Mercurial > repos > lparsons > bam_to_bigwig

diff README @ 3:b8525303b945

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Reorganized repo
author Lance Parsons <lparsons@princeton.edu>
date Wed, 24 Aug 2011 14:43:09 -0400
parents bam_to_bigwig/README@ed97c3e7e0bd
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+Galaxy tool wrapper to generate BigWig coverage files from BAM files. BigWig
+files can be displaye at UCSC directly from Galaxy. Allows user to split gapped
+reads (particularly useful for RNA-Seq with large splice regions).
+
+Requirements
+------------
+genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/)
+bedGraphToBigWig  - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/)
+
+This tool also uses the samtools fai fasta index files stored in Galaxy's shared
+tool data directory. A sample version of this file is included for completeness. 
+
+Installation
+------------
+
+1 - Install genomeCoverageBed and bedGraphToBigWig and make sure they in the PATH 
+2 - Copy bam_to_bigwig.xml to $GALAXY_HOME/tools/bam_to_bigwig
+3 - Add the tool to the $GALAXY_HOME/tool_conf.xml tool-registry file