- galaxy-dev - lists.galaxyproject.org

invoking galaxy standalone
by Sean Rogers 10 Dec '10

10 Dec '10

Hello, I downloaded and set up galaxy yesterday. It opened up the local host fine at that time. I went to reopen galaxy today by using run.sh from the command line. Galaxy did not open and I got the message: File "/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/SocketServer.py", line 413, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: [Errno 48] Address already in use Sean A. Rogers ************************************** Visiting Research Associate Department of Horticulture A314 - Plant & Soil Sciences Building Michigan State University East Lansing, MI 48824-1325 Phone: (517) 355-5191 x1373 **************************************

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Installing Galaxy on SGE cluster
by Zachariah Z 09 Dec '10

09 Dec '10

Hello gurus, This is my first attempt at installing Galaxy on a Solaris10 x86 platform with SGE 6.2 cluster that I had set up. I am using the unified method on an NFS mounted directory called /gtools. I first proceeded to download and install Python 2.6.6 onto /gtools. After this, I proceeded to download the latest source of galaxy using mercurial check out. I set the following environment variables: DRMAA_LIBRARY_PATH=/share/sgeroot/lib/sol-amd64/lbdrmaa.so.1.0 TEMP=/gtools/galaxy/galaxy-dist/database/tmp Upon running the startup script run.sh I get the error : Exception: DRMAAJobRunner requires drmaa module which could not be loaded: No module named _ctypes. The following is the transcript, I appreciate any help in resolving this Thanks in advance --Zac sh run.sh python path is: /gtools/galaxy/galaxy-dist/eggs/numpy-1.3.0-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/pysam-0.1.1_kanwei_90e03180969d-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/Whoosh-0.3.18-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/pycrypto-2.0.1-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/python_lzo-1.08_2.03_static-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/amqplib-0.6.1-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/pexpect-2.4-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Babel-0.9.4-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Beaker-1.4-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Mako-0.2.5-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/WebHelpers-0.2-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/simplejson-2.1.1-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/wchartype-0.1-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/docutils-0.4-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/WebOb-0.8.5-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Routes-1.12.3-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.6-solaris-2.10-i86pc_32-ucs2.egg, /gtools/galaxy/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/PasteScript-1.7.3-py2.6.egg, /gtools/galaxy/galaxy-dist/eggs/Paste-1.6-py2.6.egg, /gtools/galaxy/galaxy-dist/lib, /gtools/src/galaxy_env/lib/python2.6/site-packages/setuptools-0.6c11-py2.6.egg, /gtools/src/galaxy_env/lib/python2.6/site-packages/pip-0.8.2-py2.6.egg, /gtools/src/galaxy_env/lib/python26.zip, /gtools/src/galaxy_env/lib/python2.6, /gtools/src/galaxy_env/lib/python2.6/plat-sunos5, /gtools/src/galaxy_env/lib/python2.6/lib-tk, /gtools/src/galaxy_env/lib/python2.6/lib-old, /gtools/src/galaxy_env/lib/python2.6/lib-dynload, /gtools/python/current/lib/python2.6, /gtools/python/current/lib/python2.6/plat-sunos5, /gtools/python/current/lib/python2.6/lib-tk, /gtools/src/galaxy_env/lib/python2.6/site-packages galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,330 Loading datatypes from datatypes_conf.xml galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,339 Loaded display application 'ucsc_bam' for datatype 'bam', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,345 Loaded display application 'ensembl_bam' for datatype 'bam', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,347 Loaded display application 'genetrack_interval' for datatype 'bed', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,354 Loaded display application 'ucsc_bigbed' for datatype 'bigbed', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,360 Loaded display application 'ucsc_bigwig' for datatype 'bigwig', inherit=False galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,378 Loaded display application 'ensembl_gff' for datatype 'gff', inherit=True galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,380 Loaded display application 'genetrack_interval' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,392 Loaded display application 'ensembl_interval' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,397 Loaded display application 'gbrowse_interval_as_bed' for datatype 'interval', inherit=True galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,403 Loaded display application 'ucsc_maf_customtrack' for datatype 'mafcustomtrack', inherit=False galaxy.datatypes.assembly DEBUG 2010-12-08 17:19:21,406 Velvet log info JJ __init__ galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,421 Loaded sniffer for datatype: galaxy.datatypes.binary:Bam galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,422 Loaded sniffer for datatype: galaxy.datatypes.binary:Sff galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,422 Loaded sniffer for datatype: galaxy.datatypes.xml:BlastXml galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,422 Loaded sniffer for datatype: galaxy.datatypes.sequence:Maf galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,422 Loaded sniffer for datatype: galaxy.datatypes.sequence:Lav galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.sequence:csFasta galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScoreSOLiD galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.qualityscore:QualityScore454 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fasta galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,423 Loaded sniffer for datatype: galaxy.datatypes.sequence:Fastq galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.interval:Wiggle galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.images:Html galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.images:Pdf galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.sequence:Axt galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,424 Loaded sniffer for datatype: galaxy.datatypes.interval:Bed galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,425 Loaded sniffer for datatype: galaxy.datatypes.interval:CustomTrack galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,425 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,425 Loaded sniffer for datatype: galaxy.datatypes.interval:Gff3 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,425 Loaded sniffer for datatype: galaxy.datatypes.tabular:Pileup galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,426 Loaded sniffer for datatype: galaxy.datatypes.interval:Interval galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,426 Loaded sniffer for datatype: galaxy.datatypes.tabular:Sam galaxy.datatypes.registry DEBUG 2010-12-08 17:19:21,426 Loaded sniffer for datatype: galaxy.datatypes.tabular:Vcf galaxy.model.migrate.check DEBUG 2010-12-08 17:19:21,538 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.model.migrate.check INFO 2010-12-08 17:19:21,622 At database version 62 galaxy.model.custom_types DEBUG 2010-12-08 17:19:21,630 pysqlite>=2 egg successfully loaded for sqlite dialect galaxy.tools.data DEBUG 2010-12-08 17:19:21,636 Loaded tool data table 'all_fasta galaxy.tools.data DEBUG 2010-12-08 17:19:21,637 Loaded tool data table 'bfast_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,638 Loaded tool data table 'blastdb galaxy.tools.data DEBUG 2010-12-08 17:19:21,638 Loaded tool data table 'blastdb_p galaxy.tools.data DEBUG 2010-12-08 17:19:21,639 Loaded tool data table 'bowtie_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,640 Loaded tool data table 'bowtie_indexes_color galaxy.tools.data DEBUG 2010-12-08 17:19:21,641 Loaded tool data table 'bwa_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,642 Loaded tool data table 'indexed_maf_files galaxy.tools.data DEBUG 2010-12-08 17:19:21,642 Loaded tool data table 'ngs_sim_fasta galaxy.tools.data DEBUG 2010-12-08 17:19:21,643 Loaded tool data table 'lastz_seqs galaxy.tools.data DEBUG 2010-12-08 17:19:21,644 Loaded tool data table 'perm_base_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,644 Loaded tool data table 'perm_color_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,645 Loaded tool data table 'srma_indexes galaxy.tools.data DEBUG 2010-12-08 17:19:21,645 Loaded tool data table 'tophat_indexes galaxy.tools INFO 2010-12-08 17:19:21,645 parsing the tool configuration galaxy.tools DEBUG 2010-12-08 17:19:21,660 Loading section: Get Data galaxy.tools DEBUG 2010-12-08 17:19:21,997 Loaded tool: upload1 1.1.2 galaxy.tools DEBUG 2010-12-08 17:19:22,002 Loaded tool: ucsc_table_direct1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,007 Loaded tool: ucsc_table_direct_test1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,011 Loaded tool: ucsc_table_direct_archaea1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,015 Loaded tool: bx_browser 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,095 Loaded tool: microbial_import1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,099 Loaded tool: biomart 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,103 Loaded tool: biomart_test 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,107 