1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/463fc935b97c/ changeset: 463fc935b97c user: dannon date: 2012-03-23 13:59:34 summary: Convert loc file examples to use tabs instead of spaces. affected #: 22 files diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/all_fasta.loc.sample --- a/tool-data/all_fasta.loc.sample +++ b/tool-data/all_fasta.loc.sample @@ -4,13 +4,13 @@ #all_fasta.loc. This file has the format (white space characters are #TAB characters): # -#<unique_build_id><dbkey><display_name><file_path> +#<unique_build_id><dbkey><display_name><file_path> # #So, all_fasta.loc could look something like this: # -#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa -#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa -#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa +#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa +#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa +#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa # #Your all_fasta.loc file should contain an entry for each individual #fasta file. So there will be multiple fasta files for each build, diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb.loc.sample --- a/tool-data/blastdb.loc.sample +++ b/tool-data/blastdb.loc.sample @@ -2,7 +2,7 @@ #list of nucleotide BLAST databases, using three columns tab separated #(longer whitespace are TAB characters): # -#<unique_id><database_caption><base_name_path> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, @@ -25,9 +25,9 @@ #Your blastdb.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk -#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk -#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test +#nt_02_Dec_2009 nt 02 Dec 2009 /depot/data2/galaxy/blastdb/nt/nt.chunk +#wgs_30_Nov_2009 wgs 30 Nov 2009 /depot/data2/galaxy/blastdb/wgs/wgs.chunk +#test_20_Sep_2008 test 20 Sep 2008 /depot/data2/galaxy/blastdb/test/test #...etc... # #See also blastdb_p.loc which is for any protein BLAST database. diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/blastdb_p.loc.sample --- a/tool-data/blastdb_p.loc.sample +++ b/tool-data/blastdb_p.loc.sample @@ -2,25 +2,25 @@ #list of protein BLAST databases, using three columns tab separated #(longer whitespace are TAB characters): # -#<unique_id><database_caption><base_name_path> +#<unique_id><database_caption><base_name_path> # #The captions typically contain spaces and might end with the build date. #It is important that the actual database name does not have a space in it, #and that the first tab that appears in the line is right before the path. # -#So, for example, if your database is NR and the path to your base name +#So, for example, if your database is NR and the path to your base name #is /data/blastdb/nr, then the blastdb_p.loc entry would look like this: # -#nr NCBI NR (non redundant) /data/blastdb/nr +#nr NCBI NR (non redundant) /data/blastdb/nr # #and your /data/blastdb directory would contain all of the files associated #with the database, /data/blastdb/nr.*. # -#Your blastdb_p.loc file should include an entry per line for each "base name" +#Your blastdb_p.loc file should include an entry per line for each "base name" #you have stored. For example: # -#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr -#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr +#nr_05Jun2010 NCBI NR (non redundant) 05 Jun 2010 /data/blastdb/05Jun2010/nr +#nr_15Aug2010 NCBI NR (non redundant) 15 Aug 2010 /data/blastdb/15Aug2010/nr #...etc... # #See also blastdb.loc which is for any nucleotide BLAST database. diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bowtie_indices_color.loc.sample --- a/tool-data/bowtie_indices_color.loc.sample +++ b/tool-data/bowtie_indices_color.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The bowtie_indices.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_base_path> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/bowtie/hg18/, @@ -25,9 +25,9 @@ #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: # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon +#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full +#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index.loc.sample --- a/tool-data/bwa_index.loc.sample +++ b/tool-data/bwa_index.loc.sample @@ -25,10 +25,10 @@ #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 +#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 diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/bwa_index_color.loc.sample --- a/tool-data/bwa_index_color.loc.sample +++ b/tool-data/bwa_index_color.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The bwa_index_color.loc #file has this format (longer white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_path> +#<unique_build_id><dbkey><display_name><file_path> # #So, for example, if you had phiX indexed stored in #/depot/data2/galaxy/phiX/color/, @@ -25,10 +25,10 @@ #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/color/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa +#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa +#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa +#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa +#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa #...etc... # #Note that for backwards compatibility with workflows, the unique ID of diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/faseq.loc.sample --- a/tool-data/faseq.loc.sample +++ b/tool-data/faseq.loc.sample @@ -20,7 +20,7 @@ #Your faseq.loc file should include an entry per line for each set of fasta #sequence files you have stored. For example: # -#hg18 /depot/data2/galaxy/faseq/hg18 -#mm9 /depot/data2/galaxy/faseq/mm9 -#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis +#hg18 /depot/data2/galaxy/faseq/hg18 +#mm9 /depot/data2/galaxy/faseq/mm9 +#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gatk_sorted_picard_index.loc.sample --- a/tool-data/gatk_sorted_picard_index.loc.sample +++ b/tool-data/gatk_sorted_picard_index.loc.sample @@ -5,13 +5,13 @@ #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> +#<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/, +#/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 +#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: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.chrlens.loc.sample --- a/tool-data/gd.chrlens.loc.sample +++ b/tool-data/gd.chrlens.loc.sample @@ -6,17 +6,17 @@ # file has the following format (white space characters are TAB # characters): # -#<species><reference_species_file_path> +#<species><reference_species_file_path> # # So, for example, if you used Monodelphis domestica as the reference # species for a collection of Sarcophilus harrisii SNPs, then the # gd.chrlens.loc entry would look like this: # -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt +#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt # # Your gd.chrlens.loc file should include an entry for each pair of # species SNPs and reference species. For example: # -#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt -#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt +#bighorn /galaxy/data/location/gd/chrlens/cow_chr_lengths.txt +#tasmanian_devil /galaxy/data/location/gd/chrlens/mondom_chr_lengths.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.primers.loc.sample --- a/tool-data/gd.primers.loc.sample +++ b/tool-data/gd.primers.loc.sample @@ -5,18 +5,18 @@ # primers files are stored. The gd.primers.loc file has the following # format (white space characters are TAB characters): # -#<species><primers_file_path> +#<species><primers_file_path> # # So, for example, if you had a primers file located at # /galaxy/data/location/gd/primers/bighorn_primers.txt for a collection of # Ovis canadensis SNPs, then the gd.primers.loc entry would look like # this: # -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt +#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt # # Your gd.primers.loc file should include an entry for each pair of # species SNPs and primers file. For example: # -#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt -#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt +#bighorn /galaxy/data/location/gd/primers/bighorn_primers.txt +#tasmanian_devil /galaxy/data/location/gd/primers/tasmanian_devil_primers.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/gd.snps.loc.sample --- a/tool-data/gd.snps.loc.sample +++ b/tool-data/gd.snps.loc.sample @@ -5,17 +5,17 @@ # SNP call files are stored. The gd.snps.loc file has the following # format (white space characters are TAB characters): # -#<species><SNP_call_file_path> +#<species><SNP_call_file_path> # # So, for example, if you had a SNP call file located at # /galaxy/data/location/gd/snps/bighorn_snps.txt for a collection of # Ovis canadensis SNPs, then the gd.snps.loc entry would look like this: # -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt +#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt # # Your gd.snps.loc file should include an entry for each pair of species # SNPs and SNP call file. For example: # -#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt -#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt +#bighorn /galaxy/data/location/gd/snps/bighorn_snps.txt +#tasmanian_devil /galaxy/data/location/gd/snps/tasmanian_devil_snps.txt #...etc... diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/lastz_seqs.loc.sample --- a/tool-data/lastz_seqs.loc.sample +++ b/tool-data/lastz_seqs.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The lastz_seqs.loc #file has this format (white space characters are TAB characters): # -#<unique_build_id><display_name><file_path> +#<unique_build_id><display_name><file_path> # #So, for example, if your lastz_seqs.loc began like this: # -#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit -#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit -#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit +#hg18 Human (Homo sapiens): hg18 /depot/data2/galaxy/twobit/hg18.2bit +#hg19 Human (Homo sapiens): hg19 /depot/data2/galaxy/twobit/hg19.2bit +#mm9 Mouse (Mus musculus): mm9 /depot/data2/galaxy/twobit/mm9.2bit # #then your /depot/data2/galaxy/twobit/ directory #would need to contain the following 2bit files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/liftOver.loc.sample --- a/tool-data/liftOver.loc.sample +++ b/tool-data/liftOver.loc.sample @@ -8,7 +8,7 @@ #located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain, #then the liftOver.loc entry would look like this: # -#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain +#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain # #and your /depot/data2/galaxy/anoCar1/liftOver directory would #contain all of your "chain" files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/mosaik_index.loc.sample --- a/tool-data/mosaik_index.loc.sample +++ b/tool-data/mosaik_index.loc.sample @@ -5,13 +5,13 @@ #the directories in which those files are stored. The mosaik_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<unique_build_id><dbkey><display_name><fasta_file_path> # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/mosaik/hg18/ #then the mosaik_index.loc entry would look like this: # -#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa # #and your /depot/data2/galaxy/mosaik/hg18/ directory #would contain the following files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/ngs_sim_fasta.loc.sample --- a/tool-data/ngs_sim_fasta.loc.sample +++ b/tool-data/ngs_sim_fasta.loc.sample @@ -4,17 +4,17 @@ #in this directory) that