Hi,
can you point me to the MACS2 wrapper you are using? If you find the correct wrapper file you can simply replace simplejson with json and it should work.
Thanks,
Bjoern
Am 13.03.2014 13:22, schrieb changyu:
Hi,___________________________________________________________
I also have problems with macs and macs2 with updated galaxy.
I got this error which seems a python version issue. But I can not find this file.
File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond
ImportError: No module named simplejson
Any suggestions?
Thanks a lot.
Changyu
Traceback (most recent call last):
File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/runners/__init__.py", line 152, in prepare_job
job_wrapper.prepare()
File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/jobs/__init__.py", line 697, in prepare
config_filenames = self.tool.build_config_files( param_dict, self.working_directory )
File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/tools/__init__.py", line 2757, in build_config_files
f.write( fill_template( template_text, context=param_dict ) )
File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/lib/galaxy/util/template.py", line 9, in fill_template
return str( Template( source=template_text, searchList=[context] ) )
File "/ifs/rcgroups/webapps/galaxy/rcapps/rcapps-galaxy-dist03/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__
return getattr(self, mainMethName)()
File "cheetah_DynamicallyCompiledCheetahTemplate_1394672664_28_93644.py", line 82, in respond
ImportError: No module named simplejson
On 3/4/14 8:01 PM, ruiwang.sz wrote:
Hi Martin,
So, after some effort, things seem to be working. Thanks for the help along
the way.
However, one more error happened.
Originally, I installed macs dependency for galaxy myself. The version is
1.4.2. It worked well.
Now, after galaxy upgrading removed it, and I installed it back from
tool_shed, things broke. In the galaxy tool panel, it looks the same like
before(as expected), but when I click on macs, it will show an option of MACS
'version 1.0.0' and 'version 1.0.1'. Be default it is 1.0.1, which is defined
in migrated_tools_conf.xml:
<section id="peak_calling" name="NGS: Peak Calling" version="">
<tool
file="toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>"
guid="toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1>">
<tool_shed>toolshed.g2.bx.psu.edu
<http://toolshed.g2.bx.psu.edu></tool_shed>
<repository_name>macs</repository_name>
<repository_owner>devteam</repository_owner>
<installed_changeset_revision>ae2ec275332a</installed_changeset_revision>
<id>toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/peakcalling_macs/1.0.1></id>
<version>1.0.1</version>
</tool>
</section>
if we dive in this file
toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs/macs_wrapper.xml>,
we could see that in this dir
/home/bioinfoadmin/app/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs
<http://toolshed.g2.bx.psu.edu/repos/devteam/macs/ae2ec275332a/macs>, there is
a tool_dependency xml file that has following content:
<?xml version="1.0"?>
<tool_dependency>
<package name="macs" version="1.3.7.1">
<repository changeset_revision="a7ea583a35d2"
name="package_macs_1_3_7_1" owner="devteam"
prior_installation_required="False" toolshed="http://toolshed.g2.bx.psu.edu" />
</package>
<package name="R" version="2.15.0">
<repository changeset_revision="8ab0d08a3da1" name="package_r_2_15_0"
owner="devteam" prior_installation_required="False"
toolshed="http://toolshed.g2.bx.psu.edu" />
</package>
</tool_dependency>
These versions are both older than what we installed before(1.4.2 and 3.0.2).
could we manually modify that to use our own? wouldn't that be a bad practice?
while in the same dir, macs_wrapper.xml has:
<requirements>
<requirement type="package" version="1.3.7.1">macs</requirement>
<requirement type="package" version="2.15.0">R</requirement>
</requirements>
Seems that this is the tool_shed version of macs(which is identical to the one
on main galaxy server, I think?). However this one does not work with our
input data. Additionally, when I click to switch from 1.0.1 to 1.0.0 of macs,
it immediately reports error.
So, what if I want to keep using the one I installed myself? I know that
tool_shed is a cleaner way to manage tools, but in our situation the upgrade
and elimination actually broke the thing that worked before. I want to ask the
proper way to handle this kind of situation. could I simply drop the entry
from migrated_tools_conf.xml about macs, and restore the old tools_conf.xml
entry? in that way we could continue using the 1.4.2 we have. However next
time when we do the upgrade, things will break again I guess?
I think that I shouldn't be the only person that has this concern? how to
handle multiple version/dependency version for a tool? is there an option to
not use the tool_shed but keep own version?
Thanks,
Rui
On Fri, Feb 28, 2014 at 12:44 PM, Martin Čech <marten@bx.psu.edu
<mailto:marten@bx.psu.edu>> wrote:
Rui,
it might be that your shed_tool_conf.xml is inconsistent and doesn't
actually reflect tools installed in Galaxy. Please log in as an admin and
check 'Manage installed tool shed repositories' menu. Try to find a tool
that is installed and in tool_conf.xml but is not showing up in the tool
panel. Uninstall and install this tool again. That should create entry in
shed_tool_conf.xml and the tool should display properly.