Loaded tool: cbi_rice_mart 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,111 Loaded tool: gramenemart 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,114 Loaded tool: modENCODEfly 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,117 Loaded tool: flymine 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,121 Loaded tool: flymine_test 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,123 Loaded tool: modmine 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,126 Loaded tool: ratmine 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,130 Loaded tool: modENCODEworm 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,134 Loaded tool: wormbase 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,137 Loaded tool: wormbase_test 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,140 Loaded tool: eupathdb 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,143 Loaded tool: encode_db1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,146 Loaded tool: epigraph_import 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,150 Loaded tool: epigraph_import_test 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,155 Loaded tool: hbvar 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,167 Loaded tool: fix_errors 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,168 Loading section: Send Data galaxy.tools DEBUG 2010-12-08 17:19:22,199 Loaded tool: epigraph_export 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,234 Loaded tool: epigraph_test_export 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,234 Loading section: ENCODE Tools galaxy.tools DEBUG 2010-12-08 17:19:22,293 Loaded tool: gencode_partition1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,349 Loaded tool: random_intervals1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,349 Loading section: Lift-Over galaxy.tools DEBUG 2010-12-08 17:19:22,381 Loaded tool: liftOver1 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:22,382 Loading section: Text Manipulation galaxy.tools DEBUG 2010-12-08 17:19:22,412 Loaded tool: addValue 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,456 Loaded tool: Add_a_column1 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:22,481 Loaded tool: cat1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,541 Loaded tool: Cut1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,569 Loaded tool: mergeCols1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,597 Loaded tool: Convert characters1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,620 Loaded tool: createInterval 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,683 Loaded tool: Cut1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,722 Loaded tool: ChangeCase 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,746 Loaded tool: Paste1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,763 Loaded tool: Remove beginning1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,781 Loaded tool: random_lines1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,799 Loaded tool: Show beginning1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,826 Loaded tool: Show tail1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:22,875 Loaded tool: trimmer 0.0.1 galaxy.tools DEBUG 2010-12-08 17:19:22,970 Loaded tool: dna_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,024 Loaded tool: tables_arithmetic_operations 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,025 Loading section: Filter and Sort galaxy.tools DEBUG 2010-12-08 17:19:23,111 Loaded tool: Filter1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,149 Loaded tool: sort1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,379 Loaded tool: Grep1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,406 Loaded tool: Extract_features1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,453 Loaded tool: gff_filter_by_attribute 0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,472 Loaded tool: gff_filter_by_feature_count 0.1 galaxy.tools DEBUG 2010-12-08 17:19:23,472 Loading section: Join, Subtract and Group galaxy.tools DEBUG 2010-12-08 17:19:23,521 Loaded tool: join1 2.0.2 galaxy.tools DEBUG 2010-12-08 17:19:23,550 Loaded tool: comp1 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:23,607 Loaded tool: subtract_query1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,656 Loaded tool: Grouping1 1.9.1 galaxy.tools DEBUG 2010-12-08 17:19:23,688 Loaded tool: column_join 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:23,688 Loading section: Convert Formats galaxy.tools DEBUG 2010-12-08 17:19:23,753 Loaded tool: axt_to_concat_fasta 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,814 Loaded tool: axt_to_fasta 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,891 Loaded tool: axt_to_lav_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,920 Loaded tool: bed2gff1 2.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,941 Loaded tool: fasta2tab 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:23,971 Loaded tool: gff2bed1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,014 Loaded tool: lav_to_bed1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,132 Loaded tool: MAF_To_BED1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,227 Loaded tool: MAF_To_Interval1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,345 Loaded tool: MAF_To_Fasta1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,367 Loaded tool: tab2fasta 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:24,382 Loaded tool: fastq_to_fasta_python 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,434 Loaded tool: wiggle2simple1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,450 Loaded tool: Sff_extractor 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,500 Loaded tool: gtf2bedgraph 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,540 Loaded tool: wig_to_bigWig 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,540 Loading section: Extract Features galaxy.tools DEBUG 2010-12-08 17:19:24,571 Loaded tool: gene2exon1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,572 Loading section: Fetch Sequences galaxy.tools DEBUG 2010-12-08 17:19:24,637 Loaded tool: Extract genomic DNA 1 2.2.1 galaxy.tools DEBUG 2010-12-08 17:19:24,637 Loading section: Fetch Alignments galaxy.tools DEBUG 2010-12-08 17:19:24,679 Loaded tool: Interval2Maf_pairwise1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,709 Loaded tool: Interval2Maf1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,789 Loaded tool: MAF_split_blocks_by_species1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:24,833 Loaded tool: Interval_Maf_Merged_Fasta2 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,879 Loaded tool: GeneBed_Maf_Fasta2 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,962 Loaded tool: maf_stats1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:24,980 Loaded tool: MAF_Thread_For_Species1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,012 Loaded tool: MAF_Limit_To_Species1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,027 Loaded tool: maf_limit_size1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:25,043 Loaded tool: maf_by_block_number1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:25,061 Loaded tool: MAF_Reverse_Complement_1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:25,112 Loaded tool: MAF_filter 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:25,112 Loading section: Get Genomic Scores galaxy.tools DEBUG 2010-12-08 17:19:25,161 Loaded tool: wiggle2simple1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,317 Loaded tool: aggregate_scores_in_intervals2 1.1.2 galaxy.tools DEBUG 2010-12-08 17:19:25,371 Loaded tool: phastOdds_for_intervals 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,371 Loading section: Operate on Genomic Intervals galaxy.tools DEBUG 2010-12-08 17:19:25,422 Loaded tool: gops_intersect_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,576 Loaded tool: gops_subtract_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,606 Loaded tool: gops_merge_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,643 Loaded tool: gops_concat_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,669 Loaded tool: gops_basecoverage_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,710 Loaded tool: gops_coverage_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,750 Loaded tool: gops_complement_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,806 Loaded tool: gops_cluster_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,884 Loaded tool: gops_join_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,936 Loaded tool: get_flanks1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:25,972 Loaded tool: flanking_features_1 4.