Mercurial > repos > jjohnson > gatk2
diff gatk2_sorted_picard_index.loc.sample @ 0:74c05070a3f8 draft
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| author | jjohnson |
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| date | Thu, 01 Nov 2012 13:53:22 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk2_sorted_picard_index.loc.sample Thu Nov 01 13:53:22 2012 -0400 @@ -0,0 +1,30 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of Picard dict and associated files. You will need +#to create these data files and then create a picard_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The picard_index.loc +#file has this format (longer white space is the TAB character): +# +#<unique_build_id> <dbkey> <display_name> <fasta_file_path> +# +#So, for example, if you had hg18 indexed and stored in +#/depot/data2/galaxy/srma/hg18/, +#then the srma_index.loc entry would look like this: +# +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa +# +#and your /depot/data2/galaxy/srma/hg18/ directory +#would contain the following three files: +#hg18.fa +#hg18.dict +#hg18.fa.fai +# +#The dictionary file for each reference (ex. hg18.dict) must be +#created via Picard (http://picard.sourceforge.net). Note that +#the dict file does not have the .fa extension although the +#path list in the loc file does include it. +# +hg18 hg18 hg18 /data/galaxy/ext-tool-data/picard/hg18.fa +hg19 hg19 hg19 /data/galaxy/ext-tool-data/picard/hg19.fa +mm8 mm8 mm8 /data/galaxy/ext-tool-data/picard/mm8.fa +mm9 mm9 mm9 /data/galaxy/ext-tool-data/picard/mm9.fa