Mercurial > repos > elixir-it > mutect2
changeset 5:aedc908f8ec9 draft
Uploaded
| author | elixir-it |
|---|---|
| date | Mon, 02 Jul 2018 04:44:59 -0400 |
| parents | bf507641cc5f |
| children | 5345d2d688d9 |
| files | tool-data/mutect2_indexes.loc tool-data/mutect2_indexes.loc.sample |
| diffstat | 2 files changed, 35 insertions(+), 35 deletions(-) [+] |
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--- a/tool-data/mutect2_indexes.loc Thu Jun 28 06:29:37 2018 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of MuTect2 indexed sequences data files. You will need -#to create these data files and then create a mutect2_indexes.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The mutect2_indexes.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id> <dbkey> <display_name> <file_path> -# -#So, for example, if you had phiX indexed stored in -#/depot/data2/galaxy/phiX/base/, -#then the bwa_index.loc entry would look like this: -# -#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa -# -#and your /depot/data2/galaxy/phiX/base/ directory -#would contain phiX.dict, phiX.fa.fai files. -# -# -#Your mutect2_indexes.loc file should include an entry per line for each -#index set you have stored. The "file" in the path does not actually -#exist, but it is the prefix for the actual index files. For example: -# -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa -#...etc... -# -#Note that for backwards compatibility with workflows, the unique ID of -#an entry must be the path that was in the original loc file, because that -#is the value stored in the workflow for that parameter. That is why the -#hg19 entry above looks odd. New genomes can be better-looking. -# -hg38 hg38 hg38_GDC /export/gatkhg38pl/GRCh38.d1.vd1.fa
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/mutect2_indexes.loc.sample Mon Jul 02 04:44:59 2018 -0400 @@ -0,0 +1,35 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of MuTect2 indexed sequences data files. You will need +#to create these data files and then create a mutect2_indexes.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The mutect2_indexes.loc +#file has this format (longer white space characters are TAB characters): +# +#<unique_build_id> <dbkey> <display_name> <file_path> +# +#So, for example, if you had phiX indexed stored in +#/depot/data2/galaxy/phiX/base/, +#then the bwa_index.loc entry would look like this: +# +#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa +# +#and your /depot/data2/galaxy/phiX/base/ directory +#would contain phiX.dict, phiX.fa.fai files. +# +# +#Your mutect2_indexes.loc file should include an entry per line for each +#index set you have stored. The "file" in the path does not actually +#exist, but it is the prefix for the actual index files. For example: +# +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa +#...etc... +# +#Note that for backwards compatibility with workflows, the unique ID of +#an entry must be the path that was in the original loc file, because that +#is the value stored in the workflow for that parameter. That is why the +#hg19 entry above looks odd. New genomes can be better-looking. +# +hg38 hg38 hg38_GDC /export/gatkhg38pl/GRCh38.d1.vd1.fa