details: http://www.bx.psu.edu/hg/galaxy/rev/ebe3e881ac25 changeset: 2843:ebe3e881ac25 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Wed Oct 07 15:31:18 2009 -0400 description: Updated several sample index loc files to make it clearer how the actual loc files should appear 4 file(s) affected in this change: tool-data/bowtie_indices.loc.sample tool-data/sam_fa_indices.loc.sample tool-data/sequence_index_base.loc.sample tool-data/sequence_index_color.loc.sample diffs (89 lines): diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/bowtie_indices.loc.sample --- a/tool-data/bowtie_indices.loc.sample Wed Oct 07 15:25:16 2009 -0400 +++ b/tool-data/bowtie_indices.loc.sample Wed Oct 07 15:31:18 2009 -0400 @@ -1,8 +1,8 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of Bowtie indexed sequences data files. You will need #to create these data files and then create a bowtie_indices.loc file -#similar to this one (store it in this directory ) that points to -#the directories in which those files are stored. The bowtie_indices.loc +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The bowtie_indices.loc #file has this format (white space characters are TAB characters): # #<build> <file_base> @@ -26,3 +26,4 @@ #exist, but it is the prefix for the actual index files. For example: # #hg18 /depot/data2/galaxy/bowtie/hg18/hg18 +#hg19 /depot/data2/galaxy/bowtie/hg19/hg19 diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sam_fa_indices.loc.sample --- a/tool-data/sam_fa_indices.loc.sample Wed Oct 07 15:25:16 2009 -0400 +++ b/tool-data/sam_fa_indices.loc.sample Wed Oct 07 15:31:18 2009 -0400 @@ -1,17 +1,17 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of Samtools indexed sequences data files. You will need #to create these data files and then create a sam_fa_indices.loc file -#similar to this one (store it in this directory ) that points to -#the directories in which those files are stored. The sam_fa_indices.loc +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sam_fa_indices.loc #file has this format (white space characters are TAB characters): # -#<index> <seq> <location> +#index <seq> <location> # #So, for example, if you had hg18 indexed stored in #/depot/data2/galaxy/sam/, #then the sam_fa_indices.loc entry would look like this: # -#hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg18 /depot/data2/galaxy/sam/hg18.fa # #and your /depot/data2/galaxy/sam/ directory #would contain hg18.fa and hg18.fa.fai files: @@ -24,4 +24,5 @@ #exist, but it should never be directly used. Instead, the name serves #as a prefix for the index file. For example: # -#hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg18 /depot/data2/galaxy/sam/hg18.fa +#index hg19 /depot/data2/galaxy/sam/hg19.fa diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sequence_index_base.loc.sample --- a/tool-data/sequence_index_base.loc.sample Wed Oct 07 15:25:16 2009 -0400 +++ b/tool-data/sequence_index_base.loc.sample Wed Oct 07 15:31:18 2009 -0400 @@ -1,8 +1,8 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of BWA indexed sequences data files. You will need #to create these data files and then create a sequence_index_base.loc file -#similar to this one (store it in this directory ) that points to -#the directories in which those files are stored. The sequence_index_base.loc +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sequence_index_base.loc #file has this format (white space characters are TAB characters): # #<build> <file_base> @@ -26,3 +26,4 @@ #exist, but it is the prefix for the actual index files. For example: # #phiX /depot/data2/galaxy/phiX/base/phiX.fa +#hg18 /depot/data2/galaxy/hg18/base/hg18.fa diff -r 31c577c6fd49 -r ebe3e881ac25 tool-data/sequence_index_color.loc.sample --- a/tool-data/sequence_index_color.loc.sample Wed Oct 07 15:25:16 2009 -0400 +++ b/tool-data/sequence_index_color.loc.sample Wed Oct 07 15:31:18 2009 -0400 @@ -1,8 +1,8 @@ #This is a sample file distributed with Galaxy that enables tools #to use a directory of BWA indexed sequences data files. You will need #to create these data files and then create a sequence_index_color.loc file -#similar to this one (store it in this directory ) that points to -#the directories in which those files are stored. The sequence_index_color.loc +#similar to this one (store it in this directory) that points to +#the directories in which those files are stored. The sequence_index_color.loc #file has this format (white space characters are TAB characters): # #<build> <file_base> @@ -26,3 +26,4 @@ #exist, but it is the prefix for the actual index files. For example: # #phiX /depot/data2/galaxy/phiX/color/phiX.fa +#hg18 /depot/data2/galaxy/hg18/color/hg18.fa