Mercurial > repos > iuc > package_stringtie_0_97
comparison tool_dependencies.xml @ 0:09b1ece7f3e9 draft
Imported from capsule None
| author | devteam |
|---|---|
| date | Tue, 01 Jul 2014 19:08:38 -0400 |
| parents | |
| children | 0627e8e30873 |
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| -1:000000000000 | 0:09b1ece7f3e9 |
|---|---|
| 1 <?xml version="1.0"?> | |
| 2 <tool_dependency> | |
| 3 <package name="samtools" version="0.1.19"> | |
| 4 <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu" /> | |
| 5 </package> | |
| 6 <package name="stringtie" version="0.97"> | |
| 7 <install version="1.0"> | |
| 8 <actions_group> | |
| 9 <actions architecture="x86_64" os="linux"> | |
| 10 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action> | |
| 11 <action type="move_file"> | |
| 12 <source>stringtie</source> | |
| 13 <destination>$INSTALL_DIR/bin</destination> | |
| 14 </action> | |
| 15 </actions> | |
| 16 <actions architecture="x86_64" os="darwin"> | |
| 17 <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action> | |
| 18 <action type="move_file"> | |
| 19 <source>stringtie</source> | |
| 20 <destination>$INSTALL_DIR/bin</destination> | |
| 21 </action> | |
| 22 </actions> | |
| 23 <actions> | |
| 24 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action> | |
| 25 <action type="set_environment_for_install"> | |
| 26 <repository changeset_revision="233326db3402" name="package_samtools_0_1_19" owner="devteam" toolshed="https://testtoolshed.g2.bx.psu.edu"> | |
| 27 <package name="samtools" version="0.1.19" /> | |
| 28 </repository> | |
| 29 </action> | |
| 30 <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action> | |
| 31 <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action> | |
| 32 <action type="shell_command">make</action> | |
| 33 <action type="move_file"> | |
| 34 <source>stringtie</source> | |
| 35 <destination>$INSTALL_DIR/bin</destination> | |
| 36 </action> | |
| 37 </actions> | |
| 38 <action type="set_environment"> | |
| 39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 40 </action> | |
| 41 </actions_group> | |
| 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> |