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,051 Loaded tool: Annotation_Profiler_0 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,052 Loading section: Statistics galaxy.tools DEBUG 2010-12-08 17:19:26,130 Loaded tool: Summary_Statistics1 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:26,179 Loaded tool: Count1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,253 Loaded tool: cor2 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,295 Loaded tool: generate_matrix_for_pca_and_lda1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,334 Loaded tool: lda_analy1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:26,348 Loaded tool: plot_for_lda_output1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:26,395 Loaded tool: t_test_two_samples 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,491 Loaded tool: compute_q_values 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,491 Loading section: Wavelet Analysis galaxy.tools DEBUG 2010-12-08 17:19:26,539 Loaded tool: compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,588 Loaded tool: compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,639 Loaded tool: compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,702 Loaded tool: compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,703 Loading section: Graph/Display Data galaxy.tools DEBUG 2010-12-08 17:19:26,771 Loaded tool: histogram_rpy 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:26,820 Loaded tool: scatterplot_rpy 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,846 Loaded tool: barchart_gnuplot 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,892 Loaded tool: XY_Plot_1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:26,910 Loaded tool: qual_stats_boxplot 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,948 Loaded tool: gmaj_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:26,974 Loaded tool: laj_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,000 Loaded tool: build_ucsc_custom_track_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,024 Loaded tool: vcf_to_maf_customtrack1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,056 Loaded tool: mutation_visualize 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,056 Loading section: Regional Variation galaxy.tools DEBUG 2010-12-08 17:19:27,111 Loaded tool: winSplitter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,171 Loaded tool: featureCoverage1 2.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,211 Loaded tool: qualityFilter 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:27,242 Loaded tool: cpgFilter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,280 Loaded tool: getIndels_2way 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,304 Loaded tool: indels_3way 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:27,327 Loaded tool: indelRates_3way 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,349 Loaded tool: substitutions1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,386 Loaded tool: subRate1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,423 Loaded tool: microsats_align1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,452 Loaded tool: microsats_mutability1 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:27,497 Loaded tool: delete_overlapping_indels 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,598 Loaded tool: compute_motifs_frequency 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,769 Loaded tool: compute_motif_frequencies_for_all_motifs 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,806 Loaded tool: categorize_elements_satisfying_criteria 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,841 Loaded tool: draw_stacked_barplots 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:27,841 Loading section: Multiple regression galaxy.tools DEBUG 2010-12-08 17:19:27,901 Loaded tool: LinearRegression1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:27,968 Loaded tool: BestSubsetsRegression1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,024 Loaded tool: rcve1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,024 Loading section: Multivariate Analysis galaxy.tools DEBUG 2010-12-08 17:19:28,079 Loaded tool: pca1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:28,150 Loaded tool: cca1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,185 Loaded tool: kpca1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,219 Loaded tool: kcca1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,219 Loading section: Evolution galaxy.tools DEBUG 2010-12-08 17:19:28,241 Loaded tool: hyphy_branch_lengths_wrapper1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,259 Loaded tool: hyphy_nj_tree_wrapper1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,289 Loaded tool: hyphy_dnds_wrapper1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,354 Loaded tool: mutate_snp_codon_1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,405 Loaded tool: hgv_codingSnps 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,448 Loaded tool: hgv_add_scores 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,448 Loading section: Metagenomic analyses galaxy.tools DEBUG 2010-12-08 17:19:28,489 Loaded tool: Fetch Taxonomic Ranks 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:28,515 Loaded tool: t2t_report 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,594 Loaded tool: Draw_phylogram 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,649 Loaded tool: find_diag_hits 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,688 Loaded tool: lca1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:28,767 Loaded tool: poisson2test 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,767 Loading section: FASTA manipulation galaxy.tools DEBUG 2010-12-08 17:19:28,787 Loaded tool: fasta_compute_length 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,815 Loaded tool: fasta_filter_by_length 1.1 galaxy.tools DEBUG 2010-12-08 17:19:28,839 Loaded tool: fasta_concatenate0 0.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,859 Loaded tool: fasta2tab 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,879 Loaded tool: tab2fasta 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:28,902 Loaded tool: cshl_fasta_formatter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,922 Loaded tool: cshl_fasta_nucleotides_changer 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,945 Loaded tool: cshl_fastx_collapser 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:28,945 Loading section: NGS: QC and manipulation galaxy.tools DEBUG 2010-12-08 17:19:28,998 Loaded tool: fastq_groomer 1.0.3 galaxy.tools DEBUG 2010-12-08 17:19:29,019 Loaded tool: fastq_paired_end_splitter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,041 Loaded tool: fastq_paired_end_joiner 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,138 Loaded tool: fastq_stats 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,188 Loaded tool: quality_score_distribution 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:29,220 Loaded tool: trim_reads 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,240 Loaded tool: fastq_combiner 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:29,280 Loaded tool: solid2fastq 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,354 Loaded tool: solid_qual_stats 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,400 Loaded tool: solid_qual_boxplot 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,482 Loaded tool: fastq_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,510 Loaded tool: fastq_trimmer 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,537 Loaded tool: fastq_quality_trimmer 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,554 Loaded tool: fastq_masker_by_quality 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,633 Loaded tool: fastq_manipulation 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:29,647 Loaded tool: fastq_to_fasta_python 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,663 Loaded tool: fastq_to_tabular 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,679 Loaded tool: tabular_to_fastq 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,710 Loaded tool: cshl_fastq_quality_converter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,805 Loaded tool: cshl_fastx_quality_statistics 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,856 Loaded tool: cshl_fastq_quality_boxplot 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,899 Loaded tool: cshl_fastx_nucleotides_distribution 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,927 Loaded tool: cshl_fastq_to_fasta 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,967 Loaded tool: cshl_fastq_quality_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:29,999 Loaded tool: cshl_fastq_to_fasta 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,137 Loaded tool: cshl_fastx_artifacts_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,163 Loaded tool: cshl_fastx_barcode_splitter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,199 Loaded tool: cshl_fastx_clipper 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:30,222 Loaded tool: cshl_fastx_collapser 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,253 Loaded tool: cshl_fastx_renamer 0.0.11 galaxy.tools DEBUG 2010-12-08 17:19:30,278 Loaded tool: cshl_fastx_reverse_complement 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,312 Loaded tool: cshl_fastx_trimmer 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:30,312 Loading section: NCBI BLAST+ galaxy.tools DEBUG 2010-12-08 17:19:30,387 Loaded tool: ncbi_blastn_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,464 Loaded tool: ncbi_blastp_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,544 Loaded tool: ncbi_blastx_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,620 Loaded tool: ncbi_tblastn_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,699 Loaded tool: ncbi_tblastx_wrapper 0.0.5 galaxy.tools DEBUG 2010-12-08 17:19:30,756 Loaded tool: blastxml_to_tabular 0.0.1 galaxy.tools DEBUG 2010-12-08 17:19:30,757 Loading section: NGS: Mapping galaxy.tools DEBUG 2010-12-08 17:19:30,829 Loaded tool: lastz_wrapper_2 1.2.0 galaxy.tools DEBUG 2010-12-08 17:19:30,870 Loaded tool: lastz_paired_reads_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:30,967 Loaded tool: bowtie_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,070 Loaded tool: bowtie_color_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,130 