Mercurial > repos > jjohnson > package_rsem_1_2_7
changeset 0:37fc24869870 draft default tip
Uploaded
| author | jjohnson |
|---|---|
| date | Fri, 22 Nov 2013 16:27:37 -0500 |
| parents | |
| children | |
| files | tool_dependencies.xml |
| diffstat | 1 files changed, 134 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Fri Nov 22 16:27:37 2013 -0500 @@ -0,0 +1,134 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="rsem" version="1.2.7"> + <install version="1.0"> + <actions> + <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.7.tar.gz</action> + <action type="shell_command">make</action> + + <action type="move_file"> + <source>convert-sam-for-rsem</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>extract-transcript-to-gene-map-from-trinity</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-bam2readdepth</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-bam2wig</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-build-read-index</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-calculate-credibility-intervals</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-calculate-expression</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-extract-reference-transcripts</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-gen-transcript-plots</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-get-unique</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-parse-alignments</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-plot-model</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-plot-transcript-wiggles</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-prepare-reference</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-preref</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-run-em</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-run-gibbs</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-simulate-reads</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-synthesis-reference-transcripts</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-tbam2gbam</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-control-fdr</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-generate-data-matrix</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-generate-ngvector</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-run-ebseq</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-sam-validator</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem-scan-for-paired-end-reads</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="move_file"> + <source>rsem_perl_utils.pm</source> + <destination>$INSTALL_DIR/bin</destination> + </action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + </action> + </actions> + </install> + <readme> +RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly +interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, +variable-length reads and RSPD estimation. In addition, it provides posterior mean and 95X credibility interval estimates for expression levels. +For visualization,It can generate BAM and Wiggle files in both transcript-coordinate and genomic-coordinate. Genomic-coordinate files +can be visualized by both UCSC Genome browser and Broad InstituteXs Integrative Genomics Viewer (IGV). +Transcript-coordinate files can be visualized by IGV. + +http://deweylab.biostat.wisc.edu/rsem/README.html +http://deweylab.biostat.wisc.edu/rsem/ + </readme> + </package> +</tool_dependency>