# HG changeset patch
# User jjohnson
# Date 1391728049 18000
# Node ID cd7f70d4c6870d0c01cba62e70e79041385c5e7f

Uploaded

diff -r 000000000000 -r cd7f70d4c687 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Thu Feb 06 18:07:29 2014 -0500
@@ -0,0 +1,110 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="rsem" version="1.1.17">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.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="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>