I used Get Data and Upload file from your computer...and this just started this Feb, actually a couple days ago it was fine. It happened always, no matter we load from localhost or remote host, and other means like paste the path etc didn't work either.
Actually, I found that there are many released change on the galaxy release and then I ran a 'hg pull -u'. However I had some error message saying many of the tools installed are eliminated in the new distribution and I could install them back from toolshed. I'm quite confused.
Here is the command I ran:
1. hg pull -u
2. ./run.sh --daemon (many error msg, follow the suggestion,then )
3. sh manage_db.sh upgrade (update db to 118 version, start again)
4. ./run.sh --daemon (many error msg, I'll paste it below, but next I did)
5. sh ./scripts/migrate_tools/0009_tools.sh
now after 5, I run it again, it started, but when I log in, seems this page is hanging for few hours:
so the error message in step 4 above was:
The list of files at the end of this message refers to tools that are configured to load into the tool panel for
this Galaxy instance, but have been removed from the Galaxy distribution. These tools and their dependencies can be
automatically installed from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.
To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,
be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should
be removed from your file named ./tool_conf.xml
...migrate 7->8
...migrate 8->9
from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu
and will be installed into your local Galaxy instance at the
location discussed above by running the following command.
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
sh ./scripts/migrate_tools/0009_tools.sh
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The tool dependencies listed above will be installed along with the repositories if you add the 'install_dependencies'
option to the above command like this:
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
sh ./scripts/migrate_tools/0009_tools.sh install_dependencies
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Tool dependencies can be installed after the repositories have been installed as well.
After the installation process finishes, you can start your Galaxy server. As part of this installation process,
entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these
tools will continue to be loaded into your tool panel. Because of this, existing entries for these tools have been
removed from your file named ./tool_conf.xml.
fastq_to_fasta.xml
execute_dwt_var_perFeature.xml
GMAJ.xml
rgWebLogo3.xml
rgClustalw.xml
gi2taxonomy.xml
t2t_report.xml
t2ps_wrapper.xml
find_diag_hits.xml
lca.xml
poisson2test.xml
rgFastQC.xml
fastq_groomer.xml
fastq_paired_end_splitter.xml
fastq_paired_end_joiner.xml
fastq_stats.xml
fastq_combiner.xml
fastq_filter.xml
fastq_trimmer.xml
fastq_trimmer_by_quality.xml
fastq_masker_by_quality.xml
fastq_paired_end_interlacer.xml
fastq_paired_end_deinterlacer.xml
fastq_manipulation.xml
fastq_to_tabular.xml
tabular_to_fastq.xml
bowtie2_wrapper.xml
tophat_wrapper.xml
tophat2_wrapper.xml
express_wrapper.xml
filter_transcripts_via_tracking.xml
macs_wrapper.xml
sicer_wrapper.xml
ccat_wrapper.xml
freebayes.xml
I ran the command
sh ./scripts/migrate_tools/0009_tools.sh
and after that, the start up still shows some errors like:
galaxy.tools ERROR 2014-02-27 18:08:16,514 Error reading tool from path: data_source/CR.xml
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool
tree = load_tool( config_file )
File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml
tree = ElementTree.parse(fname)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml'
galaxy.tools ERROR 2014-02-27 18:08:16,539 Error reading tool from path: data_source/genomespace_file_browser_prod.xml
Traceback (most recent call last):
File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 502, in load_tool_tag_set
tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id )
File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/__init__.py", line 615, in load_tool
tree = load_tool( config_file )
File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/tools/loader.py", line 13, in load_tool
tree = parse_xml(path)
File "/home/bioinfoadmin/app/galaxy-dist/lib/galaxy/util/__init__.py", line 151, in parse_xml
tree = ElementTree.parse(fname)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 859, in parse
tree.parse(source, parser)
File "/home/bioinfoadmin/app/galaxy-dist/eggs/elementtree-1.2.6_20050316-py2.7.egg/elementtree/ElementTree.py", line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml'
galaxy.tools WARNING 2014-02-27 18:08:16,548 Tool peakcalling_macs: a when tag has been defined for 'genome_size_cond (genome_size) --> 90300000', but does not appear to be selectable.
