Re: [galaxy-dev] Unicode in tool stderr crashing galaxy? - solved, patch attached
At Thu, 10 Oct 2013 00:31:56 -0500, John Chilton wrote: > > Simon, using your test tools I was able to reproduce your errors. Pull > request 233 is my attempt to fix them with a lighter touch than just > immediately converting outputs to ascii. Do these patches work on your > end? > > Bjoern, do these patches fix your problem as well? > > If I don't hear anything from anyone, I will merge these changes in a few > days. Hi John, That works nicely, and is better than what I did, thanks! cheers, Simon ___ 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/
[galaxy-dev] Configurable toolshed package installation to support tool-dependency-resolver-plugins
At Fri, 4 Oct 2013 23:12:01 -0500, John Chilton wrote: > I understand the desire to not want to try to execute the tool shed > actions if tool_shed_packages are not specified in the dependency > resolvers list. I have created a Trello card for it > (https://trello.com/c/CPeU3VlR). It sounds like the new status quo > will be functional it will just be kind of annoying to have those > actions try and fail and then marked as errors, right? If that is > right then for this reason I don't think implementing this behavior > will be a high priority for the team, but if you send another > brilliant patch or pull request I will be happy to test it and merge > it. Hi John, I have now implemented this. Mercurial changeset attached. This adds another configuration item for universe_wsgi.ini as documented in the updated universe_wsgi.ini.sample: # This option may be used to disable installation of package # dependencies from tool sheds, which usually means downloading a # source tarball and compiling it locally. You would disable this if # you want to make use of system installed packages for example. In # that case, alternative tool dependency resolvers should be # configured in dependency_resolvers_conf.xml #enable_tool_shed_package_dependency_installation = True The default behaviour is per standard toolshed. If configured to False, then the package components of tool dependencies will never be installed from the toolshed. Rather, they will rely on the tool dependency manager to resolve the requirement. This is integrated with the missing_tool_dependencies status, so that if dependency resolution fails, the repository gets flagged with "missing tool dependencies" on the installed tool shed repositories page, and the paster.log file contains a warning of exactly what wasn't found. Of course, if the dependency can be satisfied, then it's green lights all the way, and everything should work fine. I've tested this interactively by installing the standard emboss_5 repository, with various combinations of environment module available and not. It looks to work fine. I'm afraid I haven't yet read up on the Galaxy unit testing framework, so no unit tests for now. What do you think? cheers, Simon configurable-toolshed-package-installation.patch Description: Binary data ___ 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/
[galaxy-dev] RFC: remove trailing semicolons from command line -> Broken bowtie2_wrapper on some SGE systems
Dear all,
some SGE instances will add automatically an semicolon add the end of
each command, resulting in a disrupted job, because ';;' are not
allowed.
The latest changes to the Bowtie2 wrapper resulting in such a case and a
crash in our instance. An easy solution would be to fix the wrapper and
omitting the trailing ';' but maybe its better to fix it once for all in
the corresponding tools code, patched attached.
I'm not familiar with other Job schedulers so I'm seeking for
comments ... it there any disadvantage of removing trailing ';' from the
command line?
Ciao,
Bjoern
diff -r 384240b8cd29 lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py Fri Oct 04 16:11:45 2013 -0400
+++ b/lib/galaxy/tools/__init__.py Thu Oct 10 22:08:56 2013 +0200
@@ -2677,6 +2677,9 @@
command_line = fill_template( self.command, context=param_dict )
# Remove newlines from command line, and any leading/trailing white space
command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip()
+# Remove trailing semicolon
+# Some SGE versions add automatically an semicolon at the end, which will result in an ';;' - SGE error
+command_line = command_line.rstrip(';')
except Exception:
# Modify exception message to be more clear
#e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ), )
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Re: [galaxy-dev] Fastx toolkit broken pipe
Hi Ian, what mean broken pipe error, can you post the error message here? Thanks, Bjoern > Hello, > > I've got a local install of galaxy with fastx tools installed. I'm getting a > broken pipe error but I'm not sure why. I install fastx using the compiler > outside galaxy and it was working fine inside galaxy previously. Fastx works > fine via the command line. I've checked the xml files and I don't see how > galaxy cannot find the commands. I am running this off and external volume, > but I don't think that matters. > > Cheers > Ian > > > > > > ___ > 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/
Re: [galaxy-dev] Frames issue with tool shed README links?
