Mercurial > repos > jjohnson > package_rsem_1_2_8

changeset 0:bb5e68f15713 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Fri, 13 Dec 2013 10:12:16 -0500
parents
children
files tool_dependencies.xml
diffstat 1 files changed, 164 insertions(+), 0 deletions(-) [+]
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Dec 13 10:12:16 2013 -0500
@@ -0,0 +1,164 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="R_3_0_1" version="3.0.1">
+        <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="rsem" version="1.2.8">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.2.8.tar.gz</action>
+                <action type="shell_command">make</action>
+                <action type="make_directory">$INSTALL_DIR/bin/sam</action> 
+                <action type="move_file">
+                    <source>sam/samtools</source>
+                    <destination>$INSTALL_DIR/bin/sam</destination>
+                </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>$INSTALL_DIR/bin</destination>
+                </action>
+                <action type="set_environment_for_install">
+                    <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu/">
+                        <package name="R_3_0_1" version="3.0.1" />
+                    </repository>
+                </action>
+                <action type="shell_command">make ebseq</action>
+                <action type="make_directory">$INSTALL_DIR/bin/EBSeq</action> 
+                <action type="move_directory_files">
+                    <source_directory>EBSeq/EBSeq</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin/EBSeq</destination_directory>
+                </action>
+                <action type="move_directory_files">
+                    <source_directory>EBSeq/blockmodeling</source_directory>
+                    <destination_directory>$INSTALL_DIR/bin/EBSeq</destination_directory>
+                </action>
+                <action type="move_file">
+                    <source>EBSeq/rsem-for-ebseq-find-DE</source>
+                    <destination>$INSTALL_DIR/bin/EBSeq</destination>
+                </action>
+                <action type="move_file">
+                    <source>EBSeq/rsem-for-ebseq-generate-ngvector-from-clustering-info</source>
+                    <destination>$INSTALL_DIR/bin/EBSeq</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>