Mercurial > repos > iuc > package_stringtie_0_97
view tool_dependencies.xml @ 0:bbcdfb50d3f0 draft
Imported from capsule None
author | iuc |
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date | Thu, 03 Jul 2014 18:38:00 -0400 |
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children | cfe1d3cb41d5 |
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<?xml version="1.0"?> <tool_dependency> <package name="samtools" version="0.1.19"> <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> </package> <package name="stringtie" version="0.97"> <install version="1.0"> <actions_group> <actions architecture="x86_64" os="linux"> <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.Linux_x86_64.tar.gz</action> <action type="move_file"> <source>stringtie</source> <destination>$INSTALL_DIR/bin</destination> </action> </actions> <actions architecture="x86_64" os="darwin"> <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/stringtie/stringtie-0.97-Darwin-x86_64.tgz</action> <action type="move_file"> <source>stringtie</source> <destination>$INSTALL_DIR/bin</destination> </action> </actions> <actions> <action type="download_by_url">http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz</action> <action type="set_environment_for_install"> <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu"> <package name="samtools" version="0.1.19" /> </repository> </action> <action type="shell_command">ln -s $SAMTOOLS_ROOT_DIR/src samtools</action> <action type="shell_command">cp $SAMTOOLS_ROOT_DIR/lib/libbam.* samtools/</action> <action type="shell_command">make</action> <action type="move_file"> <source>stringtie</source> <destination>$INSTALL_DIR/bin</destination> </action> </actions> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> </actions_group> </install> <readme>StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de novo genome assembly to help with transcript assembly. Its input can include not only the spliced read alignments used by reference-based assemblers, but also longer contigs that were assembled de novo from unambiguous, non-branching parts of a transcript.</readme> </package> </tool_dependency>