Loaded tool: bwa_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,198 Loaded tool: bfast_wrapper 0.1.2 galaxy.tools DEBUG 2010-12-08 17:19:31,271 Loaded tool: megablast_wrapper 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,294 Loaded tool: megablast_xml_parser 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,362 Loaded tool: PerM 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,407 Loaded tool: srma_wrapper 0.2.0 galaxy.tools DEBUG 2010-12-08 17:19:31,407 Loading section: NGS: Indel Analysis galaxy.tools DEBUG 2010-12-08 17:19:31,436 Loaded tool: sam_indel_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,462 Loaded tool: indel_sam2interval 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,487 Loaded tool: indel_table 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,520 Loaded tool: indel_analysis 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,520 Loading section: NGS: RNA Analysis galaxy.tools DEBUG 2010-12-08 17:19:31,619 Loaded tool: tophat 1.2.0 galaxy.tools DEBUG 2010-12-08 17:19:31,683 Loaded tool: cufflinks 0.9.1 galaxy.tools DEBUG 2010-12-08 17:19:31,747 Loaded tool: cuffcompare 0.9.1 galaxy.tools DEBUG 2010-12-08 17:19:31,833 Loaded tool: cuffdiff 0.9.1 galaxy.tools DEBUG 2010-12-08 17:19:31,851 Loaded tool: filter_combined_via_tracking 0.1 galaxy.tools DEBUG 2010-12-08 17:19:31,851 Loading section: NGS: SAM Tools galaxy.tools DEBUG 2010-12-08 17:19:31,892 Loaded tool: sam_bw_filter 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,921 Loaded tool: sam2interval 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:31,941 Loaded tool: sam_to_bam 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:31,959 Loaded tool: bam_to_sam 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:31,978 Loaded tool: sam_merge 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:32,022 Loaded tool: sam_pileup 1.1.0 galaxy.tools DEBUG 2010-12-08 17:19:32,175 Loaded tool: pileup_parser 1.0.2 galaxy.tools DEBUG 2010-12-08 17:19:32,217 Loaded tool: pileup_interval 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,218 Loading section: NGS: Peak Calling galaxy.tools DEBUG 2010-12-08 17:19:32,248 Loaded tool: peakcalling_macs 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,273 Loaded tool: bed2genetrack 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:32,304 Loaded tool: predict2genetrack 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,304 Loading section: NGS: Simulation galaxy.tools DEBUG 2010-12-08 17:19:32,336 Loaded tool: ngs_simulation 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,337 Loading section: SNP/WGA: Data; Filters galaxy.tools DEBUG 2010-12-08 17:19:32,500 Loaded tool: upload1 1.1.2 galaxy.tools DEBUG 2010-12-08 17:19:32,502 Loaded tool: library_access1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,707 Loaded tool: rgClean1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,774 Loaded tool: rgPedSub1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,865 Loaded tool: rgLDIndep1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,911 Loaded tool: fakePhe1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,941 Loaded tool: rgfakePed1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:32,941 Loading section: SNP/WGA: QC; LD; Plots galaxy.tools DEBUG 2010-12-08 17:19:32,989 Loaded tool: rgQC1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,047 Loaded tool: rgEigPCA1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,101 Loaded tool: rgHaploView1 0.3 galaxy.tools DEBUG 2010-12-08 17:19:33,167 Loaded tool: rgManQQ1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:33,215 Loaded tool: rgGRR1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,215 Loading section: SNP/WGA: Statistical Models galaxy.tools DEBUG 2010-12-08 17:19:33,276 Loaded tool: rgCaCo1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,329 Loaded tool: rgTDT1 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,414 Loaded tool: rgGLM1 0.2 galaxy.tools DEBUG 2010-12-08 17:19:33,479 Loaded tool: rgManQQ1 1.0.1 galaxy.tools DEBUG 2010-12-08 17:19:33,479 Loading section: Human Genome Variation galaxy.tools DEBUG 2010-12-08 17:19:33,535 Loaded tool: hgv_codingSnps 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,583 Loaded tool: hgv_add_scores 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,634 Loaded tool: hgv_sift 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,662 Loaded tool: hgv_linkToGProfile 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,698 Loaded tool: hgv_david 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,784 Loaded tool: hgv_ctdBatch 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,816 Loaded tool: hgv_funDo 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,857 Loaded tool: hgv_snpFreq 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,897 Loaded tool: hgv_ldtools 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:33,948 Loaded tool: hgv_pass 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:34,015 Loaded tool: hgv_gpass 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:34,070 Loaded tool: hgv_beam 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:34,142 Loaded tool: hgv_lps 1.0.0 galaxy.tools DEBUG 2010-12-08 17:19:34,184 Loaded tool: hgv_hilbertvis 1.0.0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,603 Loaded converter: CONVERTER_Bam_Bai_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,615 Loaded converter: CONVERTER_bam_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,627 Loaded converter: CONVERTER_bed_to_gff_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,639 Loaded converter: CONVERTER_interval_to_coverage_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,651 Loaded converter: CONVERTER_bed_to_interval_index_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,663 Loaded converter: CONVERTER_bed_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,674 Loaded converter: CONVERTER_BedGraph_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,686 Loaded converter: CONVERTER_bed_to_genetrack_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,698 Loaded converter: CONVERTER_fasta_to_tabular galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,710 Loaded converter: CONVERTER_fasta_to_bowtie_base_index galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,723 Loaded converter: CONVERTER_fasta_to_bowtie_color_index galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,735 Loaded converter: CONVERTER_gff_to_bed_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,747 Loaded converter: CONVERTER_gff_to_interval_index_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,766 Loaded converter: CONVERTER_gff_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,778 Loaded converter: CONVERTER_interval_to_bed_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,789 Loaded converter: CONVERTER_interval_to_bedstrict_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,802 Loaded converter: CONVERTER_interval_to_bed6_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,814 Loaded converter: CONVERTER_interval_to_bed12_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,826 Loaded converter: CONVERTER_maf_to_fasta_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,839 Loaded converter: CONVERTER_maf_to_interval_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,851 Loaded converter: CONVERTER_vcf_to_interval_index_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,862 Loaded converter: CONVERTER_vcf_to_summary_tree_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,874 Loaded converter: CONVERTER_Wiggle_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,876 Loaded converter: CONVERTER_wiggle_to_interval_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,888 Loaded converter: lped2fpedconvert galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,899 Loaded converter: lped2pbedconvert galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,911 Loaded converter: pbed2lpedconvert galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,923 Loaded converter: pbed2ldindepconvert galaxy.tools.imp_exp DEBUG 2010-12-08 17:19:36,928 Loaded history export tool: __EXPORT_HISTORY__ galaxy.tools.imp_exp DEBUG 2010-12-08 17:19:36,930 Loaded history import tool: __IMPORT_HISTORY__ galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,934 Loaded external metadata tool: __SET_METADATA__ galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,952 Loaded indexer: INDEXER_Coverage_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,963 Loaded indexer: INDEXER_Coverage_0 galaxy.datatypes.registry DEBUG 2010-12-08 17:19:36,974 Loaded indexer: INDEXER_Interval_0 galaxy.jobs.runners.local INFO 2010-12-08 17:19:36,984 starting workers galaxy.jobs.runners.local DEBUG 2010-12-08 17:19:36,986 5 workers ready Traceback (most recent call last): File "/gtools/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/gtools/galaxy/galaxy-dist/lib/galaxy/app.py", line 79, in __init__ self.job_manager = jobs.JobManager( self ) File "/gtools/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 41, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/gtools/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1005, in __init__ self.job_runners[runner_name] = runners.drmaa.DRMAAJobRunner( app ) File "/gtools/galaxy/galaxy-dist/lib/galaxy/jobs/runners/drmaa.py", line 72, in __init__ raise Exception( "DRMAAJobRunner requires drmaa module which could not be loaded: %s" % drmaa ) Exception: DRMAAJobRunner requires drmaa module which could not be loaded: No module named _ctypes

