# HG changeset patch # User Lance Parsons # Date 1314211222 14400 # Node ID ed97c3e7e0bde5a5f688088ec6de374a14e7ecc5 # Parent 8018e2acf4e5e06e440b2c379a28692ca91d8c2f Clarified use of sam_fa_indices.loc file in README diff -r 8018e2acf4e5 -r ed97c3e7e0bd bam_to_bigwig/README --- a/bam_to_bigwig/README Wed Aug 24 14:36:09 2011 -0400 +++ b/bam_to_bigwig/README Wed Aug 24 14:40:22 2011 -0400 @@ -4,8 +4,11 @@ Requirements ------------ - genomeCoverageBed - part of BedTools (http://code.google.com/p/bedtools/) - bedGraphToBigWig - from UCSC (http://hgdownload.cse.ucsc.edu/admin/exe/) +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 ------------ @@ -13,4 +16,3 @@ 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 - diff -r 8018e2acf4e5 -r ed97c3e7e0bd bam_to_bigwig/sam_fa_indices.loc.sample --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/bam_to_bigwig/sam_fa_indices.loc.sample Wed Aug 24 14:40:22 2011 -0400 @@ -0,0 +1,28 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Samtools indexed sequences data files. You will need +#to create these data files and then create a sam_fa_indices.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_indices.loc +#file has this format (white space characters are TAB characters): +# +#index +# +#So, for example, if you had hg18 indexed stored in +#/depot/data2/galaxy/sam/, +#then the sam_fa_indices.loc entry would look like this: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +# +#and your /depot/data2/galaxy/sam/ directory +#would contain hg18.fa and hg18.fa.fai files: +# +#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa +#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai +# +#Your sam_fa_indices.loc file should include an entry per line for +#each index set you have stored. The file in the path does actually +#exist, but it should never be directly used. Instead, the name serves +#as a prefix for the index file. For example: +# +#index hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg19 /depot/data2/galaxy/sam/hg19.fa diff -r 8018e2acf4e5 -r ed97c3e7e0bd sam_fa_indices.loc.sample --- a/sam_fa_indices.loc.sample Wed Aug 24 14:36:09 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,28 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Samtools indexed sequences data files. You will need -#to create these data files and then create a sam_fa_indices.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The sam_fa_indices.loc -#file has this format (white space characters are TAB characters): -# -#index -# -#So, for example, if you had hg18 indexed stored in -#/depot/data2/galaxy/sam/, -#then the sam_fa_indices.loc entry would look like this: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -# -#and your /depot/data2/galaxy/sam/ directory -#would contain hg18.fa and hg18.fa.fai files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai -# -#Your sam_fa_indices.loc file should include an entry per line for -#each index set you have stored. The file in the path does actually -#exist, but it should never be directly used. Instead, the name serves -#as a prefix for the index file. For example: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -#index hg19 /depot/data2/galaxy/sam/hg19.fa