Hello Peter, I've created teh following Trello card for this: https://trello.com/c/Vg12cS7o/1174-toolshed-frames-issue-with-readme-file-links Thanks, Greg Von Kuster On Oct 8, 2013, at 10:44 AM, Peter Cock wrote: > Consider the following sequence: > > 1. Goto http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan > > 2. The README file explains this is for InterProScan 4, and has > a link to http://toolshed.g2.bx.psu.edu/view/bgruening/interproscan5 > for Bjoern's InterProScan 45 wrapper. > > 3. Click the link for InterProScan 5. > > 4. Notice the link opened within the frame, and you now have a > nested tool shed menu. > > 5. Click on the link to InterPro itself, > http://www.ebi.ac.uk/interpro/interproscan.html > > 6. Notice the double nested frame remains, and now the InterPro > page is squeezed into the bottom left. > > - > > This isn't specific to these repositories, e.g. > > 1. Goto http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go > > 2. The README file introduction refers to the tool being available > on the main tool shed, > > "It is available from the Galaxy Tool Shed at: > http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go " > > 3. Click on that link > > 4. Observe a double nested tool shed interface, with the Test > Tool Shed at the top, and the Main Tool Shed nested within. > > - > > Suggested fix: All links within Tool Shed README files should be > modified to open full frame by adding target="_top" to them. > > Peter > ___ > 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/
Re: [galaxy-dev] AttributeError: type object 'InvalidJobException' has no attribute 'name'
Hi all, The recent changes to the DRMAA runner are for better handling of job-ending conditions under slurm, but it looks like SGE has different behavior when a job finishes. I'll provide a fix for this shortly, in the meantime, it's fine to use a slightly older version of drmaa.py. --nate On Oct 10, 2013, at 10:31 AM, Peter Cock wrote: > On Tue, Oct 8, 2013 at 5:03 PM, Adhemar wrote: >> Hi, >> After the last update I'm getting the following error. >> The job is submitted to SGE e executed, but galaxy doesn't get the result >> and keeps showing the job is executing (yellow box). >> Any clues? >> Thanks, >> Adhemar >> >> >> >> galaxy.jobs.runners ERROR 2013-10-08 13:01:18,488 Unhandled exception >> checking active jobs >> Traceback (most recent call last): >> File >> "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/__init__.py", >> line 362, in monitor >>self.check_watched_items() >> File >> "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/drmaa.py", >> line 217, in check_watched_items >>log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, >> external_job_id, e.__class__.name, e ) >> AttributeError: type object 'InvalidJobException' has no attribute 'name' > > > Same here, running galaxy-central with an SGE cluster (actually UGE > but the same DRMAA wrapper etc) when cancelling several jobs via > qdel at the command line: > > Galaxy.jobs.runners ERROR 2013-10-10 15:16:35,731 Unhandled exception > checking active jobs > Traceback (most recent call last): > File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/__init__.py", > line 362, in monitor >self.check_watched_items() > File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", > line 217, in check_watched_items >log.warning( "(%s/%s) job check resulted in %s: %s", > galaxy_id_tag, external_job_id, e.__class__.name, e ) > AttributeError: type object 'InvalidJobException' has no attribute 'name' > > $ hg branch > default > [galaxy@ppserver galaxy-central]$ hg heads | more > changeset: 11871:c8b55344e779 > tag: tip > user:Ross Lazarus > date:Tue Oct 08 16:30:54 2013 +1100 > summary: Proper removal of rgenetics deprecated tool wrappers > > changeset: 11818:1f0e7ae9e324 > branch: stable > parent: 11761:a477486bf18e > user:Daniel Blankenberg > date:Sun Sep 29 16:04:31 2013 +1000 > summary: Add additional check and slice to _sniffnfix_pg9_hex(). > Fixes issue seen when attempting to view saved visualizations. Further > investigation may be needed. > ... > > Killing Galaxy and restarting didn't fix this, the errors persist. > I tried this fix to solve the attribute error in the logging call: > > $ hg diff /mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py > diff -r c8b55344e779 lib/galaxy/jobs/runners/drmaa.py > --- a/lib/galaxy/jobs/runners/drmaa.pyTue Oct 08 16:30:54 2013 +1100 > +++ b/lib/galaxy/jobs/runners/drmaa.pyThu Oct 10 15:21:56 2013 +0100 > @@ -214,7 +214,10 @@ > state = self.ds.jobStatus( external_job_id ) > # TODO: probably need to keep track of > InvalidJobException count and remove after it exceeds some > configurable > except ( drmaa.DrmCommunicationException, > drmaa.InternalException, drmaa.InvalidJobException ), e: > -log.warning( "(%s/%s) job check resulted in %s: %s", > galaxy_id_tag, external_job_id, e.__class__.name, e ) > +if hasattr(e.