Hello,

I am trying to have all functional tests on our production server (galaxy-dist 
6621:26920e20157f) run successfully but I do still have failures that I do not 
know how to solve. 

Theses failures are related to unexpected differences probably due to versions 
of software that have been upgraded recently.

( Extract genomic DNA 1 ) > Test-1
( Extract genomic DNA 1 ) > Test-2
( Extract genomic DNA 1 ) > Test-3
( Extract genomic DNA 1 ) > Test-4
( Extract genomic DNA 1 ) > Test-5
( GeneBed_Maf_Fasta2 ) > Test-1
( Interval2Maf1 ) > Test-1
( Interval2Maf1 ) > Test-3
( Interval_Maf_Merged_Fasta2 ) > Test-1
( Interval_Maf_Merged_Fasta2 ) > Test-2
( LinearRegression1 ) > Test-1
( XY_Plot_1 ) > Test-1
( cca1 ) > Test-1
( histogram_rpy ) > Test-1
( kpca1 ) > Test-1
( pca1 ) > Test-1
( pca1 ) > Test-2
( pca1 ) > Test-3
( plot_for_lda_output1 ) > Test-1
( qual_stats_boxplot ) > Test-1
    AssertionError: History item 2 different than expected, difference (using 
diff)

( gops_join_1 ) > Test-4
   TwillAssertionError: code is 500 != 200

I do also have failures due to missing data but I am struggling to find out 
where to download them.

( gd_select_snps ) > Test-1
   AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset 
blurb: error
   'bighorn' does not appear in location file 
'/opt/local/home/webapp/galaxy/tool-data/gd.chrlens.loc'

( Annotation_Profiler_0 ) > Test-1
( Annotation_Profiler_0 ) > Test-2
   AssertionError: Configuration error: Table directory is missing 
(/opt/local/home/webapp/galaxy/tool-data/annotation_profiler/hg18)

( Interval2Maf_pairwise1 ) > Test-1
   AssertionError: Attempting to set field 'mafType' to value 
'['PAIRWISE_hg17_fr1']' in form 'tool_form' threw exception: cannot find 
value/label "PAIRWISE_hg17_fr1" in list control

( maf_stats1 ) > Test-1
( maf_stats1 ) > Test-2
   AssertionError: Attempting to set field 'maf_source_type|mafType' to value 
'['8_WAY_MULTIZ_hg17']' in form 'tool_form' threw exception: cannot find 
value/label "8_WAY_MULTIZ_hg17" in list control

( phastOdds_for_intervals ) > Test-1
   AssertionError: Attempting to set field 'score_file' to value 
'['/galaxy/data/phastOdds_precomputed/encode_SEP-2005_\
tba.v2_phastOdds']' in form 'tool_form' threw exception: cannot find 
value/label "/galaxy/data/phas..2_phastOdds" in li\
st control

( aggregate_scores_in_intervals2 ) > Test-1
( aggregate_scores_in_intervals2 ) > Test-2
   AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset 
blurb: error

( gencode_partition1 ) > Test-1
   Expecting dataset state 'ok', but state is 'error'. Dataset blurb: error
   Error loading partitioning dataset.

( lda_analy1 ) > Test-1
   AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset 
blurb: error

The last failure is related to genome diversity and the fact that it calls 
python2.5. I've changed it to python for testing but the test still fails.

( gd_extract_flanking_dna ) > Test-1
( gd_extract_primers ) > Test-1
( gd_select_restriction_enzymes ) > Test-1
   AssertionError: Expecting dataset state 'ok', but state is 'error'. Dataset 
blurb: error
   python2.5: command not found
   > if changed to python: ERROR: 'NoneType' object has no attribute 'rfind'


Is there a way to fix these failures? Any help would be very much appreciated. 
Thanks,
Anne.

--
Anne Pajon, Ph.D.
Cancer Research UK - Cambridge Research Institute
Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE
anne.pa...@cancer.org.uk | +44 (0)1223 404 334



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