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

planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5

<?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>