details: http://www.bx.psu.edu/hg/galaxy/rev/ea7f4e4b7214 changeset: 3443:ea7f4e4b7214 user: Nate Coraor <nate@bx.psu.edu> date: Thu Feb 25 12:27:07 2010 -0500 description: Fix locations of cached data for tests diffstat: buildbot_setup.sh | 3 ++- test/base/twilltestcase.py | 2 +- tools/annotation_profiler/annotation_profiler.xml | 2 +- tools/annotation_profiler/annotation_profiler_for_interval.py | 2 +- tools/extract/liftOver_wrapper.xml | 2 +- tools/extract/phastOdds/phastOdds_tool.xml | 2 +- tools/filters/axt_to_lav.xml | 2 +- tools/filters/lav_to_bed.xml | 6 +++--- tools/metag_tools/rmap_wrapper.xml | 2 +- tools/metag_tools/rmapq_wrapper.xml | 2 +- tools/samtools/sam_to_bam.py | 8 ++++---- tools/stats/aggregate_binned_scores_in_intervals.xml | 4 ++-- 12 files changed, 19 insertions(+), 18 deletions(-) diffs (176 lines): diff -r 983d70363eeb -r ea7f4e4b7214 buildbot_setup.sh --- a/buildbot_setup.sh Thu Feb 25 11:28:14 2010 -0500 +++ b/buildbot_setup.sh Thu Feb 25 12:27:07 2010 -0500 @@ -26,6 +26,7 @@ LINKS=" /galaxy/data/location/alignseq.loc +/galaxy/data/annotation_profiler /galaxy/data/annotation_profiler/annotation_profiler.loc /galaxy/data/annotation_profiler/annotation_profiler_options.xml /galaxy/data/annotation_profiler/annotation_profiler_valid_builds.txt @@ -45,7 +46,7 @@ /galaxy/data/location/quality_scores.loc /galaxy/data/location/regions.loc /galaxy/data/location/sam_fa_indices.loc -/galaxy/data/location/taxonomy +/galaxy/data/taxonomy /galaxy/data/location/twobit.loc " diff -r 983d70363eeb -r ea7f4e4b7214 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Feb 25 11:28:14 2010 -0500 +++ b/test/base/twilltestcase.py Thu Feb 25 12:27:07 2010 -0500 @@ -1674,7 +1674,7 @@ url += "&ldda_ids=%s" % ldda_id self.visit_url( url ) tc.code( 200 ) - archive = self.write_temp_file( self.last_page(), suffix=format ) + archive = self.write_temp_file( self.last_page(), suffix='.' + format ) self.home() return archive def check_archive_contents( self, archive, lddas ): diff -r 983d70363eeb -r ea7f4e4b7214 tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/annotation_profiler/annotation_profiler.xml Thu Feb 25 12:27:07 2010 -0500 @@ -1,6 +1,6 @@ <tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0"> <description>for a set of genomic intervals</description> - <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${chromInfo} -b 3 -t $table_names</command> + <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p ${GALAXY_DATA_INDEX_DIR}/annotation_profiler/$dbkey $summary -l ${chromInfo} -b 3 -t $table_names</command> <inputs> <param format="interval" name="input1" type="data" label="Choose Intervals"> <validator type="dataset_metadata_in_file" filename="annotation_profiler_valid_builds.txt" metadata_name="dbkey" metadata_column="0" message="Profiling is not currently available for this species."/> diff -r 983d70363eeb -r ea7f4e4b7214 tools/annotation_profiler/annotation_profiler_for_interval.py --- a/tools/annotation_profiler/annotation_profiler_for_interval.py Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/annotation_profiler/annotation_profiler_for_interval.py Thu Feb 25 12:27:07 2010 -0500 @@ -290,7 +290,7 @@ parser.add_option( '-p','--path', dest='path', - type='str',default='/depot/data2/galaxy/annotation_profiler/hg18', + type='str',default='/galaxy/data/annotation_profiler/hg18', help='Path to profiled data for