Mercurial > repos > iuc > package_stringtie_0_97
annotate tool_dependencies.xml @ 1:cfe1d3cb41d5 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
author | iuc |
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date | Fri, 17 Jul 2015 11:16:34 -0400 |
parents | bbcdfb50d3f0 |
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0 | 1 <?xml version="1.0"?> |
2 <tool_dependency> | |
3 <package name="stringtie" version="0.97"> | |
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cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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4 <install version="1.0"> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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5 <actions_group> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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6 <actions architecture="x86_64" os="linux"> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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7 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action> |
0 | 8 <action type="move_file"> |
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cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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9 <source>stringtie</source> |
0 | 10 <destination>$INSTALL_DIR/bin</destination> |
11 </action> | |
12 </actions> | |
13 <actions architecture="x86_64" os="darwin"> | |
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cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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14 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action> |
0 | 15 <action type="move_file"> |
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cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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16 <source>stringtie</source> |
0 | 17 <destination>$INSTALL_DIR/bin</destination> |
18 </action> | |
19 </actions> | |
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cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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20 <actions> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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21 <package name="samtools" version="0.1.19"> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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22 <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://toolshed.g2.bx.psu.edu" /> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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23 </package> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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24 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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25 <action type="set_environment_for_install"> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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26 <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://toolshed.g2.bx.psu.edu"> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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0
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27 <package name="samtools" version="0.1.19" /> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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28 </repository> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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29 </action> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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30 <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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31 <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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32 <action type="shell_command">make</action> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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33 <action type="move_file"> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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34 <source>stringtie</source> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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35 <destination>$INSTALL_DIR/bin</destination> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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36 </action> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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37 </actions> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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38 <action type="set_environment"> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
iuc
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39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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40 </action> |
cfe1d3cb41d5
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_0_97 commit e10d6e2c4435771dc6f44d940359c1a31c0d6742-dirty
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41 </actions_group> |
0 | 42 </install> |
43 <readme>StringTie is a fast and highly efficient assembler of RNA-Seq | |
44 alignments into potential transcripts. It is primarily a genome-guided | |
45 transcriptome assembler, although it can borrow algorithmic techniques | |
46 from de novo genome assembly to help with transcript assembly. Its input | |
47 can include not only the spliced read alignments used by reference-based | |
48 assemblers, but also longer contigs that were assembled de novo from | |
49 unambiguous, non-branching parts of a transcript.</readme> | |
50 </package> | |
51 </tool_dependency> |