1 0

NGINX configuration for Galaxy production
by Richard Bruskiewich 08 Dec '10

08 Dec '10

Colleagues, I encountered a curious problem while configuring nginx as a proxy for Galaxy. I posed the question through Enis who forwarded it to one of the lists. I just want to share a solution to the issue, which could perhaps be documented in a small change to the http://bitbucket.org/galaxy/galaxy-central/wiki/Config/nginxProxydocumentat… page. The observed problem was that Galaxy proxied through NGINX would only display properly in Microsoft IE but not in Firefox or Opera. One of my colleagues noticed that a Firefox error console reported that the various cascading style sheets were observed as having MIME type "text/plain" not "text/css" hence, where not loaded by Firefox. Presumably IE assumed CSS file type by the context of retrieval but the other browsers were more strict. Anyhow, this suggested that although NGINX has a configuration file of MIME types associated with file extensions, the content-type wasn't being properly set. I don't know if this represents a bug in NGINX operations, but after perusing the NGINX wiki docs, I came across a directive that appeared to solve the problem: default_type. The "default_type" covers any files in a specified context (http, server, location) which don't otherwise have their MIME type recognized (for whatever reason) and is itself originally set "by default" to "text/plain", which may explain the observed error in content type sent back. What I therefore did is reset the default type, in the style sheet nginx "location" directive context, to "text/css". This appeared to work. In the nginxProxy wiki documentation page on BitBucket, somebody with editorial privileges to this page may wish to document this throughout the page where the style directives are documented , i.e. location /static/style { alias /home/nate/galaxy_dist/static/june_2007_style/blue; default_type text/css; # other directives... } Cheers, Richard Bruskiewich, PhD Senior Scientist, Computational and Systems Biology Applications Team for Computational Genomics T.T. Chang Genetic Resources Center International Rice Research Institute

2 3

syntax error in tophat wrapper after updating
by Glen Beane 08 Dec '10

08 Dec '10

Last week we pulled the changes from galaxy-dist (our copy was a couple months old). Now when we run tophat we get a Python syntax error: An error occurred running this job:File "/<galaxy_home>/tools/ngs_rna/tophat_wrapper.py", line 196 finally: ^ SyntaxError: invalid syntax We have no local changes to the wrapper. Has this been fixed in galaxy-central? -- Glen L. Beane Software Engineer The Jackson Laboratory Phone (207) 288-6153