this organism' ) parser.add_option( diff -r 983d70363eeb -r ea7f4e4b7214 tools/extract/liftOver_wrapper.xml --- a/tools/extract/liftOver_wrapper.xml Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/extract/liftOver_wrapper.xml Thu Feb 25 12:27:07 2010 -0500 @@ -27,7 +27,7 @@ <tests> <test> <param name="input" value="5.bed" dbkey="hg18" ftype="bed" /> - <param name="to_dbkey" value="/depot/data2/galaxy/hg18/liftOver/hg18ToPanTro2.over.chain" /> + <param name="to_dbkey" value="/galaxy/data/hg18/liftOver/hg18ToPanTro2.over.chain" /> <param name="minMatch" value="0.95" /> <output name="out_file1" file="5_liftover_mapped.bed"/> <output name="out_file2" file="5_liftover_unmapped.bed"/> diff -r 983d70363eeb -r ea7f4e4b7214 tools/extract/phastOdds/phastOdds_tool.xml --- a/tools/extract/phastOdds/phastOdds_tool.xml Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/extract/phastOdds/phastOdds_tool.xml Thu Feb 25 12:27:07 2010 -0500 @@ -26,7 +26,7 @@ <tests> <test> <param name="input" value="4.bed" dbkey="hg17" ftype="bed"/> - <param name="score_file" value="/depot/data2/galaxy/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" /> + <param name="score_file" value="/galaxy/data/phastOdds_precomputed/encode_SEP-2005_tba.v2_phastOdds" /> <param name="per_col" value="true" /> <output name="output" file="phastOdds_tool_out.interval" /> </test> diff -r 983d70363eeb -r ea7f4e4b7214 tools/filters/axt_to_lav.xml --- a/tools/filters/axt_to_lav.xml Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/filters/axt_to_lav.xml Thu Feb 25 12:27:07 2010 -0500 @@ -1,6 +1,6 @@ <tool id="axt_to_lav_1" name="AXT to LAV"> <description>Converts an AXT formatted file to LAV format</description> - <command interpreter="python">axt_to_lav.py /depot/data2/galaxy/$dbkey_1/seq/%s.nib:$dbkey_1:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_1}.len /depot/data2/galaxy/$dbkey_2/seq/%s.nib:$dbkey_2:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_2}.len $align_input $lav_file $seq_file1 $seq_file2</command> + <command interpreter="python">axt_to_lav.py /galaxy/data/$dbkey_1/seq/%s.nib:$dbkey_1:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_1}.len /depot/data2/galaxy/$dbkey_2/seq/%s.nib:$dbkey_2:${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey_2}.len $align_input $lav_file $seq_file1 $seq_file2</command> <inputs> <param name="align_input" type="data" format="axt" label="Alignment File" optional="False"/> <param name="dbkey_1" type="genomebuild" label="Genome"/> diff -r 983d70363eeb -r ea7f4e4b7214 tools/filters/lav_to_bed.xml --- a/tools/filters/lav_to_bed.xml Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/filters/lav_to_bed.xml Thu Feb 25 12:27:07 2010 -0500 @@ -33,8 +33,8 @@ #:lav s { - "/depot/data2/galaxy/hg16/seq/chr19.nib" 1 63811651 0 1 - "/depot/data2/galaxy/mm5/seq/chr11.nib" 1 121648857 0 1 + "/galaxy/data/hg16/seq/chr19.nib" 1 63811651 0 1 + "/galaxy/data/mm5/seq/chr11.nib" 1 121648857 0 1 } h { "> hg16.chr19" @@ -65,4 +65,4 @@ chr11 70573975 70574054 mm5_1 0 + </help> <code file="lav_to_bed_code.py"/> -</tool> \ No newline at end of file +</tool> diff -r 983d70363eeb -r ea7f4e4b7214 tools/metag_tools/rmap_wrapper.xml --- a/tools/metag_tools/rmap_wrapper.xml Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/metag_tools/rmap_wrapper.xml Thu Feb 25 12:27:07 2010 -0500 @@ -41,7 +41,7 @@ <!