Mercurial > repos > elixir-it > muse
changeset 7:110b3018eb2a draft default tip
Uploaded
| author | elixir-it |
|---|---|
| date | Sat, 21 Sep 2019 13:21:15 -0400 |
| parents | b48eb134cfcc |
| children | |
| files | tool-data/gatk_sorted_picard_index.loc.sample tool-data/muse_index.loc.sample tool_data_table_conf.xml.sample |
| diffstat | 3 files changed, 35 insertions(+), 37 deletions(-) [+] |
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--- a/tool-data/gatk_sorted_picard_index.loc.sample Fri Sep 20 08:25:16 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,36 +0,0 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of MuSE fasta files. You will need -#to create these data files and then create a muse_index.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The muse_index.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. -# -#hg19 hg19 hg19_GATK_bundle /cvmfs/elixir-italy.galaxy.refdata/index_GATK_bundle/ucsc.hg19/ucsc.hg19.fasta -
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/muse_index.loc.sample Sat Sep 21 13:21:15 2019 -0400 @@ -0,0 +1,34 @@ +#This is a sample file distributed with Galaxy that enables tools +#to use a directory of MuSE indexed sequences data files. You will need +#to create these data files and then create a muse_index.loc file +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The muse_index.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 muse_index.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. +#
--- a/tool_data_table_conf.xml.sample Fri Sep 20 08:25:16 2019 -0400 +++ b/tool_data_table_conf.xml.sample Sat Sep 21 13:21:15 2019 -0400 @@ -2,6 +2,6 @@ <!-- Locations of indexes in the muse_call mapper format --> <table name="muse_index" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="/cvmfs/data.galaxyproject.org/byhand/location/gatk_sorted_picard_index.loc" /> + <file path="tool-data/muse_index.loc" /> </table> </tables>