diff --git a/tool-data/all_fasta.loc.sample b/tool-data/all_fasta.loc.sample index 3daaf92a7c2..1a5a28d5e3f 100644 --- 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): # -# +# # #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 --git a/tool-data/faseq.loc.sample b/tool-data/faseq.loc.sample index e818d38fa8a..1f1d781594a 100644 --- 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 +#hg18 /depot/data2/galaxy/faseq/hg18 +#mm9 /depot/data2/galaxy/faseq/mm9 #Arabidopsis /depot/data2/galaxy/faseq/Arabidopsis #...etc... diff --git a/tool-data/liftOver.loc.sample b/tool-data/liftOver.loc.sample index c679a4b7295..777a25af461 100644 --- 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 --git a/tool-data/mosaik_index.loc.sample b/tool-data/mosaik_index.loc.sample index 16bfae6b02f..59286b0ac5f 100644 --- 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): # -# +# # #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 --git a/tool-data/ngs_sim_fasta.loc.sample b/tool-data/ngs_sim_fasta.loc.sample index 66b55390a39..70623c198e3 100644 --- a/tool-data/ngs_sim_fasta.loc.sample +++ b/tool-data/ngs_sim_fasta.loc.sample @@ -4,7 +4,7 @@ #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): # -# +# # #So, for example, if you had hg18chrM.fa in #/data/path/hg18/seq/, @@ -16,5 +16,5 @@ #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 +#phiX174 phiX phiX174 /data/path/genome/phiX/seq/phiX.fa +#pUC18 pUC18 pUC18 /data/path/genome/pUC18/seq/pUC18.fa diff --git a/tool-data/perm_base_index.loc.sample b/tool-data/perm_base_index.loc.sample index 2a06e3f2170..ff6a06bf553 100644 --- 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): # -# +# # #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 --git a/tool-data/perm_color_index.loc.sample b/tool-data/perm_color_index.loc.sample index 6c2341f55a9..00f687a65a7 100644 --- 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): # -# +# # #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 --git a/tool-data/picard_index.loc.sample b/tool-data/picard_index.loc.sample index cc326418abe..d1055684e70 100644 --- 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): # -# +# # #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 --git a/tool-data/regions.loc.sample b/tool-data/regions.loc.sample index 30117de98a3..fac1412c3c3 100644 --- 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 --git a/tool-data/srma_index.loc.sample b/tool-data/srma_index.loc.sample index b2de62f7a45..ef138333e39 100644 --- a/tool-data/srma_index.loc.sample +++ b/tool-data/srma_index.loc.sample @@ -8,7 +8,7 @@ #the directories in which those files are stored. The srma_index.loc #file has this format (longer white space is the TAB character): # -# +# # #So, for example, if you had hg18 indexed and stored in #/depot/data2/galaxy/srma/hg18/,