2 1

statistics -> cor failing on R's is.atomic() check
by Ry4an Brase 08 Dec '10

08 Dec '10

Trying to run the unmodified cor.py tool from a current galaxy-dist we're getting this output using the sample input data: % python /project/dbw-galaxy/DEVELOPMENT/tools/stats/cor.py /project/dbw-galaxy/DEVELOPMENT/test-data/cor.tabular /tmp/cor.out.ry4an 2,3 pearson Error: is.atomic(x) is not TRUE which is happening in galaxy too. The line it's triggering is: 71 # Run correlation 72 try: 73 value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method ) 74 except Exception, exc: 75 out.close() 76 stop_err("%s" %str( exc )) and tracing through the execution the inputs look fine: Breakpoint 1 at /home/msi/ry4an/cor.py:73 (Pdb) run Restarting ./cor.py with arguments: /project/dbw-galaxy/DEVELOPMENT/test-data/cor.tabular /tmp/cor.out.ry4an465 2,3 pearson > /home/msi/ry4an/cor.py(6)<module>() -> """ (Pdb) c > /home/msi/ry4an/cor.py(73)main() -> value = r.cor( array( matrix ), use="pairwise.complete.obs", method=method ) (Pdb) p matrix [[68.0, 4.0999999999999996], [71.0, 4.5999999999999996], [62.0, 3.7999999999999998], [75.0, 4.4000000000000004], [58.0, 3.2000000000000002], [60.0, 3.1000000000000001], [67.0, 3.7999999999999998], [68.0, 4.0999999999999996], [71.0, 4.2999999999999998], [69.0, 3.7000000000000002], [68.0, 3.5], [67.0, 3.2000000000000002], [63.0, 3.7000000000000002], [62.0, 3.2999999999999998], [60.0, 3.3999999999999999], [63.0, 4.0], [65.0, 4.0999999999999996], [67.0, 3.7999999999999998], [63.0, 3.3999999999999999], [61.0, 3.6000000000000001]] (Pdb) p array(matrix) array([[ 68. , 4.1], [ 71. , 4.6], [ 62. , 3.8], [ 75. , 4.4], [ 58. , 3.2], [ 60. , 3.1], [ 67. , 3.8], [ 68. , 4.1], [ 71. , 4.3], [ 69. , 3.7], [ 68. , 3.5], [ 67. , 3.2], [ 63. , 3.7], [ 62. , 3.3], [ 60. , 3.4], [ 63. , 4. ], [ 65. , 4.1], [ 67. , 3.8], [ 63. , 3.4], [ 61. , 3.6]]) The closest thing I could find ont the rpy list is: http://www.mail-archive.com/rpy-list@lists.sourceforge.net/msg02612.html which hints at an input conversion problem in rpy. We've got rpy 1.0.3 and R version 2.10.1 on this galaxy instance. Has anyone else seen this, or does anyone have a suggestion as to how the tool might be tweaked to bypass it? Thanks, -- Ry4an Brase 612-626-6575 Software Developer Application Development University of Minnesota Supercomputing Institute http://www.msi.umn.edu

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UCSC genome browser
by Rene Dreos (JIC) 08 Dec '10

08 Dec '10

Dear Developer my institute would like to run a local version of Galaxy and I managed to properly install it on my mac. We are focused on plant and especially on Arabidopsis. I managed to upgrade our local Galaxy with Arabidopsis genome and I am able to run some analysis (ChIP-seq) from mapping to peak detection with MACS. The next step would be to visualize the results on UCSC genome browser. We have a local version of it (with the latest Arabidopsis genome assembly) but MACS result hasn't got any link to UCSC GB but only to GeneTrack (that is not working). How can I make Galaxy aware of our local GB? thank you very much kind regard r

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slow execution of set_metadata.py
by Matthias Gierth 08 Dec '10

