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Fix locations of cached data for tests

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Nate Coraor
2010-02-25 12:27:07 -05:00
parent 3df11a4257
commit 0bfa58679b
12 changed files with 19 additions and 18 deletions
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buildbot_setup.sh
+2 -1
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@@ -26,6 +26,7 @@ esac
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 @@ LINKS="
/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
"
test/base/twilltestcase.py
+1 -1
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@@ -1674,7 +1674,7 @@ class TwillTestCase( unittest.TestCase ):
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 ):
tools/annotation_profiler/annotation_profiler.xml
+1 -1
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@@ -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."/>
tools/annotation_profiler/annotation_profiler_for_interval.py
+1 -1
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@@ -290,7 +290,7 @@ def __main__():
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(
tools/extract/liftOver_wrapper.xml
+1 -1
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@@ -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"/>
tools/extract/phastOdds/phastOdds_tool.xml
+1 -1
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@@ -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>
tools/filters/axt_to_lav.xml
+1 -1
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@@ -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"/>
tools/filters/lav_to_bed.xml
+3 -3
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@@ -33,8 +33,8 @@ This tool converts a LAV formatted file to the BED format.
#:lav
s {
&quot;/depot/data2/galaxy/hg16/seq/chr19.nib&quot; 1 63811651 0 1
&quot;/depot/data2/galaxy/mm5/seq/chr11.nib&quot; 1 121648857 0 1
&quot;/galaxy/data/hg16/seq/chr19.nib&quot; 1 63811651 0 1
&quot;/galaxy/data/mm5/seq/chr11.nib&quot; 1 121648857 0 1
}
h {
&quot;> hg16.chr19&quot;
@@ -65,4 +65,4 @@ This tool converts a LAV formatted file to the BED format.
chr11 70573975 70574054 mm5_1 0 +
</help>
<code file="lav_to_bed_code.py"/>
</tool>
</tool>
tools/metag_tools/rmap_wrapper.xml
+1 -1
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@@ -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" />
tools/metag_tools/rmapq_wrapper.xml
+1 -1
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@@ -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" />
tools/samtools/sam_to_bam.py
+4 -4
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@@ -45,14 +45,14 @@ def __main__():
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 ):
tools/stats/aggregate_binned_scores_in_intervals.xml
+2 -2
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@@ -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>