1 new changeset in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/8a154602ee88/ changeset: r5538:8a154602ee88 user: dan date: 2011-05-11 16:46:46 summary: Some minor fixes for 5537:1a379a0f2ecc. affected #: 3 files (38 bytes) --- a/tools/gatk/analyze_covariates.xml Wed May 11 09:38:23 2011 -0400 +++ b/tools/gatk/analyze_covariates.xml Wed May 11 10:46:46 2011 -0400 @@ -9,7 +9,7 @@ -outputDir "${output_html.files_path}" ##-log "${output_log}" ##-Rscript,--path_to_Rscript path_to_Rscript; on path is good enough - -resources "${GALAXY_DATA_INDEX_DIR}/shared/gatk/R" + -resources "${GALAXY_DATA_INDEX_DIR}/gatk/R" #if $analysis_param_type.analysis_param_type_selector == "advanced": --ignoreQ "${analysis_param_type.ignore_q}" --numRG "${analysis_param_type.num_read_groups}" --- a/tools/gatk/gatk_wrapper.py Wed May 11 09:38:23 2011 -0400 +++ b/tools/gatk/gatk_wrapper.py Wed May 11 10:46:46 2011 -0400 @@ -86,7 +86,7 @@ stderr_target.write( chunk ) else: break - + stderr.close() #generate html reports if options.html_report_from_directory: for ( html_filename, html_dir ) in options.html_report_from_directory: --- a/tools/gatk/indel_realigner.xml Wed May 11 09:38:23 2011 -0400 +++ b/tools/gatk/indel_realigner.xml Wed May 11 10:46:46 2011 -0400 @@ -277,8 +277,8 @@ <param name="knowns_only" /><param name="gatk_param_type_selector" value="basic" /><param name="analysis_param_type_selector" value="basic" /> - <output name="output_bam" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam"/> - <output name="output_log" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains" compare="contains"/> + <output name="output_bam" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.bam" ftype="bam" lines_diff="2" /> + <output name="output_log" file="gatk/gatk_indel_realigner/gatk_indel_realigner_out_1.log.contains" compare="contains" /></test></tests><help> 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.