Mercurial > repos > nml > package_stringmlst_2_1
diff tool_dependencies.xml @ 0:75d83e0939c5 draft default tip
planemo upload commit 0366addb646f1ddea484915abdeda939d7d49bd5
author | nml |
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date | Mon, 24 Oct 2016 13:14:45 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Mon Oct 24 13:14:45 2016 -0400 @@ -0,0 +1,106 @@ +<?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 king.jordan@biology.gatech.edu 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>