| Previous changeset 9:7d6658b2531a (2014-02-20) Next changeset 11:08f88205d596 (2014-02-27) |
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Commit message:
Fix bugs: (a) use value rather than dbkey to get bowtie indices and (b) point to correct bowtie table. |
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modified:
tool_data_table_conf.xml.sample tool_dependencies.xml tophat_fusion_post.xml |
| b |
| diff -r 7d6658b2531a -r 33aafd74bb31 tool_data_table_conf.xml.sample --- a/tool_data_table_conf.xml.sample Thu Feb 20 13:19:38 2014 -0500 +++ b/tool_data_table_conf.xml.sample Thu Feb 27 14:58:22 2014 -0500 |
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| @@ -1,7 +1,7 @@ <tables> - <table name="bowtie2_indexes" comment_char="#"> + <table name="bowtie_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> - <file path="tool-data/bowtie2_indices.loc" /> + <file path="tool-data/bowtie_indices.loc" /> </table> <table name="tophat_fusion_blastdb_indexes" comment_char="#"> <columns>value, dbkey, name, path</columns> |
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| diff -r 7d6658b2531a -r 33aafd74bb31 tool_dependencies.xml --- a/tool_dependencies.xml Thu Feb 20 13:19:38 2014 -0500 +++ b/tool_dependencies.xml Thu Feb 27 14:58:22 2014 -0500 |
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| @@ -1,12 +1,12 @@ <?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="tophat2" version="2.0.9"> - <repository changeset_revision="8549fd545473" name="package_tophat2_2_0_9" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository name="package_tophat2_2_0_9" owner="devteam"/> </package> <package name="bowtie" version="0.12.7"> - <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository name="package_bowtie_0_12_7" owner="devteam"/> </package> </tool_dependency> |
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| diff -r 7d6658b2531a -r 33aafd74bb31 tophat_fusion_post.xml --- a/tophat_fusion_post.xml Thu Feb 20 13:19:38 2014 -0500 +++ b/tophat_fusion_post.xml Thu Feb 27 14:58:22 2014 -0500 |
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| @@ -27,7 +27,7 @@ #end if ## Bowtie indices. - ${__get_data_table_entry__('bowtie_indexes', 'dbkey', $accepted_hits.dbkey, 'path')} + ${__get_data_table_entry__('bowtie_indexes', 'value', $accepted_hits.dbkey, 'path')} </command> <inputs> |