November 2011 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dan: Fix for 2ee4a6b8419b where chromInfo from custom dbkeys when no custom dbkeys have been defined would cause an error.

by Bitbucket

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/1638bc414549/ changeset: 1638bc414549 user: dan date: 2011-11-30 23:22:30 summary: Fix for 2ee4a6b8419b where chromInfo from custom dbkeys when no custom dbkeys have been defined would cause an error. affected #: 1 file diff -r c6f70cccce287702f18c518175bec4a5e8ace23c -r 1638bc41454922e24dfa5e01d840fbf5ea505782 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -192,7 +192,7 @@ incoming[ "chromInfo" ] = db_dataset.file_name else: # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. - if trans.user and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): + if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): # Custom build. custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) 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.

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commit/galaxy-central: dan: Add no_options validator to built-in reference genome selector in GATK tools.

by Bitbucket

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c6f70cccce28/ changeset: c6f70cccce28 user: dan date: 2011-11-30 19:29:21 summary: Add no_options validator to built-in reference genome selector in GATK tools. affected #: 13 files diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/count_covariates.xml --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -146,6 +146,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -194,6 +194,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/indel_realigner.xml --- a/tools/gatk/indel_realigner.xml +++ b/tools/gatk/indel_realigner.xml @@ -124,6 +124,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/realigner_target_creator.xml --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -112,6 +112,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/table_recalibration.xml --- a/tools/gatk/table_recalibration.xml +++ b/tools/gatk/table_recalibration.xml @@ -129,6 +129,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_bam" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/unified_genotyper.xml --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -154,6 +154,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_annotator.xml --- a/tools/gatk/variant_annotator.xml +++ b/tools/gatk/variant_annotator.xml @@ -157,6 +157,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_apply_recalibration.xml --- a/tools/gatk/variant_apply_recalibration.xml +++ b/tools/gatk/variant_apply_recalibration.xml @@ -109,6 +109,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_combine.xml --- a/tools/gatk/variant_combine.xml +++ b/tools/gatk/variant_combine.xml @@ -121,6 +121,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_eval.xml --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -160,6 +160,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_filtration.xml --- a/tools/gatk/variant_filtration.xml +++ b/tools/gatk/variant_filtration.xml @@ -110,6 +110,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variant_recalibrator.xml --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -156,6 +156,7 @@ <options from_data_table="gatk_picard_indexes"></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> diff -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 -r c6f70cccce287702f18c518175bec4a5e8ace23c tools/gatk/variants_validate.xml --- a/tools/gatk/variants_validate.xml +++ b/tools/gatk/variants_validate.xml @@ -96,6 +96,7 @@ <options from_data_table="gatk_picard_indexes"><filter type="data_meta" key="dbkey" ref="input_variant" column="dbkey"/></options> + <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/></param></when><when value="history"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Provide chromInfo correctly during conversions of datasets with custom build dbkeys.

by Bitbucket

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/2ee4a6b8419b/ changeset: 2ee4a6b8419b user: jgoecks date: 2011-11-30 19:06:12 summary: Provide chromInfo correctly during conversions of datasets with custom build dbkeys. affected #: 1 file diff -r 665853dfd9e12e137f26777d1a2d2167df4b4275 -r 2ee4a6b8419b3da2b95e1600a92099fe547cd070 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -191,7 +191,16 @@ db_datasets[ "chromInfo" ] = db_dataset incoming[ "chromInfo" ] = db_dataset.file_name else: - incoming[ "chromInfo" ] = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) + # For custom builds, chrom info resides in converted dataset; for built-in builds, chrom info resides in tool-data/shared. + if trans.user and ( input_dbkey in trans.user.preferences[ 'dbkeys' ] ): + # Custom build. + custom_build_dict = from_json_string( trans.user.preferences[ 'dbkeys' ] )[ input_dbkey ] + build_fasta_dataset = trans.app.model.HistoryDatasetAssociation.get( custom_build_dict[ 'fasta' ] ) + chrom_info = build_fasta_dataset.get_converted_dataset( trans, 'len' ).file_name + else: + # Default to built-in build. + chrom_info = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) + incoming[ "chromInfo" ] = chrom_info inp_data.update( db_datasets ) # Determine output dataset permission/roles list 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.