now if I do a 'grep IOError paster.log', I got the following:
IOError: [Errno 2] No such file or directory: './tools/data_source/CR.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/genomespace_file_browser_prod.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/bx_browser.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/flymine.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/flymine_test.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/modmine.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/mousemine.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/ratmine.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/yeastmine.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/metabolicmine.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/encode_db.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import.xml'
IOError: [Errno 2] No such file or directory: './tools/data_source/epigraph_import_test.xml'
IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph.xml'
IOError: [Errno 2] No such file or directory: './tools/data_destination/epigraph_test.xml'
IOError: [Errno 2] No such file or directory: './tools/encode/gencode_partition.xml'
IOError: [Errno 2] No such file or directory: './tools/encode/random_intervals.xml'
IOError: [Errno 2] No such file or directory: './tools/new_operations/column_join.xml'
IOError: [Errno 2] No such file or directory: './tools/extract/phastOdds/phastOdds_tool.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/t_test_two_samples.xml'
IOError: [Errno 2] No such file or directory: './tools/plotting/xy_plot.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/getIndels_3way.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/delete_overlapping_indels.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motifs_frequency.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/compute_motif_frequencies_for_all_motifs.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/categorize_elements_satisfying_criteria.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/draw_stacked_barplots.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/multispecies_MicrosatDataGenerator_interrupted_GALAXY.xml'
IOError: [Errno 2] No such file or directory: './tools/regVariation/microsatellite_birthdeath.xml'
IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_branch_lengths_wrapper.xml'
IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_nj_tree_wrapper.xml'
IOError: [Errno 2] No such file or directory: './tools/hyphy/hyphy_dnds_wrapper.xml'
IOError: [Errno 2] No such file or directory: './tools/evolution/mutate_snp_codon.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_formatter.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fasta_nucleotide_changer.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_converter.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_quality_statistics.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_boxplot.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_nucleotides_distribution.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastq_quality_filter.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_artifacts_filter.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_barcode_splitter.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_clipper.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_collapser.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_renamer.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_reverse_complement.xml'
IOError: [Errno 2] No such file or directory: './tools/fastx_toolkit/fastx_trimmer.xml'
IOError: [Errno 2] No such file or directory: './tools/indels/sam_indel_filter.xml'
IOError: [Errno 2] No such file or directory: './tools/indels/indel_sam2interval.xml'
IOError: [Errno 2] No such file or directory: './tools/indels/indel_table.xml'
IOError: [Errno 2] No such file or directory: './tools/indels/indel_analysis.xml'
IOError: [Errno 2] No such file or directory: './tools/ngs_rna/tophat_color_wrapper.xml'
IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cufflinks_wrapper.xml'
IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffcompare_wrapper.xml'
IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffmerge_wrapper.xml'
IOError: [Errno 2] No such file or directory: './tools/ngs_rna/cuffdiff_wrapper.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/sam_bitwise_flag_filter.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/sam2interval.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/sam_to_bam.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/bam_to_sam.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/sam_merge.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_mpileup.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/sam_pileup.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_parser.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/pileup_interval.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_flagstat.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_rmdup.xml'
IOError: [Errno 2] No such file or directory: './tools/samtools/samtools_slice_bam.xml'
IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_indexer.xml'
IOError: [Errno 2] No such file or directory: './tools/genetrack/genetrack_peak_prediction.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgClean.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgPedSub.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgLDIndep.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePhe.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgfakePed.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgQC.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgEigPCA.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgHaploView.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGRR.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgCaCo.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgTDT.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgGLM.xml'
IOError: [Errno 2] No such file or directory: './tools/rgenetics/rgManQQ.xml'
IOError: [Errno 2] No such file or directory: './tools/phenotype_association/ctd.xml'
IOError: [Errno 2] No such file or directory: './tools/phenotype_association/funDo.xml'
IOError: [Errno 2] No such file or directory: './tools/phenotype_association/hilbertvis.xml'
IOError: [Errno 2] No such file or directory: './tools/phenotype_association/dividePgSnpAlleles.xml'
IOError: [Errno 2] No such file or directory: './tools/vcf_tools/intersect.xml'
I'm not sure if I successfully updated galaxy source...since right now the screen is always hanging. I think I miss some config files or so.
Could you please advise?
Thanks,
Rui