M.
On Fri, Feb 28, 2014 at 3:26 PM, ruiwang.sz <http://ruiwang.sz>
<ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
I'm seeing a lot of messages like:
galaxy.model.migrate.check INFO 2014-02-28 12:10:18,201 At database
version 118
migrate.versioning.repository DEBUG 2014-02-28 12:10:18,220 Loading
repository lib/tool_shed/galaxy_install/migrate...
migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading
script lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py...
migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script
lib/tool_shed/galaxy_install/migrate/versions/0001_tools.py loaded
successfully
migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Loading
script lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py...
migrate.versioning.script.base DEBUG 2014-02-28 12:10:18,220 Script
lib/tool_shed/galaxy_install/migrate/versions/0002_tools.py loaded
successfully
and then
tool_shed.galaxy_install.installed_repository_manager DEBUG 2014-02-28
12:10:18,683 Adding an entry for revision 96d2e31a3938 of repository
bowtie2 owned by devteam to
repository_dependencies_of_installed_repositories.
I noticed that some tools disappeared from the side panel, like bowtie
and samtools, etc. So, should I remove the corresponding entries in
the tool_conf.xml? Now seems many of the tools were installed back by
the toolshed but I don't see them on the panel, how to enable them? I
thought this would be done by the migration script?
Thanks,
Rui
On Fri, Feb 28, 2014 at 10:24 AM, Martin Čech <marten@bx.psu.edu
<mailto:marten@bx.psu.edu>> wrote:
Question mark means 'untracked' so no problems there.
Please try removing tool_conf.xml (make backup) and run Galaxy
again. It might trigger the migration again.
M.
On Fri, Feb 28, 2014 at 1:08 PM, ruiwang.sz <http://ruiwang.sz>
<ruiwang.sz@gmail.com <mailto:ruiwang.sz@gmail.com>> wrote:
oh, I took that back, I think these are the tools that I
installed but does not come with Galaxy. probably that's the ?
means -- it is not part of the distribution?
thanks,
Rui
On Fri, Feb 28, 2014 at 10:07 AM, ruiwang.sz
<http://ruiwang.sz> <ruiwang.sz@gmail.com
<mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Here you go. there are 493 files missing, seems.
Thanks,
Rui
On Fri, Feb 28, 2014 at 9:59 AM, Martin Čech
<marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Rui,
could you please try 'hg status' and tell us what it
outputs? Thanks
Martin
On Fri, Feb 28, 2014 at 12:27 PM, ruiwang.sz
<http://ruiwang.sz> <ruiwang.sz@gmail.com
<mailto:ruiwang.sz@gmail.com>> wrote:
Hi Martin,
Thanks. I'll read the manual.
Best,
Rui
On Fri, Feb 28, 2014 at 8:47 AM, Martin Čech
<marten@bx.psu.edu <mailto:marten@bx.psu.edu>> wrote:
Hello Rui,
the process of migrating tools from Galaxy
itself to the ToolShed (Galaxy's appstore) is
ongoing and is well described here:
https://wiki.galaxyproject.org/MigratingToolsFromGalaxyDistribution
Please check the page and let us know if it
helps you with your instance.
Afterwards we can continue to troubleshoot the
upload problems.
goodluck
Martin
On Fri, Feb 28, 2014 at 12:20 AM, ruiwang.sz
<http://ruiwang.sz> <ruiwang.sz@gmail.com
<mailto:ruiwang.sz@gmail.com>> wrote:
Hi Sam,
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:
Inline image 1
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
On Thu, Feb 27, 2014 at 7:21 PM, sam
guerler <aysam.guerler@gmail.com
<mailto:aysam.guerler@gmail.com>> wrote:
Hi Rui,
Are you using the upload tool
available in the tool panel under 'Get
Data' > 'Upload file from your
computer'? Or the new upload dialog by
clicking on 'Load Data'? Could you
also please let me know if this error
occurs always or just sometimes?
Thanks Sam
On Thu, Feb 27, 2014 at 8:50 PM,
ruiwang.sz <http://ruiwang.sz>
<ruiwang.sz@gmail.com
<mailto:ruiwang.sz@gmail.com>> wrote:
Hi Guys,
Our galaxy instance has been in
use for a couple years but since
Feb 2014 it started to show us
some weird behavior. Recently the
upload function suddenly stopped
working properly. We are getting
messages like the following. I'm
not sure if this only happens to
us. If someone has seen this
before, please give me some hints.
P.S., I searched online and many
says that this is because the
browser does not wait till all the
data from the server is received
and closes the socket. However it
happens both in firefox and
chrome. I'm wondering if it is
because galaxy has any change
recently but when I do 'hg update
stable' it reported that it is up
to date.
Thanks!