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commit/galaxy-central: richard_burhans: python version of "phyloP interspecies conservation scores" tool

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1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/665853dfd9e1/ changeset: 665853dfd9e1 user: richard_burhans date: 2011-11-30 18:05:59 summary: python version of "phyloP interspecies conservation scores" tool affected #: 3 files diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tool-data/add_scores.loc.sample --- a/tool-data/add_scores.loc.sample +++ b/tool-data/add_scores.loc.sample @@ -1,21 +1,20 @@ -#This is a sample file distributed with Galaxy that enables tools to use a -#directory of gzipped genome files for use with add_scores. You will need to -#supply these files and then create a add_scores.loc file similar to this one -#(store it in this directory) that points to the directories in which those -#files are stored. The add_scores.loc file has this format (white space -#characters are TAB characters): +#This is a sample file distributed with Galaxy that lists the BigWig files +#available for use with the add_scores (phyloP interspecies conservation +#scores) tool. You will need to supply these BigWig files and then create +#an add_scores.loc file similar to this one (store it in this directory) +#that lists their locations. The add_scores.loc file has the following +#format (white space characters are TAB characters): # -#<build><file_path> +#<build><BigWig_file_path> # #So, for example, if your add_scores.loc began like this: # -#hg18 /galaxy/data/hg18/misc/phyloP +#hg18 /galaxy/data/hg18/misc/phyloP44way.primate.bw # -#then your /galaxy/data/hg18/misc/phyloP directory would need to contain -#the following gzipped files, among others: +#then your /galaxy/data/hg18/misc/ directory would need to contain a +#BigWig file named phyloP44way.primate.bw, among others: # -#-rw-r--r-- 1 g2data g2data 161981190 2010-03-19 12:48 chr10.phyloP44way.primate.wigFix.gz -#-rw-r--r-- 1 g2data g2data 54091 2010-03-19 12:56 chr10_random.phyloP44way.primate.wigFix.gz -#-rw-r--r-- 1 g2data g2data 158621990 2010-03-19 12:46 chr11.phyloP44way.primate.wigFix.gz +#-rw-r--r-- 1 g2data g2data 6057387572 Nov 23 10:11 phyloP44way.primate.bw # -#hg18 /galaxy/data/hg18/misc/phyloP +#hg18 /galaxy/data/hg18/misc/phyloP44way.primate.bw +#hg19 /galaxy/data/hg19/misc/phyloP46way.primate.bw diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tools/evolution/add_scores.py --- /dev/null +++ b/tools/evolution/add_scores.py @@ -0,0 +1,120 @@ +#!/usr/bin/env python + +import sys +from galaxy import eggs +import pkg_resources +pkg_resources.require( "bx-python" ) +pkg_resources.require( "numpy" ) +from bx.bbi.bigwig_file import BigWigFile +import os + +################################################################################ + +def die( message ): + print >> sys.stderr, message + sys.exit(1) + +def open_or_die( filename, mode='r', message=None ): + if message is None: + message = 'Error opening {0}'.format( filename ) + try: + fh = open( filename, mode ) + except IOError, err: + die( '{0}: {1}'.format( message, err.strerror ) ) + return fh + +################################################################################ + +class LocationFile( object ): + def __init__( self, filename, comment_chars=None, delimiter='\t', key_column=0 ): + self.filename = filename + if comment_chars is None: + self.comment_chars = ( '#' ) + else: + self.comment_chars = tuple( comment_chars ) + self.delimiter = delimiter + self.key_column = key_column + self._map = {} + self._populate_map() + + def _populate_map( self ): + try: + with