galaxy-commits March 2012

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commit/galaxy-central: dan: Fix for GATK Depth of coverage tool when using advanced GATK options with one or more target interval inputs defined.
by Bitbucket 01 Mar '12

01 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/35be930b21be/ changeset: 35be930b21be user: dan date: 2012-03-01 16:11:55 summary: Fix for GATK Depth of coverage tool when using advanced GATK options with one or more target interval inputs defined. affected #: 1 file diff -r 49f8ed2c6109024446b30e9110aea274e60378c3 -r 35be930b21bea104bd574d4e9854c6e9c1a58cdb tools/gatk/depth_of_coverage.xml --- a/tools/gatk/depth_of_coverage.xml +++ b/tools/gatk/depth_of_coverage.xml @@ -129,7 +129,7 @@ && mv ${output_per_locus_coverage}.sample_summary ${output_summary_sample} && mv ${output_per_locus_coverage}.sample_statistics ${output_statistics_sample} #end if - #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "": + #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.sample_interval_summary ${output_interval_summary_sample} && mv ${output_per_locus_coverage}.sample_interval_statistics ${output_interval_statistics_sample} #end if @@ -148,7 +148,7 @@ && mv ${output_per_locus_coverage}.read_group_summary ${output_summary_readgroup} && mv ${output_per_locus_coverage}.read_group_statistics ${output_statistics_readgroup} #end if - #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "": + #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.read_group_interval_summary ${output_interval_summary_readgroup} && mv ${output_per_locus_coverage}.read_group_interval_statistics ${output_interval_statistics_readgroup} #end if @@ -167,7 +167,7 @@ && mv ${output_per_locus_coverage}.library_summary ${output_summary_library} && mv ${output_per_locus_coverage}.library_statistics ${output_statistics_library} #end if - #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and str( $gatk_param_type.omit_interval_statistics ) == "": + #if $gatk_param_type.gatk_param_type_selector == "advanced" and len( $gatk_param_type.input_interval_repeat ) and ( str( $analysis_param_type.analysis_param_type_selector ) == "basic" or str( $analysis_param_type.omit_interval_statistics ) == "" ): && mv ${output_per_locus_coverage}.library_interval_summary ${output_interval_summary_library} && mv ${output_per_locus_coverage}.library_interval_statistics ${output_interval_statistics_library} #end if 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: Quick fix for ftp upload unicode normalization failure.
by Bitbucket 01 Mar '12

01 Mar '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/49f8ed2c6109/ changeset: 49f8ed2c6109 user: dannon date: 2012-03-01 15:31:18 summary: Quick fix for ftp upload unicode normalization failure. TODO: Refactor, shouldn't happen this way. affected #: 1 file diff -r 384549bf99307fed758ea5f3a336e23bf63bc835 -r 49f8ed2c6109024446b30e9110aea274e60378c3 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -309,7 +309,7 @@ if ftp_files is not None: # Normalize input paths to ensure utf-8 encoding is normal form c. # This allows for comparison when the filesystem uses a different encoding than the browser. - ftp_files = [unicodedata.normalize('NFC', f) for f in ftp_files] + ftp_files = [unicodedata.normalize('NFC', f) for f in ftp_files if isinstance(f, unicode)] if trans.user is None: log.warning( 'Anonymous user passed values in ftp_files: %s' % ftp_files ) ftp_files = [] @@ -321,7 +321,11 @@ path = relpath( os.path.join( dirpath, filename ), user_ftp_dir ) if not os.path.islink( os.path.join( dirpath, filename ) ): # Normalize filesystem paths - valid_files.append( unicodedata.normalize('NFC', path )) + if isinstance(path, unicode): + valid_files.append(unicodedata.normalize('NFC', path )) + else: + valid_files.append(path) + else: ftp_files = [] for ftp_file in ftp_files: 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 March 2012