Rui
Error messages:
Exception happened during
processing of request from
('127.0.0.1'----------------------------------------
Exception happened during
processing of request from (,
52259'127.0.0.1', 52260)
Traceback (most recent call last):
)
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in
process_request_in_thread
----------------------------------------
Exception happened during
processing of request from
(----------------------------------------
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in
process_request_in_thread
Exception happened during
processing of request
from'127.0.0.1' ,
('127.0.0.1'52264,
52262----------------------------------------
)
Exception happened during
processing of request from
('127.0.0.1'----------------------------------------
, )
Traceback (most recent call last):
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in
process_request_in_thread
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in
process_request_in_thread
Exception happened during
processing of request from
52261('127.0.0.1',
----------------------------------------
)Exception happened during
processing of request from
Traceback (most recent call last):
52263('127.0.0.1')
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in
process_request_in_thread
Traceback (most recent call last):
, 52265)
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in
process_request_in_thread
Traceback (most recent call last):
File
"/home/bioinfoadmin/app/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py",
line 1068, in
process_request_in_thread
self.finish_request(request,
client_address)
File
"/usr/lib/python2.7/SocketServer.py",
line 323, in finish_request
self.finish_request(request,
client_address)
File
"/usr/lib/python2.7/SocketServer.py",
line 323, in finish_request
self.finish_request(request,
client_address)
self.finish_request(request,
client_address)
self.finish_request(request,
client_address)
File
"/usr/lib/python2.7/SocketServer.py",
line 323, in finish_request
self.finish_request(request,
client_address)
File
"/usr/lib/python2.7/SocketServer.py",
line 323, in finish_request
File
"/usr/lib/python2.7/SocketServer.py",
line 323, in finish_request
File
"/usr/lib/python2.7/SocketServer.py",
line 323, in finish_request
self.finish_request(request,
client_address)
File
"/usr/lib/python2.7/SocketServer.py",
line 323, in finish_request
127.0.0.1 - -
[27/Feb/2014:16:59:36 -0700] "GET
/tool_runner?tool_id=upload1
HTTP/1.1" 200 -
"http://localhost:20020/root"
"Mozilla/5.0 (X11; Ubuntu; Linux
x86_64; rv:27.0) Gecko/20100101
Firefox/27.0"
self.RequestHandlerClass(request,
client_address, self)
self.RequestHandlerClass(request,
client_address, self)
File
"/usr/lib/python2.7/SocketServer.py",
line 640, in __init__
File
"/usr/lib/python2.7/SocketServer.py",
line 640, in __init__
self.RequestHandlerClass(request,
client_address, self)
self.RequestHandlerClass(request,
client_address, self)
File
"/usr/lib/python2.7/SocketServer.py",
line 640, in __init__
self.finish()
self.RequestHandlerClass(request,
client_address, self)
self.finish()
self.RequestHandlerClass(request,
client_address, self)
self.finish()
File
"/usr/lib/python2.7/SocketServer.py",
line 693, in finish
File
"/usr/lib/python2.7/SocketServer.py",
line 640, in __init__
File
"/usr/lib/python2.7/SocketServer.py",
line 693, in finish
File
"/usr/lib/python2.7/SocketServer.py",
line 640, in __init__
self.RequestHandlerClass(request,
client_address, self)
File
"/usr/lib/python2.7/SocketServer.py",
line 693, in finish
File
"/usr/lib/python2.7/SocketServer.py",
line 640, in __init__
File
"/usr/lib/python2.7/SocketServer.py",
line 640, in __init__
self.finish()
self.finish()
File
"/usr/lib/python2.7/SocketServer.py",
line 693, in finish
self.wfile.flush()
self.wfile.flush()
File
"/usr/lib/python2.7/SocketServer.py",
line 693, in finish
self.wfile.flush()
self.finish()
File
"/usr/lib/python2.7/SocketServer.py",
line 693, in finish
File
"/usr/lib/python2.7/socket.py",
line 303, in flush
File
"/usr/lib/python2.7/socket.py",
line 303, in flush
self.wfile.flush()
self.finish()
self.wfile.flush()
File
"/usr/lib/python2.7/socket.py",
line 303, in flush
self.wfile.flush()
File
"/usr/lib/python2.7/SocketServer.py",
line 693, in finish
File
"/usr/lib/python2.7/socket.py",
line 303, in flush
File
"/usr/lib/python2.7/socket.py",
line 303, in flush
File
"/usr/lib/python2.7/socket.py",
line 303, in flush
self.wfile.flush()
File
"/usr/lib/python2.7/socket.py",
line 303, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
error: [Errno 32] Broken pipe
----------------------------------------
self._sock.sendall(view[write_offset:write_offset+buffer_size])
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
error: [Errno 32] Broken pipe
----------------------------------------
___________________________________________________________
Please keep all replies on the
list by using "reply all"
in your mail client. To manage
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and other Galaxy lists, please use
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the unified search at:
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___________________________________________________________
Please keep all replies on the list by
using "reply all"
in your mail client. To manage your
subscriptions to this
and other Galaxy lists, please use the
interface at:
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To search Galaxy mailing lists use the
unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/