1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c19fa5da36cc/ changeset: c19fa5da36cc user: jgoecks date: 2013-02-13 17:04:54 summary: Improved documentation in bowtie2 loc file. affected #: 1 file diff -r 7bf8f6a1da9c7d6148712e574f16a34a2c6e1525 -r c19fa5da36cc51fd5ee6005ed801a7e2c9aba229 tool-data/bowtie2_indices.loc.sample --- a/tool-data/bowtie2_indices.loc.sample +++ b/tool-data/bowtie2_indices.loc.sample @@ -1,37 +1,37 @@ -#This is a sample file distributed with Galaxy that enables tools -#to use a directory of Bowtie2 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 bowtie2_indices.loc -#file has this format (longer white space characters are TAB characters): +# bowtie2_indices.loc.sample +# This is a *.loc.sample file distributed with Galaxy that enables tools +# to use a directory of indexed data files. This one is for Bowtie2 and Tophat2. +# See the wiki: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup +# First create these data files and save them in your own data directory structure. +# Then, create a bowtie_indices.loc file to use those indexes with tools. +# Copy this file, save it with the same name (minus the .sample), +# follow the format examples, and store the result in this directory. +# The file should include an one line entry for each index set. +# The path points to the "basename" for the set, not a specific file. +# It has four text columns seperated by TABS. # -#<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/bowtie2/hg18/, -#then the bowtie2_indices.loc entry would look like this: +# So, for example, if you had hg18 indexes stored in: # -#hg18 hg18 hg18 /depot/data2/galaxy/bowtie2/hg18/hg18 +# /depot/data2/galaxy/hg19/bowtie2/ # -#and your /depot/data2/galaxy/bowtie2/hg18/ directory -#would contain hg18.*.ebwt files: +# containing hg19 genome and hg19.*.bt2 files, such as: +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.fa +# -rw-rw-r-- 1 james james 914M Feb 10 18:56 hg19canon.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.bt2 +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.bt2 +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.bt2 +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.bt2 # -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.1.ebwt -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.2.ebwt -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 hg18.3.ebwt -#...etc... +# then the bowtie2_indices.loc entry could look like this: # -#Your bowtie2_indices.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: +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie2/hg19canon # -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie2/hg18/hg18canon -#hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie2/hg18/hg18full -#/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 -#...etc... +#More examples: # -#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. +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie2/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie2/dm3 # +# 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.