| Next changeset 1:cfe1d3cb41d5 (2015-07-17) |
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Commit message:
Imported from capsule None |
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added:
tool_dependencies.xml |
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| diff -r 000000000000 -r bbcdfb50d3f0 tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Thu Jul 03 18:38:00 2014 -0400 |
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| @@ -0,0 +1,51 @@ +<?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> |