open( self.filename ) as fh: + line_number = 0 + for line in fh: + line_number += 1 + line = line.rstrip( '\r\n' ) + if not line.startswith( self.comment_chars ): + elems = line.split( self.delimiter ) + if len( elems ) <= self.key_column: + die( 'Location file {0} line {1}: less than {2} columns'.format( self.filename, line_number, self.key_column + 1 ) ) + else: + key = elems.pop( self.key_column ) + if key in self._map: + if self._map[key] != elems: + die( 'Location file {0} line {1}: duplicate key "{2}"'.format( self.filename, line_number, key ) ) + else: + self._map[key] = elems + except IOError, err: + die( 'Error opening location file {0}: {1}'.format( self.filename, err.strerror ) ) + + def get_values( self, key ): + if key in self._map: + rval = self._map[key] + if len( rval ) == 1: + return rval[0] + else: + return rval + else: + die( 'key "{0}" not found in location file {1}'.format( key, self.filename ) ) + +################################################################################ + +def main(): + input_filename, output_filename, loc_filename, loc_key, chrom_col, start_col = sys.argv[1:] + + # open input, output, and bigwig files + location_file = LocationFile( loc_filename ) + bigwig_filename = location_file.get_values( loc_key ) + bwfh = open_or_die( bigwig_filename, message='Error opening BigWig file {0}'.format( bigwig_filename ) ) + bw = BigWigFile( file=bwfh ) + ifh = open_or_die( input_filename, message='Error opening input file {0}'.format( input_filename ) ) + ofh = open_or_die( output_filename, mode='w', message='Error opening output file {0}'.format( output_filename ) ) + + # make column numbers 0-based + chrom_col = int( chrom_col ) - 1 + start_col = int( start_col ) - 1 + min_cols = max( chrom_col, start_col ) + + # add score column to imput file + line_number = 0 + for line in ifh: + line_number += 1 + line = line.rstrip( '\r\n' ) + elems = line.split( '\t' ) + if len( elems ) > min_cols: + chrom = elems[chrom_col].strip() + # base-0 position in chrom + start = int( elems[start_col] ) + score_list = bw.get( chrom, start, start + 1 ) + score_list_len = len( score_list ) + if score_list_len == 1: + beg, end, score = score_list[0] + score_val = '{0:1.3f}'.format( score ) + elif score_list_len == 0: + score_val = 'NA' + else: + die( '{0} line {1}: chrom={2}, start={3}, score_list_len = {4}'.format( input_filename, line_number, chrom, start, score_list_len ) ) + print >> ofh, '\t'.join( [line, score_val] ) + else: + print >> ofh, line + + bwfh.close() + ifh.close() + ofh.close() + +################################################################################ + +if __name__ == "__main__": + main() + diff -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 -r 665853dfd9e12e137f26777d1a2d2167df4b4275 tools/evolution/add_scores.xml --- a/tools/evolution/add_scores.xml +++ b/tools/evolution/add_scores.xml @@ -1,8 +1,8 @@ <tool id="hgv_add_scores" name="phyloP" version="1.0.0"><description>interspecies conservation scores</description> - <command> - add_scores $input1 ${input1.metadata.dbkey} ${input1.metadata.chromCol} ${input1.metadata.startCol} ${GALAXY_DATA_INDEX_DIR}/add_scores.loc $out_file1 + <command interpreter="python"> + add_scores.py "$input1" "$out_file1" "${GALAXY_DATA_INDEX_DIR}/add_scores.loc" "${input1.metadata.dbkey}" "${input1.metadata.chromCol}" "${input1.metadata.startCol}" </command><inputs> @@ -34,7 +34,7 @@ <help> .. class:: warningmark -This currently works only for build hg18. +This currently works only for builds hg18 and hg19. ----- Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for frames inside of frames issue introduced in 5db0da0007fc. Seen when require_login=True.

