Mercurial > repos > david-hoover > garbage1
changeset 4:6a81b7acaad4 draft
Uploaded
| author | david-hoover |
|---|---|
| date | Tue, 11 Sep 2012 15:53:53 -0400 |
| parents | 2de9956e59d2 |
| children | 23fc4a7dcf37 |
| files | gatk2_sorted_picard_index.loc.sample |
| diffstat | 1 files changed, 38 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/gatk2_sorted_picard_index.loc.sample Tue Sep 11 15:53:53 2012 -0400 @@ -0,0 +1,38 @@ +#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. +# +dm3 dm3 dm3 /data/galaxy/ext-tool-data/picard/dm3.fa +equCab2 equCab2 equCab2 /data/galaxy/ext-tool-data/picard/equCab2.fa +hg17 hg17 hg17 /data/galaxy/ext-tool-data/picard/hg17.fa +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 +mm10 mm10 mm10 /data/galaxy/ext-tool-data/picard/mm10.fa +rn4 rn4 rn4 /data/galaxy/ext-tool-data/picard/rn4.fa +sacCer2 sacCer2 sacCer2 /data/galaxy/ext-tool-data/picard/sacCer2.fa +sacCer3 sacCer3 sacCer3 /data/galaxy/ext-tool-data/picard/sacCer3.fa +xenTro2 xenTro2 xenTro2 /data/galaxy/ext-tool-data/picard/xenTro2.fa