Mercurial > repos > devteam > tophat_fusion_post
changeset 3:2f75d0317ee5
Use Bowtie rather than Bowtie2 and update wrapper to fix Cheetah syntax bug.
| author | devteam@galaxyproject.org |
|---|---|
| date | Mon, 10 Feb 2014 12:13:22 -0500 |
| parents | 664f7d964231 |
| children | 51ede4e7d4f0 |
| files | tool-data/bowtie_indices.loc.sample tool_dependencies.xml tophat_fusion_post.xml |
| diffstat | 3 files changed, 44 insertions(+), 7 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool-data/bowtie_indices.loc.sample Mon Feb 10 12:13:22 2014 -0500 @@ -0,0 +1,37 @@ +# bowtie_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 Bowtie and Tophat. +# 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> +# +# So, for example, if you had hg18 indexes stored in: +# +# /depot/data2/galaxy/hg19/bowtie/ +# +# containing hg19 genome and hg19.*.ewbt 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.ewbt +# -rw-rw-r-- 1 james james 683M Feb 10 18:56 hg19canon.2.ewbt +# -rw-rw-r-- 1 james james 3.3K Feb 10 16:54 hg19canon.3.ewbt +# -rw-rw-r-- 1 james james 683M Feb 10 16:54 hg19canon.4.ewbt +# -rw-rw-r-- 1 james james 914M Feb 10 20:45 hg19canon.rev.1.ewbt +# -rw-rw-r-- 1 james james 683M Feb 10 20:45 hg19canon.rev.2.ewbt +# +# then the bowtie2_indices.loc entry could look like this: +# +#hg19 hg19 Human (hg19) /depot/data2/galaxy/hg19/bowtie/hg19canon +# +#More examples: +# +#mm10 mm10 Mouse (mm10) /depot/data2/galaxy/mm10/bowtie/mm10 +#dm3 dm3 D. melanogaster (dm3) /depot/data2/galaxy/mm10/bowtie/dm3 +# +#
--- a/tool_dependencies.xml Sun Feb 09 15:48:15 2014 -0500 +++ b/tool_dependencies.xml Mon Feb 10 12:13:22 2014 -0500 @@ -1,9 +1,9 @@ <?xml version="1.0"?> <tool_dependency> <package name="blast+" version="2.2.28"> - <repository changeset_revision="23b9ba41ad00" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository name="package_blast_plus_2_2_28" owner="iuc"/> </package> - <package name="bowtie2" version="2.1.0"> - <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <package name="bowtie" version="0.12.7"> + <repository name="package_bowtie_0_12_7" owner="devteam"/> </package> </tool_dependency>
--- a/tophat_fusion_post.xml Sun Feb 09 15:48:15 2014 -0500 +++ b/tophat_fusion_post.xml Mon Feb 10 12:13:22 2014 -0500 @@ -3,14 +3,14 @@ <version_command>tophat-fusion-post --version</version_command> <requirements> <requirement type="package" version="2.2.28">blast+</requirement> - <requirement type="package" version="2.1.0">bowtie2</requirement> + <requirement type='package' version="0.12.7">bowtie</requirement> </requirements> <command> ## Set up tophat_out structure. mkdir tophat_out; ln -s $accepted_hits tophat_out/accepted_hits.bam; ln -s $fusions tophat_out/fusions.out; ## Set up blast directory structure. - #set blast_db_path = ${__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} + #set blast_db_path = $__get_data_table_entry__('tophat_fusion_blastdb_indexes', 'dbkey', $accepted_hits.dbkey, 'path') ln -s ${blast_db_path}/ blast; ## Set up additional files: @@ -25,8 +25,8 @@ --non-human #end if - ## Bowtie2 indices. - ${__get_data_table_entry__('bowtie2_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} + ## Bowtie indices. + ${__get_data_table_entry__('bowtie_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} </command> <inputs>