1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/cfd26c91f6c3/ changeset: cfd26c91f6c3 user: inithello date: 2012-09-28 21:35:44 summary: Migrate BWA to the tool shed. affected #: 6 files diff -r 203e3e1592439dcb8c0eb890545ed38a66f08f2c -r cfd26c91f6c3bb8b6365e7835263e11fc3013004 lib/galaxy/tool_shed/migrate/versions/0005_tools.py --- /dev/null +++ b/lib/galaxy/tool_shed/migrate/versions/0005_tools.py @@ -0,0 +1,15 @@ +""" +The tools "Map with BWA for Illumina" and "Map with BWA for SOLiD" have +been eliminated from the distribution. The tools are now available +in the repository named bwa_wrappers from the main Galaxy tool shed at +http://toolshed.g2.bx.psu.edu, and will be installed into your local +Galaxy instance at the location discussed above by running the following +command. +""" + +import sys + +def upgrade(): + print __doc__ +def downgrade(): + pass diff -r 203e3e1592439dcb8c0eb890545ed38a66f08f2c -r cfd26c91f6c3bb8b6365e7835263e11fc3013004 scripts/migrate_tools/0005_tools.sh --- /dev/null +++ b/scripts/migrate_tools/0005_tools.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/migrate_tools/migrate_tools.py 0005_tools.xml $@ diff -r 203e3e1592439dcb8c0eb890545ed38a66f08f2c -r cfd26c91f6c3bb8b6365e7835263e11fc3013004 scripts/migrate_tools/0005_tools.xml --- /dev/null +++ b/scripts/migrate_tools/0005_tools.xml @@ -0,0 +1,7 @@ +<?xml version="1.0"?> +<toolshed name="toolshed.g2.bx.psu.edu"> + <repository name="bwa_wrappers" description="Galaxy wrappers for the BWA short read aligner." changeset_revision="ffa8aaa14f7c"> + <tool id="bwa_wrapper" version="1.2.3" file="bwa_wrapper.xml"/> + <tool id="bwa_color_wrapper" version="1.0.2" file="bwa_color_wrapper.xml"/> + </repository> +</toolshed> diff -r 203e3e1592439dcb8c0eb890545ed38a66f08f2c -r cfd26c91f6c3bb8b6365e7835263e11fc3013004 tool-data/bwa_index.loc.sample --- a/tool-data/bwa_index.loc.sample +++ /dev/null @@ -1,38 +0,0 @@ -#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 bwa_index.loc file -#similar to this one (store it in this directory) that points to -#the directories in which those files are stored. The bwa_index.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id><dbkey><display_name><file_path> -# -#So, for example, if you had phiX indexed stored in -#/depot/data2/galaxy/phiX/base/, -#then the bwa_index.loc entry would look like this: -# -#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/base/phiX.fa -# -#and your /depot/data2/galaxy/phiX/base/ directory -#would contain phiX.fa.* files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt -#...etc... -# -#Your bwa_index.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: -# -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/base/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/base/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/base/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/base/hg19.fa -#...etc... -# -#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. -# diff -r 203e3e1592439dcb8c0eb890545ed38a66f08f2c -r cfd26c91f6c3bb8b6365e7835263e11fc3013004 tool-data/bwa_index_color.loc.sample --- a/tool-data/bwa_index_color.loc.sample +++ /dev/null @@ -1,38 +0,0 @@ -#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 bwa_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 bwa_index_color.loc -#file has this format (longer white space characters are TAB characters): -# -#<unique_build_id><dbkey><display_name><file_path> -# -#So, for example, if you had phiX indexed stored in -#/depot/data2/galaxy/phiX/color/, -#then the bwa_index.loc entry would look like this: -# -#phiX174 phiX phiX Pretty /depot/data2/galaxy/phiX/color/phiX.fa -# -#and your /depot/data2/galaxy/phiX/color/ directory -#would contain phiX.fa.* files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 phiX.fa.amb -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 phiX.fa.ann -#-rw-r--r-- 1 james universe 269808 2005-09-13 10:12 phiX.fa.bwt -#...etc... -# -#Your bwa_index_color.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: -# -#phiX174 phiX phiX174 /depot/data2/galaxy/phiX/color/phiX.fa -#hg18canon hg18 hg18 Canonical /depot/data2/galaxy/hg18/color/hg18canon.fa -#hg18full hg18 hg18 Full /depot/data2/galaxy/hg18/color/hg18full.fa -#/orig/path/hg19.fa hg19 hg19 /depot/data2/galaxy/hg19/color/hg19.fa -#...etc... -# -#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. -# diff -r 203e3e1592439dcb8c0eb890545ed38a66f08f2c -r cfd26c91f6c3bb8b6365e7835263e11fc3013004 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -330,8 +330,6 @@ <tool file="sr_mapping/bowtie_wrapper.xml" /><tool file="sr_mapping/bowtie2_wrapper.xml" /><tool file="sr_mapping/bowtie_color_wrapper.xml" /> - <tool file="sr_mapping/bwa_wrapper.xml" /> - <tool file="sr_mapping/bwa_color_wrapper.xml" /><tool file="sr_mapping/bfast_wrapper.xml" /><tool file="metag_tools/megablast_wrapper.xml" /><tool file="metag_tools/megablast_xml_parser.xml" /> 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.