__class__, "name"): > +log.warning( "(%s/%s) job check resulted in %s: > %s", galaxy_id_tag, external_job_id, e.__class__.name, e ) > +else: > +log.warning( "(%s/%s) job check resulted in: %s", > galaxy_id_tag, external_job_id, e ) > new_watched.append( ajs ) > continue > except Exception, e: > > > Now I get lots of these lines instead: > > galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:16,489 (251/11372) > job check resulted in: code 18: The job specified by the 'jobid' does > not exist. > galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:16,533 (252/11373) > job check resulted in: code 18: The job specified by the 'jobid' does > not exist. > galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:17,580 (253/11374) > job check resulted in: code 18: The job specified by the 'jobid' does > not exist. > galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:17,624 (254/11375) > job check resulted in: code 18: The job specified by the 'jobid' does > not exist. > galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:17,668 (255/11376) > job check resulted in: code 18: The job specified by the 'jobid' does > not exist. > galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:17,712 (256/11377) > job check resulted in: code 18: The job specified by the 'jobid' does > not exist. > (this seems to repeat, endlessly) > > I manually killed the jobs from the Galaxy history, an
[galaxy-dev] Trouble viewing History from a particular laptop
Hi Olivia, Our development team suggests checking the paster.log, plus, if applicable, proxy server logs. From what we know, this kind of issue generally indicate a firewall issue, but without more information, it is difficult to diagnose. Please keep replies on this mailing list instead (is the one for local install questions). Thanks! Jen Galaxy team On 10/9/13 2:31 PM, Olivia Choudhury wrote: Hello, I am a graduate student in the University of Notre Dame. I have installed a personal instance of Galaxy and have been developing tools there as a part of my research. Everything worked well on my laptop until recently, when I could not view the 'History' panel, no matter which browser (Firefox, Chrome, Safari) I used on my laptop (Windows 7 OS). Everything works absolutely fine and I can view 'History' when I am using a desktop or any other laptop. I have checked this across different operating systems and also ensured that no changes were made with the Firewall setup of my laptop. I have attached a print screen of what the Galaxy page looks like. It would be great if I could get some help with this. Thanks a lot in advance, Olivia ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev 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/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/
[galaxy-dev] Fastx toolkit broken pipe
Hello, I've got a local install of galaxy with fastx tools installed. I'm getting a broken pipe error but I'm not sure why. I install fastx using the compiler outside galaxy and it was working fine inside galaxy previously. Fastx works fine via the command line. I've checked the xml files and I don't see how galaxy cannot find the commands. I am running this off and external volume, but I don't think that matters. Cheers Ian ___ 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/
Re: [galaxy-dev] UCSC Main table browser invalid link
On Oct 9, 2013, at 5:40 PM, Gonsky, Rivkah, Ph.D wrote: > Link doesn’t work Hi Rivkah, If you're referring to the Galaxy instance at usegalaxy.org, this has been fixed. Thanks, --nate > > Rivkah Gonsky > Inflammatory Bowel and Immunobiology Research Institute > Davis 4063 > 8700 Beverly Blvd > Los Angeles, CA 90048 > 310-423-7624 > gon...@cshs.org > > IMPORTANT WARNING: This message is intended for the use of the person or > entity to which it is addressed and may contain information that is > privileged and confidential, the disclosure of which is governed by > applicable law. If the reader of this message is not the intended recipient, > or the employee or agent responsible for delivering it to the intended > recipient, you are hereby notified that any dissemination, distribution or > copying of this information is STRICTLY PROHIBITED. If you have received this > message in error, please notify us immediately by calling (310) 423-6428 and > destroy the related message. Thank You for your cooperation. > ___ > 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/
[galaxy-dev] Dealing with cluster job preemption
Hi, Our Galaxy instance is configured to use LSF. The problem is that sometimes our jobs get preempted (stopped and re-queued to let higher-priority jobs run) and Galaxy thinks that those jobs have failed. Is there any way around that by any chance? Thanks, Ilya ___ 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/
Re: [galaxy-dev] FASTQ converter not working