-- <tests> <test> - <param name="database" value="/depot/data2/galaxy/faseq/test" /> + <param name="database" value="/galaxy/data/faseq/test" /> <param name="input_seq" value="rmap_wrapper_test1.fasta" ftype="fasta"/> <param name="read_len" value="36" /> <param name="align_len" value="36" /> diff -r 983d70363eeb -r ea7f4e4b7214 tools/metag_tools/rmapq_wrapper.xml --- a/tools/metag_tools/rmapq_wrapper.xml Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/metag_tools/rmapq_wrapper.xml Thu Feb 25 12:27:07 2010 -0500 @@ -44,7 +44,7 @@ <!-- <tests> <test> - <param name="database" value="/depot/data2/galaxy/faseq/test" /> + <param name="database" value="/galaxy/data/faseq/test" /> <param name="input_seq" value="rmapq_wrapper_test1.fasta" ftype="fasta"/> <param name="input_score" value="rmapq_wrapper_test1.qual" ftype="qualsolexa" /> <param name="high_score" value="40" /> diff -r 983d70363eeb -r ea7f4e4b7214 tools/samtools/sam_to_bam.py --- a/tools/samtools/sam_to_bam.py Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/samtools/sam_to_bam.py Thu Feb 25 12:27:07 2010 -0500 @@ -45,14 +45,14 @@ cached_seqs_pointer_file = '%s/sam_fa_indices.loc' % options.index_dir if not os.path.exists( cached_seqs_pointer_file ): stop_err( 'The required file (%s) does not exist.' % cached_seqs_pointer_file ) - # If found for the dbkey, seq_path will look something like /depot/data2/galaxy/equCab2/sam_index/equCab2.fa, + # If found for the dbkey, seq_path will look something like /galaxy/data/equCab2/sam_index/equCab2.fa, # and the equCab2.fa file will contain fasta sequences. seq_path = check_seq_file( options.dbkey, cached_seqs_pointer_file ) tmp_dir = tempfile.mkdtemp() if options.ref_file == 'None': - # We're using locally cached reference sequences( e.g., /depot/data2/galaxy/equCab2/sam_index/equCab2.fa ). - # The indexes for /depot/data2/galaxy/equCab2/sam_index/equCab2.fa will be contained in - # a file named /depot/data2/galaxy/equCab2/sam_index/equCab2.fa.fai + # We're using locally cached reference sequences( e.g., /galaxy/data/equCab2/sam_index/equCab2.fa ). + # The indexes for /galaxy/data/equCab2/sam_index/equCab2.fa will be contained in + # a file named /galaxy/data/equCab2/sam_index/equCab2.fa.fai fai_index_file_base = seq_path fai_index_file_path = '%s.fai' % seq_path if not os.path.exists( fai_index_file_path ): diff -r 983d70363eeb -r ea7f4e4b7214 tools/stats/aggregate_binned_scores_in_intervals.xml --- a/tools/stats/aggregate_binned_scores_in_intervals.xml Thu Feb 25 11:28:14 2010 -0500 +++ b/tools/stats/aggregate_binned_scores_in_intervals.xml Thu Feb 25 12:27:07 2010 -0500 @@ -42,13 +42,13 @@ <test> <param name="input1" value="6.bed" dbkey="hg17" ftype="bed"/> <param name="score_source" value="cached"/> - <param name="datasets" value="/depot/data2/galaxy/binned_scores/hg17/phastcons_encode_sep2005_tba" /> + <param name="datasets" value="/galaxy/data/binned_scores/hg17/phastcons_encode_sep2005_tba" /> <output name="out_file1" file="aggregate_binned_scores_in_intervals.out" /> </test> <test> <param name="input1" value="9_hg18.bed" dbkey="hg18" ftype="bed"/> <param name="score_source" value="cached"/> - <param name="datasets" value="/depot/data2/galaxy/binned_scores/hg18/phastCons17way/ba" /> + <param name="datasets" value="/galaxy/data/binned_scores/hg18/phastCons17way/ba" /> <output name="out_file1" file="aggregate_binned_scores_in_intervals2.interval" /> </test> <test>