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Per @yhoogstrate's suggestion https://github.com/galaxyproject/galaxy/commit/c0c286a9c69dcb23a50a0b9b249cd6e5b09a3aad#commitcomment-12594774, retab .loc.samples
This commit is contained in:
Dannon Baker
@@ -4,13 +4,13 @@
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#all_fasta.loc. This file has the format (white space characters are
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#TAB characters):
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#
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#<unique_build_id> <dbkey> <display_name> <file_path>
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#<unique_build_id> <dbkey> <display_name> <file_path>
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#
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#So, all_fasta.loc could look something like this:
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#
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#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
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#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
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#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
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#apiMel3 apiMel3 Honeybee (Apis mellifera): apiMel3 /path/to/genome/apiMel3/apiMel3.fa
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#hg19canon hg19 Human (Homo sapiens): hg19 Canonical /path/to/genome/hg19/hg19canon.fa
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#hg19full hg19 Human (Homo sapiens): hg19 Full /path/to/genome/hg19/hg19full.fa
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#
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#Your all_fasta.loc file should contain an entry for each individual
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#fasta file. So there will be multiple fasta files for each build,
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@@ -20,7 +20,7 @@
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#Your faseq.loc file should include an entry per line for each set of fasta
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#sequence files you have stored. For example:
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#
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#hg18 /depot/data2/galaxy/faseq/hg18
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#mm9 /depot/data2/galaxy/faseq/mm9
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#hg18 /depot/data2/galaxy/faseq/hg18
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#mm9 /depot/data2/galaxy/faseq/mm9
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#Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis
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#...etc...
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@@ -8,7 +8,7 @@
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#located at /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain,
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#then the liftOver.loc entry would look like this:
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#
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#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
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#anoCar1 galGal3 /depot/data2/galaxy/anoCar1/liftOver/anoCar1ToGalGal3.over.chain
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#
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#and your /depot/data2/galaxy/anoCar1/liftOver directory would
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#contain all of your "chain" files (e.g.):
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@@ -5,13 +5,13 @@
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#the directories in which those files are stored. The mosaik_index.loc
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#file has this format (longer white space is the TAB character):
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#
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#<unique_build_id> <dbkey> <display_name> <fasta_file_path>
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#<unique_build_id> <dbkey> <display_name> <fasta_file_path>
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#
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#So, for example, if you had hg18 indexed and stored in
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#/depot/data2/galaxy/mosaik/hg18/
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#then the mosaik_index.loc entry would look like this:
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#
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#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa
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#hg18 hg18 hg18 Pretty /depot/data2/galaxy/mosaik/hg18/hg18.fa
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#
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#and your /depot/data2/galaxy/mosaik/hg18/ directory
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#would contain the following files:
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@@ -4,7 +4,7 @@
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#in this directory) that points to the locations of those files. The ngs_sim.loc
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#file has this format (white space characters are TAB characters):
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#
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#<unique_build_id> <dbkey> <display_name> <file_base_path>
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#<unique_build_id> <dbkey> <display_name> <file_base_path>
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#
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#So, for example, if you had hg18chrM.fa in
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#/data/path/hg18/seq/,
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@@ -16,5 +16,5 @@
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#have stored.
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#
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#hg18chrM hg18 hg18chrM /data/path/hg18/seq/hg18chrM.fa
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#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa
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#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa
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#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa
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#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa
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@@ -5,7 +5,7 @@
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#the directories in which those files are stored. The perm_base_index.loc
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#file has this format (longer white space characters are TAB characters):
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#
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#<build_seed_readlength> <display_name> <file_base>
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#<build_seed_readlength> <display_name> <file_base>
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#
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#Because each PerM index is built with a specific seed and a specific read
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#length, this needs to be specified so the user can choose the appropriate
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@@ -13,7 +13,7 @@
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#50, and stored in /depot/data/galaxy/phiX/perm_index/,
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#then the perm_base_index.loc entry would look something like this:
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#
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#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
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#phiX_F3_50 phiX: seed=F3, read length=50 /depot/data/galaxy/phiX/perm_index/phiX_base_F3_50.index
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#
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#and your /depot/data/galaxy/phiX/perm_index/ directory
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#would contain the file phiX_base_F3_50.index:
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@@ -21,7 +21,7 @@
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#Your perm_base_index.loc file should include an entry per line for each
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#index set you have stored. For example:
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#
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#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
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#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
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#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
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#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
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#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
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#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_base_F3_50.index
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#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
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#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_base_F3_50.index
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@@ -5,7 +5,7 @@
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#the directories in which those files are stored. The perm_color_index.loc
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#file has this format (white space characters are TAB characters):
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#
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#<build_seed_readlength> <display_name> <file_base>
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#<build_seed_readlength> <display_name> <file_base>
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#
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#Because each PerM index is built with a specific seed and a specific read
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#length, this needs to be specified so the user can choose the appropriate
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@@ -13,7 +13,7 @@
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#50, and stored in /depot/data/galaxy/phiX/perm_index/,
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#then the perm_color_index.loc entry would look something like this:
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#
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#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
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#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
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#
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#and your /depot/data/galaxy/phiX/perm_index/ directory
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#would contain the file phiX_color_F3_50.index:
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@@ -21,8 +21,8 @@
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#Your perm_color_index.loc file should include an entry per line for each
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#index set you have stored. For example:
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#
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#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
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#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
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#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
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#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
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#phiX_F3_50 phiX: seed=F3, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
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#phiX_F4_50 phiX: seed=F4, read length=50 /data/galaxy/phiX/perm_index/phiX_color_F3_50.index
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#hg19_F3_50 hg19: seed=F3, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
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#hg19_F4_50 hg19: seed=F4, read length=50 /data/galaxy/hg19/perm_index/hg19_color_F3_50.index
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#
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@@ -5,13 +5,13 @@
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#the directories in which those files are stored. The picard_index.loc
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#file has this format (longer white space is the TAB character):
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#
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#<unique_build_id> <dbkey> <display_name> <fasta_file_path>
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#<unique_build_id> <dbkey> <display_name> <fasta_file_path>
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#
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#So, for example, if you had hg18 indexed and stored in
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#/depot/data2/galaxy/srma/hg18/,
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#then the srma_index.loc entry would look like this:
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#
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#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
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#hg18 hg18 hg18 Pretty /depot/data2/galaxy/picard/hg18/hg18.fa
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#
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#and your /depot/data2/galaxy/srma/hg18/ directory
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#would contain the following three files:
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@@ -8,7 +8,7 @@
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#/depot/data2/galaxy/regions/encode_regions_coords_hg16.bed, then the
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#regions.loc entry would look like this:
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#
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#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed
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#hg16 encode_hg16 ENCODE Regions /depot/data2/galaxy/regions/encode_regions_coords_hg16.bed
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#
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#and your /depot/data2/galaxy/regions/ directory would
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#contain all of your regions files (e.g.):
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@@ -8,7 +8,7 @@
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#the directories in which those files are stored. The srma_index.loc
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#file has this format (longer white space is the TAB character):
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#
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#<unique_build_id> <dbkey> <display_name> <fasta_file_path>
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#<unique_build_id> <dbkey> <display_name> <fasta_file_path>
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#
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#So, for example, if you had hg18 indexed and stored in
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#/depot/data2/galaxy/srma/hg18/,
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