashion with minimum dependencies.
+
+Reference http://jordan.biology.gatech.edu/page/software/stringmlst/
+
+Abstract http://bioinformatics.oxfordjournals.org/content/early/2016/09/06/bioinformatics.btw586.short?rss=1
+
+Application Note http://bioinformatics.oxfordjournals.org/content/early/2016/09/06/bioinformatics.btw586.full.pdf+html
+
+
+Manual http://jordan.biology.gatech.edu/page/software/stringmlst/stringMLST-useageDocumentation.pdf
+
+Public repository https://github.com/anujg1991/stringMLST
+
+
+
+License listed below:
+
+LICENSE TERMS FOR stringMLST
+
+1. INTENT/PURPOSE:
+
+stringMLST is free for academic users and requires permission before any commercial use for any version of this code/algorithm.  
+If you are a commercial user, please contact [e-mail] for permissions.
+
+2. LICENSEE:
+
+Any person or organization who receives the software with a copy of this license.
+
+3. INTELLECTUAL PROPERTY LICENSED:
+
+The rights to use, copy, modify, and compile the software,
+subject to the restrictions described in the present document.
+
+5. SCOPE OF THE LICENSE
+
+* NON-COMMERCIAL license for research and evaluation purposes ONLY.
+
+* NO right to commercialize the software, or any derivative work, 
+ without separate agreement with the copyright owners.
+
+6. MODIFICATION
+
+* License permits licensee to modify the software for their 
+ research and evaluation purposes.
+
+7. REDISTRIBUTION
+
+* License permits licensee to redistribute verbatim copies 
+ of the software, accompanied with a copy of this license.
+
+* License does not permit licensee to redistribute 
+ modified versions of the software.
+
+* License does not permit licensee to commercialize the software
+ or any derivative work of the software.
+
+8. FEE/ROYALTY
+
+* Licensee pays no royalty for non-commercial license
+
+* Licensee and any third parties must enter a new agreement
+ for any use beyond scope of license.
+
+9. NO WARRANTY
+
+The software is provided "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 the Licensee.
+
+10. NO LIABILITY
+
+In no event unless required by applicable law or agreed to in writing
+will any copyright owner be liable to Licensee 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 Licensee 
+or third parties or a failure of the program to operate with other programs),
+even if such holder has been advised of the possibility of such damages.
+
+
+
+        </readme>
+    </package>
+</tool_dependency>