Mercurial > repos > iuc > package_stringtie_1_2_3
changeset 0:ee804c6f3b97 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stringtie_1_2_3 commit acdc3dfe5fd6317ae57899aa0e83130dff7460e7
| author | iuc |
|---|---|
| date | Wed, 13 Jul 2016 14:47:52 -0400 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 28 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Wed Jul 13 14:47:52 2016 -0400 @@ -0,0 +1,28 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="stringtie" version="1.2.3"> + <install version="1.0"> + <actions> + <action type="download_by_url" sha256sum="1a323fd17c24889748c645b3dfe5a06305236d9899e87a27939a68404d2d9d09">https://ccb.jhu.edu/software/stringtie/dl/stringtie-1.2.3.tar.gz</action> + <action type="shell_command">make release</action> + <action type="move_file"> + <source>stringtie</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> + <environment_variable action="set_to" name="STRINGTIE_ROOT_PATH">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> +StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. +It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and +quantitate full-length transcripts representing multiple splice variants for each gene locus. +Its input can include not only the alignments of raw reads used by other transcript assemblers, +but also alignments longer sequences that have been assembled from those reads. +To identify differentially expressed genes between experiments, StringTie's +output can be processed either by the Cuffdiff or Ballgown programs. + </readme> + </package> +</tool_dependency>