points to the locations of those files. The ngs_sim.loc #file has this format (white space characters are TAB characters): # -#<unique_build_id><dbkey><display_name><file_base_path> +#<unique_build_id><dbkey><display_name><file_base_path> # #So, for example, if you had hg18chrM.fa in #/data/path/hg18/seq/, #then the ngs_sim.loc entry would look like this: # -#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa +#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa # #Your ngs_sim.loc file should include an entry per line for each FASTA file you #have stored. # -#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa -#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa -#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa +#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa +#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa +#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_base_index.loc.sample --- a/tool-data/perm_base_index.loc.sample +++ b/tool-data/perm_base_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_base_index.loc #file has this format (longer white space characters are TAB characters): # -#<build_seed_readlength><display_name><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_base_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_base_F3_50.index: @@ -21,7 +21,7 @@ #Your perm_base_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index -#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index -#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/perm_color_index.loc.sample --- a/tool-data/perm_color_index.loc.sample +++ b/tool-data/perm_color_index.loc.sample @@ -5,7 +5,7 @@ #the directories in which those files are stored. The perm_color_index.loc #file has this format (white space characters are TAB characters): # -#<build_seed_readlength><display_name><file_base> +#<build_seed_readlength><display_name><file_base> # #Because each PerM index is built with a specific seed and a specific read #length, this needs to be specified so the user can choose the appropriate @@ -13,7 +13,7 @@ #50, and stored in /depot/data/galaxy/phiX/perm_index/, #then the perm_color_index.loc entry would look something like this: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index # #and your /depot/data/galaxy/phiX/perm_index/ directory #would contain the file phiX_color_F3_50.index: @@ -21,8 +21,8 @@ #Your perm_color_index.loc file should include an entry per line for each #index set you have stored. For example: # -#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index -#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index -#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index +#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index +#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index # diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/picard_index.loc.sample --- a/tool-data/picard_index.loc.sample +++ b/tool-data/picard_index.loc.sample @@ -5,13 +5,13 @@ #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> +#<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 +#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: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/quality_scores.loc.sample --- a/tool-data/quality_scores.loc.sample +++ b/tool-data/quality_scores.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/panTro2/quality_scores, then the quality_scores.loc entry #would look like this: # -#panTro2 /depot/data2/galaxy/panTro2/quality_scores +#panTro2 /depot/data2/galaxy/panTro2/quality_scores # #and your /depot/data2/galaxy/panTro2/quality_scores directory would #contain all of your quality score files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/regions.loc.sample --- a/tool-data/regions.loc.sample +++ b/tool-data/regions.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed, then the #regions.loc entry would look like this: # -#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed +#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed # #and your /depot/data2/galaxy/regions/ directory would #contain all of your regions files (e.g.): diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/srma_index.loc.sample --- a/tool-data/srma_index.loc.sample +++ b/tool-data/srma_index.loc.sample @@ -8,13 +8,13 @@ #the directories in which those files are stored. The srma_index.loc #file has this format (longer white space is the TAB character): # -#<unique_build_id><dbkey><display_name><fasta_file_path> +#<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/srma/hg18/hg18.fa +#hg18 hg18 hg18 Pretty /depot/data2/galaxy/srma/hg18/hg18.fa # #and your /depot/data2/galaxy/srma/hg18/ directory #would contain the following three files: diff -r 732c10115fdf807ada88bf83cfe8a03f0c1c599e -r 463fc935b97cf697f0fb0a48aae052a35c8e95c7 tool-data/twobit.loc.sample --- a/tool-data/twobit.loc.sample +++ b/tool-data/twobit.loc.sample @@ -8,7 +8,7 @@ #/depot/data2/galaxy/droPer1/, then the twobit.loc entry #would look like this: # -#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit # #and your /depot/data2/galaxy/droPer1/ directory would #contain all of your twobit files (e.g.): @@ -19,8 +19,8 @@ #Your twobit.loc file should include an entry per line for each twobit #file you have stored. For example: # -#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit -#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit -#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit -#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit +#droPer1 /depot/data2/galaxy/droPer1/droPer1.2bit +#apiMel2 /depot/data2/galaxy/apiMel2/apiMel2.2bit +#droAna1 /depot/data2/galaxy/droAna1/droAna1.2bit +#droAna2 /depot/data2/galaxy/droAna2/droAna2.2bit #...etc... Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.