08 Dec '10

Hello List, I have a small problem with my own local Galaxy instance. So I try to set up some workflows for NGS. Everything is working fine for now, but the process for setting the Metadata on a file takes a lot of time. Currently I created a workflow --> fastq file from Library --> fastx_groomer( convert from Illumina to sanger format)-->mapping with bwa So the grooming and mapping runs fine, but after mapping the set_metadata.py takes longer than the mapping of the 2gb fastq-file. The testing server is a Dell R710 with 2x6-core cpus and 72GB of memory Below there is my Config for Galaxy. Anybody an Idea whats going wrong with my setup? many thanks Matthias # # Galaxy is configured by default to be useable in a single-user development # environment. To tune the application for a multi-user production # environment, see the documentation at: # # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer # # Throughout this sample configuration file, except where stated otherwise, # uncommented values override the default if left unset, whereas commented # values are set to the default value. # examples of many of these options are explained in more detail in the wiki: # # Config hackers are encouraged to check there before asking for help. # ---- HTTP Server ---------------------------------------------------------- # Configuration of the internal HTTP server. [server:main] # The internal HTTP server to use. Currently only Paste is provided. This # option is required. use = egg:Paste#http # The port on which to listen. port = 8081 # The address on which to listen. By default, only listen to localhost (Galaxy # will not be accessible over the network). Use '0.0.0.0' to listen on all # available network interfaces. host = 0.0.0.0 # Use a threadpool for the web server instead of creating a thread for each # request. use_threadpool = True # Number of threads in the web server thread pool. threadpool_workers = 8 # ---- Filters -------------------------------------------------------------- # Filters sit between Galaxy and the HTTP server. # These filters are disabled by default. They can be enabled with # 'filter-with' in the [app:main] section below. # Define the gzip filter. [filter:gzip] use = egg:Paste#gzip # Define the proxy-prefix filter. [filter:proxy-prefix] use = egg:PasteDeploy#prefix prefix = /galaxy # ---- Galaxy --------------------------------------------------------------- # Configuration of the Galaxy application. [app:main] # -- Application and filtering # The factory for the WSGI application. This should not be changed. paste.app_factory = galaxy.web.buildapp:app_factory # If not running behind a proxy server, you may want to enable gzip compression # to decrease the size of data transferred over the network. If using a proxy # server, please enable gzip compression there instead. #filter-with = gzip # If running behind a proxy server and Galaxy is served from a subdirectory, # enable the proxy-prefix filter and set the prefix in the # [filter:proxy-prefix] section above. #filter-with = proxy-prefix # If proxy-prefix is enabled and you're running more than one Galaxy instance # behind one hostname, you will want to set this to the same path as the prefix # in the filter above. This value becomes the "path" attribute set in the # cookie so the cookies from each instance will not clobber each other. #cookie_path = None # -- Database # By default, Galaxy uses a SQLite database at 'database/universe.sqlite'. You # may use a SQLAlchemy connection string to specify an external database # instead. This string takes many options which are explained in detail in the # config file documentation. database_connection = mysql://xxx:xxx@localhost/galaxy?unix_socket=/data/mysql/mysql.sock # If the server logs errors about not having enough database pool connections, # you will want to increase these values, or consider running more Galaxy # processes. #database_engine_option_pool_size = 5 #database_engine_option_max_overflow = 10 # If using MySQL and the server logs the error "MySQL server has gone away", # you will want to set this to some positive value (7200 should work). database_engine_option_pool_recycle = 7200 # If large database query results are causing memory or response time issues in # the Galaxy process, leave the result on the server instead. This option is # only available for PostgreSQL and is highly recommended. #database_engine_option_server_side_cursors = False # Create only one connection to the database per thread, to reduce the # connection overhead. Recommended when not using SQLite: #database_engine_option_strategy = threadlocal # -- Files and directories # Dataset files are stored in this directory. file_path = /galaxytemp/data # Temporary files are stored in this directory. new_file_path = /galaxytemp/tmp # Tool config file, defines what tools are available in Galaxy. #tool_config_file = tool_conf.xml # Path to the directory containing the tools defined in the config. #tool_path = tools # Directory where data used by tools is located, see the samples in that # directory and the wiki for help: # http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration #tool_data_path = tool-data # Datatypes config file, defines what data (file) types are available in # Galaxy. #datatypes_config_file = datatypes_conf.xml # -- Mail and notification # Galaxy sends mail for various things: Subscribing users to the mailing list # if they request it, emailing password resets, notification from the Galaxy # Sample Tracking system, and reporting dataset errors. To do this, it needs # to send mail through an SMTP server, which you may define here. #smtp_server = None # On the user registration form, users may choose to join the mailing list. # This is the address of the list they'll be subscribed to. #mailing_join_addr = galaxy-user-join(a)bx.psu.edu # Datasets in an error state include a link to report the error. Those reports # will be sent to this address. Error reports are disabled if no address is set. #error_email_to = None # -- Display sites # Galaxy can display data at various external browsers. These options specify # which browsers should be available. URLs and builds available at these # browsers are defined in the specifield files. # UCSC browsers: tool-data/shared/ucsc/ucsc_build_sites.txt #ucsc_display_sites = main,test,archaea,ucla # GBrowse servers: tool-data/shared/gbrowse/gbrowse_build_sites.txt #gbrowse_display_sites = wormbase,tair,modencode_worm,modencode_fly # GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt #genetrack_display_sites = main,test # -- UI Localization # Append "/{brand}" to the "Galaxy" text in the masthead. #brand = None # The URL linked by the "Galaxy/brand" text. #logo_url = / # The URL linked by the "Galaxy Wiki" link in the "Help" menu. #wiki_url = http://bitbucket.org/galaxy/galaxy-central/wiki # The URL linked by the "Email comments..." link in the "Help" menu. #bugs_email = None # The URL linked by the "How to Cite..." link in the "Help" menu. #citation_url = http://bitbucket.org/galaxy/galaxy-central/wiki/Citations # Serve static content, which must be enabled if you're not serving it via a # proxy server. These options should be self explanatory and so are not # documented individually. You can use these paths (or ones in the proxy # server) to point to your own styles. static_enabled = True static_cache_time = 360 static_dir = %(here)s/static/ static_images_dir = %(here)s/static/images static_favicon_dir = %(here)s/static/favicon.ico static_scripts_dir = %(here)s/static/scripts/ static_style_dir = %(here)s/static/june_2007_style/blue # -- Logging and Debugging # Verbosity of console log messages. Acceptable values can be found here: # http://docs.python.org/library/logging.html#logging-levels #log_level = DEBUG # Print database operations to the server log (warning, quite verbose!). #database_engine_option_echo = False # Print database pool operations to the server log (warning, quite verbose!). #database_engine_option_echo_pool = False # Turn on logging of application events and some user events to the database. #log_events = True # Turn on logging of user actions to the database. Actions currently logged are # grid views, tool searches, and use of "recently" used tools menu. The # log_events and log_actions functionality will eventually be merged. #log_actions = True # Debug enables access to various config options useful for development and # debugging: use_lint, use_profile, use_printdebug and use_interactive. It # also causes the files used by PBS/SGE (submission script, output, and error) # to remain on disk after the job is complete. Debug mode is disabled if # commented, but is uncommented by default in the sample config. debug = True # Check for WSGI compliance. #use_lint = False # Run the Python profiler on each request. #use_profile = False # Intercept print statements and show them on the returned page. #use_printdebug = True # Enable live debugging in your browser. This should NEVER be enabled on a # public site. Enabled in the sample config for development. use_interactive = True # Write thread status periodically to 'heartbeat.log', (careful, uses disk # space rapidly!). Useful to determine why your processes may be consuming a # lot of CPU. #use_heartbeat = False # Enable the memory debugging interface (careful, negatively impacts server # performance). #use_memdump = False # -- Data Libraries # These library upload options are described in much more detail in the wiki: # http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles # Add an option to the library upload form which allows administrators to # upload a directory of files. library_import_dir = /data/ # Add an option to the library upload form which allows authorized # non-administrators to upload a directory of files. The configured directory # must contain sub-directories named the same as the non-admin user's Galaxy # login ( email ). The non-admin user is restricted to uploading files or # sub-directories of files contained in their directory. #user_library_import_dir = None # Add an option to the admin library upload tool allowing admins to paste # filesystem paths to files and directories in a box, and these paths will be # added to a library. Set to True to enable. Please note the security # implication that this will give Galaxy Admins access to anything your Galaxy # user has access to. allow_library_path_paste = True # -- Users and Security # Galaxy encodes various internal values when these values will be output in # some format (for example, in a URL or cookie). You should set a key to be # used by the algorithm that encodes and decodes these values. It can be any # string. If left unchanged, anyone could construct a cookie that would grant # them access to others' sessions. #id_secret = USING THE DEFAULT IS NOT SECURE! # User authentication can be delegated to an upstream proxy server (usually # Apache). The upstream proxy should set a REMOTE_USER header in the request. # Enabling remote user disables regular logins. For more information, see: # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy #use_remote_user = False # If use_remote_user is enabled and your external authentication # method just returns bare usernames, set a default mail domain to be appended # to usernames, to become your Galaxy usernames (email addresses). #remote_user_maildomain = None # If use_remote_user is enabled, you can set this to a URL that will log your # users out. #remote_user_logout_href = None # Administrative users - set this to a comma-separated list of valid Galaxy # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: # http://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface admin_users = xxxx@biotec.tu-dresden.de,xxxx@biotec.tu-dresden.de # Force everyone to log in (disable anonymous access). #require_login = False # Allow unregistered users to create new accounts (otherwise, they will have to # be created by an admin). #allow_user_creation = True # Allow administrators to delete accounts. #allow_user_deletion = False # By default, users' data will be public, but setting this to True will cause # it to be private. Does not affect existing users and data, only ones created # after this option is set. Users may still change their default back to # public. new_user_dataset_access_role_default_private = True # -- Beta features # Enable Galaxy's built-in visualization module, Trackster. #enable_tracks = False # Enable Galaxy Pages. Pages are custom webpages that include embedded Galaxy items, # such as datasets, histories, workflows, and visualizations; pages are useful for # documenting and sharing multiple analyses or workflows. Pages are created using a # WYSIWYG editor that is very similar to a word processor. #enable_pages = False # Enable the (experimental! beta!) Web API. Documentation forthcoming. #enable_api = False # -- Job Execution # If running multiple Galaxy processes, one can be designated as the job # runner. For more information, see: # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling enable_job_running = True # Should jobs be tracked through the database, rather than in memory. # Necessary if you're running the load balanced setup. track_jobs_in_database = True # Enable job recovery (if Galaxy is restarted while cluster jobs are running, # it can "recover" them when it starts). This is not safe to use if you are # running more than one Galaxy server using the same database. enable_job_recovery = True # Setting metadata on job outputs to in a separate process (or if using a # cluster, on the cluster). Thanks to Python's Global Interpreter Lock and the # hefty expense that setting metadata incurs, your Galaxy process may become # unresponsive when this operation occurs internally. set_metadata_externally = True # Although it is fairly reliable, setting metadata can occasionally fail. In # these instances, you can choose to retry setting it internally or leave it in # a failed state (since retrying internally may cause the Galaxy process to be # unresponsive). If this option is set to False, the user will be given the # option to retry externally, or set metadata manually (when possible). #retry_metadata_internally = True # Number of concurrent jobs to run (local job runner) local_job_queue_workers = 7 # Jobs can be killed after a certain amount of execution time. Format is in # hh:mm:ss. Currently only implemented for PBS. #job_walltime = None # Clustering Galaxy is not a straightforward process and requires some # pre-configuration. See the the wiki before attempting to set any of these # options: # http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster # Comma-separated list of job runners to start. local is always started. If # left commented, no jobs will be run on the cluster, even if a cluster URL is # explicitly defined in the [galaxy:tool_runners] section below. The runners # currently available are 'pbs' and 'drmaa'. #start_job_runners = None # The URL for the default runner to use when a tool doesn't explicity define a # runner below. #default_cluster_job_runner = local:/// # The cluster runners have their own thread pools used to prepare and finish # jobs (so that these sometimes lengthy operations do not block normal queue # operation). The value here is the number of worker threads available to each # started runner. #cluster_job_queue_workers = 3 # These options are only used when using file staging with PBS. #pbs_application_server = #pbs_stage_path = #pbs_dataset_server = # ---- Tool Job Runners ----------------------------------------------------- # Individual per-tool job runner overrides. If not listed here, a tool will # run with the runner defined with default_cluster_job_runner. [galaxy:tool_runners] biomart = local:/// encode_db1 = local:/// hbvar = local:/// microbial_import1 = local:/// ucsc_table_direct1 = local:/// ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// # ---- Galaxy Message Queue ------------------------------------------------- # Galaxy uses AMQ protocol to receive messages from external sources like # bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. # For Galaxy to receive messages from a message queue the RabbitMQ server has # to be set up with a user account and other parameters listed below. The 'host' # and 'port' fields should point to where the RabbitMQ server is running. [galaxy_amqp] #host = 127.0.0.1 #port = 5672 #userid = galaxy #password = galaxy #virtual_host = galaxy_messaging_engine #queue = galaxy_queue #exchange = galaxy_exchange #routing_key = bar_code_scanner -- Matthias Gierth System Administrator Applied Bioinformatics Group (ABG) TU Dresden, Biotec Tatzberg 47-51 01307 Dresden Phone: +49 (0)351 463 40020 Fax: +49 (0)351 463 40087 Email: matthias.gierth(a)biotec.tu-dresden.de

