Mercurial > repos > iuc > package_stringtie_0_97
comparison 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 |
|---|---|
| date | Fri, 17 Jul 2015 11:16:34 -0400 |
| parents | bbcdfb50d3f0 |
| children |
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| 0:bbcdfb50d3f0 | 1:cfe1d3cb41d5 |
|---|---|
| 1 <?xml version="1.0"?> | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | 2 <tool_dependency> |
| 3 <package name="samtools" version="0.1.19"> | |
| 4 <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> | |
| 5 </package> | |
| 6 <package name="stringtie" version="0.97"> | 3 <package name="stringtie" version="0.97"> |
| 7 <install version="1.0"> | 4 <install version="1.0"> |
| 8 <actions_group> | 5 <actions_group> |
| 9 <actions architecture="x86_64" os="linux"> | 6 <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> | 7 <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"> | 8 <action type="move_file"> |
| 12 <source>stringtie</source> | 9 <source>stringtie</source> |
| 13 <destination>$INSTALL_DIR/bin</destination> | 10 <destination>$INSTALL_DIR/bin</destination> |
| 14 </action> | 11 </action> |
| 15 </actions> | 12 </actions> |
| 16 <actions architecture="x86_64" os="darwin"> | 13 <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> | 14 <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"> | 15 <action type="move_file"> |
| 19 <source>stringtie</source> | 16 <source>stringtie</source> |
| 20 <destination>$INSTALL_DIR/bin</destination> | 17 <destination>$INSTALL_DIR/bin</destination> |
| 21 </action> | 18 </action> |
| 22 </actions> | 19 </actions> |
| 23 <actions> | 20 <actions> |
| 24 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action> | 21 <package name="samtools" version="0.1.19"> |
| 25 <action type="set_environment_for_install"> | 22 <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://toolshed.g2.bx.psu.edu" /> |
| 26 <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"> | 23 </package> |
| 27 <package name="samtools" version="0.1.19" /> | 24 <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action> |
| 28 </repository> | 25 <action type="set_environment_for_install"> |
| 29 </action> | 26 <repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" prior_installation_required="true" toolshed="https://toolshed.g2.bx.psu.edu"> |
| 30 <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action> | 27 <package name="samtools" version="0.1.19" /> |
| 31 <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action> | 28 </repository> |
| 32 <action type="shell_command">make</action> | 29 </action> |
| 33 <action type="move_file"> | 30 <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action> |
| 34 <source>stringtie</source> | 31 <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action> |
| 35 <destination>$INSTALL_DIR/bin</destination> | 32 <action type="shell_command">make</action> |
| 36 </action> | 33 <action type="move_file"> |
| 37 </actions> | 34 <source>stringtie</source> |
| 38 <action type="set_environment"> | 35 <destination>$INSTALL_DIR/bin</destination> |
| 39 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | 36 </action> |
| 40 </action> | 37 </actions> |
| 41 </actions_group> | 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> | 42 </install> |
| 43 <readme>StringTie is a fast and highly efficient assembler of RNA-Seq | 43 <readme>StringTie is a fast and highly efficient assembler of RNA-Seq |
| 44 alignments into potential transcripts. It is primarily a genome-guided | 44 alignments into potential transcripts. It is primarily a genome-guided |
| 45 transcriptome assembler, although it can borrow algorithmic techniques | 45 transcriptome assembler, although it can borrow algorithmic techniques |
| 46 from de novo genome assembly to help with transcript assembly. Its input | 46 from de novo genome assembly to help with transcript assembly. Its input |