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1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/36998f5a7ddb/ changeset: 36998f5a7ddb user: dan date: 2011-11-30 16:20:15 summary: Fix for frames inside of frames issue introduced in 5db0da0007fc. Seen when require_login=True. affected #: 1 file diff -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c -r 36998f5a7ddb12ee93068b8001a09b84a47944f4 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -407,6 +407,7 @@ def _ensure_logged_in_user( self, environ, session_cookie ): # The value of session_cookie can be one of # 'galaxysession' or 'galaxycommunitysession' + # Currently this method does nothing unless session_cookie is 'galaxysession' if session_cookie == 'galaxysession': # TODO: re-engineer to eliminate the use of allowed_paths # as maintenance overhead is far too high. @@ -436,8 +437,8 @@ host = None if host in UCSC_SERVERS: return - if self.request.path not in allowed_paths: - self.response.send_redirect( url_for( controller='root', action='index' ) ) + if self.request.path not in allowed_paths: + self.response.send_redirect( url_for( controller='root', action='index' ) ) def __create_new_session( self, prev_galaxy_session=None, user_for_new_session=None ): """ Create a new GalaxySession for this request, possibly with a connection 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.

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commit/galaxy-central: greg: Revert 2 changes made in 5db0da0007fc in an attempt to correct the broken behavior of rendering Galaxy correctly when using apache proxying, possibly in adition to requiring users to login.

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1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/834de698004e/ changeset: 834de698004e user: greg date: 2011-11-30 15:16:37 summary: Revert 2 changes made in 5db0da0007fc in an attempt to correct the broken behavior of rendering Galaxy correctly when using apache proxying, possibly in adition to requiring users to login. affected #: 2 files diff -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py +++ b/lib/galaxy/web/controllers/user.py @@ -358,7 +358,7 @@ else: refresh_frames = [ 'masthead', 'history' ] message, status, user, success = self.__validate_login( trans, webapp, **kwd ) - if success and referer and not referer.startswith( url_for( trans.request.base + url_for( controller='user', action='logout' ) ) ): + if success and referer and not referer.startswith( trans.request.base + url_for( controller='user', action='logout' ) ): redirect_url = referer elif success: redirect_url = url_for( '/' ) diff -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b -r 834de698004e1306b4424d0a8dbd3e7c1938ee9c templates/webapps/galaxy/base_panels.mako --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -142,7 +142,11 @@ menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user', webapp='galaxy' ), "galaxy_main" ] ) if app.config.get_bool( 'enable_tracks', False ): menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - menu_options.append( [ 'Logout', h.url_for( controller='/user', action='logout', webapp='galaxy' ), "_top" ] ) + if app.config.require_login: + logout_url = h.url_for( controller='/root', action='index', m_c='user', m_a='logout', webapp='galaxy' ) + else: + logout_url = h.url_for( controller='/user', action='logout', webapp='galaxy' ) + menu_options.append( [ 'Logout', logout_url, "_top" ] ) menu_options.append( None ) menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) 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.

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commit/galaxy-central: dannon: Fix for browsing libraries, json2 wasn't being loaded, needed in IE for jstorage to work.

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1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/de03f821784b/ changeset: de03f821784b user: dannon date: 2011-11-30 13:29:32 summary: Fix for browsing libraries, json2 wasn't being loaded, needed in IE for jstorage to work. affected #: 1 file diff -r b751663f3f64ea794951f57b2ff4686debd1b455 -r de03f821784bcbe04a7514ad3d8e43fb1b635e4b templates/library/common/browse_library.mako --- a/templates/library/common/browse_library.mako +++ b/templates/library/common/browse_library.mako @@ -48,6 +48,7 @@ <%def name="javascripts()"> ${parent.javascripts()} + ${h.js("json2")} ${h.js("jstorage")} ${common_javascripts()} ${self.grid_javascripts()} 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.

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commit/galaxy-central: dan: Minor fix for 04e8ed0cd930.

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1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b751663f3f64/ changeset: b751663f3f64 user: dan date: 2011-11-29 23:35:14 summary: Minor fix for 04e8ed0cd930. affected #: 1 file diff -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 -r b751663f3f64ea794951f57b2ff4686debd1b455 tools/sr_mapping/PerM.xml --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -13,7 +13,7 @@ #if $s.space == "color" "${s.sourceOfRef.index.fields.path}" #elif $s.space == "base" - "${s.sourceOfRef.index.fields.path" + "${s.sourceOfRef.index.fields.path}" #end if #end if #if $s.mate.singleOrPairs == "single": 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.

