1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/313da0e75a88/ Changeset: 313da0e75a88 User: Dave Bouvier Date: 2013-10-01 21:49:08 Summary: Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories. Affected #: 3 files diff -r 5aef59e6841170aa6e21794d78f709b17738595e -r 313da0e75a88883610cc878bb291b3f9f2d81a9b scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -15,16 +15,16 @@ <repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"><tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /></repository> - <repository owner="devteam" changeset_revision="9d35cf35634e" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> + <repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."><tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."><tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /></repository> - <repository owner="devteam" changeset_revision="b50aacc8ae49" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> + <repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."><tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /></repository> - <repository owner="devteam" changeset_revision="dbbd37e013aa" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> + <repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."><tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"> diff -r 5aef59e6841170aa6e21794d78f709b17738595e -r 313da0e75a88883610cc878bb291b3f9f2d81a9b tool-data/sam_fa_indices.loc.sample --- a/tool-data/sam_fa_indices.loc.sample +++ /dev/null @@ -1,28 +0,0 @@ -#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 -#file has this format (white space characters are TAB characters): -# -#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: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -# -#and your /depot/data2/galaxy/sam/ directory -#would contain hg18.fa and hg18.fa.fai files: -# -#-rw-r--r-- 1 james universe 830134 2005-09-13 10:12 hg18.fa -#-rw-r--r-- 1 james universe 527388 2005-09-13 10:12 hg18.fa.fai -# -#Your sam_fa_indices.loc file should include an entry per line for -#each index set you have stored. The file in the path does actually -#exist, but it should never be directly used. Instead, the name serves -#as a prefix for the index file. For example: -# -#index hg18 /depot/data2/galaxy/sam/hg18.fa -#index hg19 /depot/data2/galaxy/sam/hg19.fa diff -r 5aef59e6841170aa6e21794d78f709b17738595e -r 313da0e75a88883610cc878bb291b3f9f2d81a9b tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample +++ b/tool_data_table_conf.xml.sample @@ -55,11 +55,6 @@ <columns>value, name, path</columns><file path="tool-data/perm_color_index.loc" /></table> - <!-- Location of SAMTools indexes and other files --> - <table name="sam_fa_indexes" comment_char="#"> - <columns>line_type, value, path</columns> - <file path="tool-data/sam_fa_indices.loc" /> - </table><!-- Location of Picard dict file and other files --><table name="picard_indexes" comment_char="#"><columns>value, dbkey, name, path</columns> 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.