Mercurial > repos > iuc > package_rsem_1_2_28
changeset 0:987ca85aead4 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rsem_1_2_28 commit 3c4a2b13b0f3a280de4f98f4f5e0dc29e10fc7a0
| author | iuc |
|---|---|
| date | Tue, 29 Mar 2016 06:33:46 -0400 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 142 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Tue Mar 29 06:33:46 2016 -0400 @@ -0,0 +1,142 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="ncurses" version="6.0"> + <repository changeset_revision="15e2190c87ca" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="zlib" version="1.2.8"> + <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + </package> + <package name="rsem" version="1.2.28"> + <install version="1.0"> + <actions> + <action sha256sum="b54c3ac0ab44b470ab0c29852d30b5194674e36375c3b9067eb3150f569de53e" type="download_by_url"> + https://github.com/deweylab/RSEM/archive/v1.2.28.tar.gz + </action> + <action type="set_environment_for_install"> + <repository changeset_revision="15e2190c87ca" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="ncurses" version="6.0" /> + </repository> + <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu"> + <package name="zlib" version="1.2.8" /> + </repository> + </action> + <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' samtools*/Makefile samtools*/config.mk</action> + <action type="shell_command">sed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" Makefile samtools*/Makefile</action> <!-- In case you have an obsolete zlib in /usr/lib --> + <action type="shell_command">make</action> + + <action type="move_file"> + <source>rsem-bam2readdepth</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-bam2wig</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-build-read-index</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-calculate-credibility-intervals</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-calculate-expression</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-control-fdr</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-extract-reference-transcripts</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-gen-transcript-plots</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-generate-data-matrix</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-generate-ngvector</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-get-unique</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-gff3-to-gtf</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-parse-alignments</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-plot-model</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-plot-transcript-wiggles</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-prepare-reference</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-preref</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-refseq-extract-primary-assembly</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-run-ebseq</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-run-em</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-run-gibbs</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-sam-validator</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-scan-for-paired-end-reads</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-simulate-reads</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-synthesis-reference-transcripts</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem-tbam2gbam</source> + <destination>$INSTALL_DIR</destination> + </action> + <action type="move_file"> + <source>rsem_perl_utils.pm</source> + <destination>$INSTALL_DIR</destination> + </action> + + <action type="set_environment"> + <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable> + </action> + </actions> + </install> + </package> +</tool_dependency>