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uploading data from UCSC on scaled Apache configuration broken
by David Hoover 07 Dec '10

07 Dec '10

I have followed the directions for scaling at http://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling, trying both the single job-runner/single web-server and single job-runner/multiple web-server approaches. In both cases, uploading data from UCSC failed with the following error message: An error occurred running this job: The remote data source application may be off line, please try again later. Error: [Errno socket error] [Errno -3] Temporary failure in name resolution What does this mean? We have multiple web servers behind a load balancing switch. If I limit the number of web servers to one, then the data upload works. Must the remote data request return to the same server and port as it went out from? David Hoover Helix Systems Staff http://helix.nih.gov

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Error setting-up and running bowtie tasks
by Chris Cole 06 Dec '10

06 Dec '10

I have previously been able to run bowtie jobs successfully, but now I get this error: galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure running job 2248 Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 124, in queue_job job_wrapper.prepare() File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py", line 368, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py", line 1524, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 182, in respond IndexError: list index out of range I've a feeling it has something to with the bowtie_indices.loc file and it's associated entry in tool_data_table_conf.xml. I can see that the format for the .loc file has changed (it now has four columns instead of two): h_sapiens37 NCBI37 Homo sapiens ncbi37 /db/bowtie/h_sapiens_37_asm But the xml doesn't match (it only has two columns):  <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table> What should there be in the 'columns' section? Thanks, Chris

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Changing the FASTA to tabular converter
by Peter 06 Dec '10

06 Dec '10

Hello all, I ran into a problem in a work flow manipulating FASTA and tabular files. I traced this to an unexpected behaviour of the FASTA to tabular converter. In my experience most command line tools which take FASTA files as input treat the first word after the ">" as the identifier for each FASTA record, and any subsequent text as an optional description. It could then make sense to turn a FASTA file into a three column tabular file (identifier, description, sequence). Currently Galaxy does not make this distinction, so we have just two columns (identifier+description, seq). Would you all be amenable to my extending this script to allow the user to choose between 2 column output (current behaviour) and 3 column output (splitting the FASTA ">" line at the first white space)? Alternatively, I have written a less invasive patch to allow an easy way to extract the identifier (first word) and sequence: http://bitbucket.org/peterjc/galaxy-central/changeset/f57552b4f9fb Note that currently the converter does allow the ">" line to be trimmed which can achieve the same goal but ONLY when all the identifiers are the same length (rarely the case in my experience). Similarly, I'd like to extend the tabular to FASTA converter to allow a third column to be selected as the description, giving for example ">c1 c3" as the ">" line, with the sequence coming from c2. I look forward to comments, Thanks, Peter P.S. All these comments apply equally to the FASTQ to/from tabular converters.

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