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commit/galaxy-central: dan: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools.

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1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04e8ed0cd930/ changeset: 04e8ed0cd930 user: dan date: 2011-11-29 23:30:14 summary: Replace old filter() on tool_data_tables by param value hack with param.fields.path for several tools. affected #: 13 files diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/metag_tools/megablast_wrapper.xml --- a/tools/metag_tools/megablast_wrapper.xml +++ b/tools/metag_tools/megablast_wrapper.xml @@ -2,7 +2,7 @@ <description> compare short reads against htgs, nt, and wgs databases</description><command interpreter="python"> megablast_wrapper.py - --db_build="${ filter( lambda x: str( x[0] ) == str( $source_select ), $__app__.tool_data_tables[ 'blastdb' ].get_fields() )[0][-1] }" + --db_build="${source_select.fields.path}" --input=$input_query --word_size=$word_size --identity_cutoff=$iden_cutoff diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_color_wrapper.xml --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -19,7 +19,7 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes_color' ].get_fields() )[0][-1] }" + --indexes-path="${refGenomeSource.index.fields.path}" #end if ## Are reads single-end or paired? diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_rna/tophat_wrapper.xml --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -17,7 +17,7 @@ #if $refGenomeSource.genomeSource == "history": --own-file=$refGenomeSource.ownFile #else: - --indexes-path="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'tophat_indexes' ].get_fields() )[0][-1] }" + --indexes-path="${refGenomeSource.index.fields.path}" #end if ## Are reads single-end or paired? diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/ngs_simulation/ngs_simulation.xml --- a/tools/ngs_simulation/ngs_simulation.xml +++ b/tools/ngs_simulation/ngs_simulation.xml @@ -4,7 +4,7 @@ <command interpreter="python"> ngs_simulation.py #if $in_type.input_type == "built-in" - --input="${ filter( lambda x: str( x[0] ) == str( $in_type.genome ), $__app__.tool_data_tables[ 'ngs_sim_fasta' ].get_fields() )[0][-1] }" + --input="${in_type.genome.fields.path}" --genome=$in_type.genome #else --input=$in_type.input1 diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/picard/rgPicardASMetrics.xml --- a/tools/picard/rgPicardASMetrics.xml +++ b/tools/picard/rgPicardASMetrics.xml @@ -6,7 +6,7 @@ #if $genomeSource.refGenomeSource == "history": --ref-file "$genomeSource.ownFile" #else - --ref "${ filter( lambda x: str( x[0] ) == str( $genomeSource.index ), $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] }" + --ref "${genomeSource.index.fields.path}" #end if </command><requirements><requirement type="package">picard</requirement></requirements> diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/PerM.xml --- a/tools/sr_mapping/PerM.xml +++ b/tools/sr_mapping/PerM.xml @@ -11,9 +11,9 @@ $s.sourceOfRef.ref #else #if $s.space == "color" - "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_color_indexes' ].get_fields() )[0][-1] }" + "${s.sourceOfRef.index.fields.path}" #elif $s.space == "base" - "${ filter( lambda x: str( x[0] ) == str( $s.sourceOfRef.index ), $__app__.tool_data_tables[ 'perm_base_indexes' ].get_fields() )[0][-1] }" + "${s.sourceOfRef.index.fields.path" #end if #end if #if $s.mate.singleOrPairs == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_color_wrapper.xml --- a/tools/sr_mapping/bowtie_color_wrapper.xml +++ b/tools/sr_mapping/bowtie_color_wrapper.xml @@ -58,7 +58,7 @@ #end if #else ##use pre-built index - --ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes_color' ].get_fields() )[0][-1] }" + --ref="${refGenomeSource.index.fields.path}" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bowtie_wrapper.xml --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -61,8 +61,7 @@ #end if #else ##use pre-built index - ##--ref="${ filter( lambda x: str( x[0] ) == str( $refGenomeSource.index ), $__app__.tool_data_tables[ 'bowtie_indexes' ].get_fields() )[0][-1] }" - --ref="${ refGenomeSource.index.fields.path }" + --ref="${refGenomeSource.index.fields.path}" #end if --paired=$singlePaired.sPaired #if $singlePaired.sPaired == "single": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_color_wrapper.xml --- a/tools/sr_mapping/bwa_color_wrapper.xml +++ b/tools/sr_mapping/bwa_color_wrapper.xml @@ -14,7 +14,7 @@ --dbkey=$dbkey #else: ##use precomputed indexes - --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes_color' ].get_fields() )[0][-1] }" + --ref="${genomeSource.indices.fields.path}" --do_not_build_index #end if diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -17,7 +17,7 @@ --dbkey=$dbkey #else: ##use precomputed indexes - --ref="${ filter( lambda x: str( x[0] ) == str( $genomeSource.indices ), $__app__.tool_data_tables[ 'bwa_indexes' ].get_fields() )[0][-1] }" + --ref="${genomeSource.indices.fields.path}" --do_not_build_index #end if diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_paired_reads_wrapper.xml --- a/tools/sr_mapping/lastz_paired_reads_wrapper.xml +++ b/tools/sr_mapping/lastz_paired_reads_wrapper.xml @@ -12,7 +12,7 @@ --input1=$source.input1 --ref_sequences=$input1.metadata.sequences #else: - --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --input1="${source.input1_2bit.fields.path}" #end if --output=$output1 --lastz_seqs_file_dir=${GALAXY_DATA_INDEX_DIR} diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/lastz_wrapper.xml --- a/tools/sr_mapping/lastz_wrapper.xml +++ b/tools/sr_mapping/lastz_wrapper.xml @@ -12,7 +12,7 @@ --input1=$source.input1 --ref_sequences=$input1.metadata.sequences #else: - --input1="${ filter( lambda x: str( x[0] ) == str( $source.input1_2bit ), $__app__.tool_data_tables[ 'lastz_seqs' ].get_fields() )[0][-1] }" + --input1="${source.input1_2bit.fields.path}" --ref_sequences="None" #end if #if $params.source_select=="pre_set": diff -r 0532712a2708855e77d1a6a9a1099121983458a4 -r 04e8ed0cd930023fea4d7d942e1a12694c4526e6 tools/sr_mapping/mosaik.xml --- a/tools/sr_mapping/mosaik.xml +++ b/tools/sr_mapping/mosaik.xml @@ -13,7 +13,7 @@ #end if MosaikBuild -fr #if $genomeSource.refGenomeSource == 'indexed': - ${ filter( lambda x: str( x[0] ) == str( $genomeSource.indexReference ), $__app__.tool_data_tables[ 'mosaik_indexes' ].get_fields() )[0][-1] } + ${genomeSource.indexReference.fields.path} #else: $genomeSource.historyReference #end if Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix tab to 4 spaces in tool_conf.xml.sample.

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1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/0532712a2708/ changeset: 0532712a2708 user: dan date: 2011-11-29 23:07:06 summary: Fix tab to 4 spaces in tool_conf.xml.sample. affected #: 1 file diff -r 9ee4e2e41fd60c75c2b87d55648c538438809430 -r 0532712a2708855e77d1a6a9a1099121983458a4 tool_conf.xml.sample --- a/tool_conf.xml.sample +++ b/tool_conf.xml.sample @@ -469,7 +469,7 @@ <tool file="human_genome_variation/lps.xml" /><tool file="human_genome_variation/hilbertvis.xml" /><tool file="human_genome_variation/freebayes.xml" /> - <tool file="human_genome_variation/master2pg.xml" /> + <tool file="human_genome_variation/master2pg.xml" /></section><section name="Genome Diversity" id="gd"><tool file="genome_diversity/extract_primers.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.

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galaxy-commits November 2011