Hi James, The FASTX fastq to fasta conversion tool requires your input to be in one of the "fastqsanger,fastqsolexa,fastqillumina" datatypes. Please note that this does not include the base "fastq" datatype. Can you double check the datatype assigned to your datasets? Alternatively, there is also another FASTQ to FASTA converter available which does not have this restriction: https://usegalaxy.org/tool_runner?tool_id=fastq_to_fasta_python Thanks for using Galaxy, Dan On Oct 10, 2013, at 6:54 AM, James Tarver wrote: > So I have used Galaxy to convert >50 different FASTQ files into FASTA with no > problems before over the past year. The sequencer and FASTQ file format have > been identical, however, yesterday when I tired to use the the FASTQ to FASTA > converter I couldn't get it to recognise my files. > > The drop down 'FASTQ Library to convert:' tab was empty and unable to select > the dataset to convert > > I then switched histories to one where this action had already been done to > repeat it and make sure it was nothing odd with the file I uploaded. However, > again the tab was empty and I was unable to select the file to convert. > > Suggestions? > > JT > ___ > 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/
Re: [galaxy-dev] AttributeError: type object 'InvalidJobException' has no attribute 'name'
On Tue, Oct 8, 2013 at 5:03 PM, Adhemar wrote: > Hi, > After the last update I'm getting the following error. > The job is submitted to SGE e executed, but galaxy doesn't get the result > and keeps showing the job is executing (yellow box). > Any clues? > Thanks, > Adhemar > > > > galaxy.jobs.runners ERROR 2013-10-08 13:01:18,488 Unhandled exception > checking active jobs > Traceback (most recent call last): > File > "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/__init__.py", > line 362, in monitor > self.check_watched_items() > File > "/opt/bioinformatics/share/galaxy20130410/lib/galaxy/jobs/runners/drmaa.py", > line 217, in check_watched_items > log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, > external_job_id, e.__class__.name, e ) > AttributeError: type object 'InvalidJobException' has no attribute 'name' Same here, running galaxy-central with an SGE cluster (actually UGE but the same DRMAA wrapper etc) when cancelling several jobs via qdel at the command line: Galaxy.jobs.runners ERROR 2013-10-10 15:16:35,731 Unhandled exception checking active jobs Traceback (most recent call last): File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/__init__.py", line 362, in monitor self.check_watched_items() File "/mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py", line 217, in check_watched_items log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.name, e ) AttributeError: type object 'InvalidJobException' has no attribute 'name' $ hg branch default [galaxy@ppserver galaxy-central]$ hg heads | more changeset: 11871:c8b55344e779 tag: tip user:Ross Lazarus date:Tue Oct 08 16:30:54 2013 +1100 summary: Proper removal of rgenetics deprecated tool wrappers changeset: 11818:1f0e7ae9e324 branch: stable parent: 11761:a477486bf18e user:Daniel Blankenberg date:Sun Sep 29 16:04:31 2013 +1000 summary: Add additional check and slice to _sniffnfix_pg9_hex(). Fixes issue seen when attempting to view saved visualizations. Further investigation may be needed. ... Killing Galaxy and restarting didn't fix this, the errors persist. I tried this fix to solve the attribute error in the logging call: $ hg diff /mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py diff -r c8b55344e779 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.pyTue Oct 08 16:30:54 2013 +1100 +++ b/lib/galaxy/jobs/runners/drmaa.pyThu Oct 10 15:21:56 2013 +0100 @@ -214,7 +214,10 @@ state = self.ds.jobStatus( external_job_id ) # TODO: probably need to keep track of InvalidJobException count and remove after it exceeds some configurable except ( drmaa.DrmCommunicationException, drmaa.InternalException, drmaa.InvalidJobException ), e: -log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.name, e ) +if hasattr(e.__class__, "name"): +log.warning( "(%s/%s) job check resulted in %s: %s", galaxy_id_tag, external_job_id, e.__class__.name, e ) +else: +log.warning( "(%s/%s) job check resulted in: %s", galaxy_id_tag, external_job_id, e ) new_watched.append( ajs ) continue except Exception, e: Now I get lots of these lines instead: galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:16,489 (251/11372) job check resulted in: code 18: The job specified by the 'jobid' does not exist. galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:16,533 (252/11373) job check resulted in: code 18: The job specified by the 'jobid' does not exist. galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:17,580 (253/11374) job check resulted in: code 18: The job specified by the 'jobid' does not exist. galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:17,624 (254/11375) job check resulted in: code 18: The job specified by the 'jobid' does not exist. galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:17,668 (255/11376) job check resulted in: code 18: The job specified by the 'jobid' does not exist. galaxy.jobs.runners.drmaa WARNING 2013-10-10 15:22:17,712 (256/11377) job check resulted in: code 18: The job specified by the 'jobid' does not exist. (this seems to repeat, endlessly) I manually killed the jobs from the Galaxy history, and restarted Galaxy again. That seemed to fix this. If the DRMAA layer says the job was invalid (which is what I am assuming InvalidJobException means) then surely it failed? Perhaps something like this (untested)? $ hg diff /mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py diff -r c8b55344e779 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.pyTue Oct 08 16:30:54 2013 +1100 +++ b/lib/galaxy/jobs/runners/drmaa.pyThu Oct 10 15:27:28 2013 +0100 @@ -213,10 +213,15 @@ assert ext
Re: [galaxy-dev] Visualizations broken after Aug. 12 update
Thank you Jeremy, It turned out the issue was our version of bedtools. We updated to 2.17.0 and no longer have the errors. Cheers, Liisa From: Jeremy Goecks To: Liisa Koski Cc: "galaxy-dev@lists.bx.psu.edu Galaxy-dev" Date: 05/10/2013 08:08 PM Subject:Re: [galaxy-dev] Visualizations broken after Aug. 12 update You'll need to do two things: (1) Install wigToBigWig and bedtools; see steps 2 and 3 here: http://wiki.galaxyproject.org/Visualization%20Setup (2) Update your datatypes_conf.xml file: If you haven't made changes to your datatypes_conf.xml file, you can just copy datatypes_conf.xml.sample to datatypes_conf.xml to get the needed converters. If you've made changes to datatypes_conf.xml, you'll need to manually add the needed converters. We recently transitioned all the *_to_summary_tree converters to *_to_bigwig, so you'll want to remove the summary_tree converters and replace them with the bigwig converters. Let us know if you have any problems/questions. Best, J. On Oct 3, 2013, at 1:33 PM, Liisa Koski wrote: Hello, We recently updated to the Aug.12 distribution. I u commented the visualizations_config_directory = config/visualizations in the universe file and when I restarted and tried to view past Trackster Visualizations none of my tracks load. I get the error displayed in the track itself: Cannot display dataset due to an error. View error. Try again. When I click on View error I get pop up with this for my gff3 track: Input error: Cannot split into blocks. Found interval with fewer than 12 columns. needLargeMem: trying to allocate 0 bytes (limit: 17179869184) With this for my BAM track: grep: /Galaxy/galaxy_dist/database/files/016/dataset_16392.dat: No such file or directory needLargeMem: trying to allocate 0 bytes (limit: 17179869184) All tracks in all published Visualizations are no longer loading. I do not see any errors in the log files. I have also updated my datatypes.conf file by copying over datatypes.conf.sample Any help would be much appreciated. Thanks in advance, Liisa ___ 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/
[galaxy-dev] masthead and history lost when embedding Galaxy in iframe
Hi all, I really can't understand why this should be, but in recent versions of Galaxy if you have a simple html page with an iframe embedding Galaxy, you loose the masthead (no login, workflow etc) and the history panel no longer works. eg (newer Galaxy Versions) https://galaxy.cbio.mskcc.org/"; width="800px" height="600px"> https://galaxy.cbio.mskcc.org/"; width="800px" height="600px"> You can see the problems, whereas older versions of galaxy show no problems: http://galaxy.berkeleybop.org:8080/"; width="800px" height="600px"> What could be causing this so that I can try to make amends? Thanks Andy ___ 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/
[galaxy-dev] FASTQ converter not working
So I have used Galaxy to convert >50 different FASTQ files into FASTA with no problems before over the past year. The sequencer and FASTQ file format have been identical, however, yesterday when I tired to use the the FASTQ to FASTA converter I couldn't get it to recognise my files. The drop down 'FASTQ Library to convert:' tab was empty and unable to select the dataset to convert I then switched histories to one where this action had already been done to repeat it and make sure it was nothing odd with the file I uploaded. However, again the tab was empty and I was unable to select the file to convert. Suggestions? JT ___ 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/
Re: [galaxy-dev] Test Toolshed Biopython package dependency & NumPy
On Wed, Oct 9, 2013 at 10:01 PM, Björn Grüning wrote: > Am Mittwoch, den 09.10.2013, 19:15 +0100 schrieb Peter Cock: >> On Tue, Oct 8, 2013 at 9:57 PM, Dave Bouvier wrote: >> > Peter, Björn, >> > >> > I have restored gfortran to the repository test host. I believe it was >> > inadvertently removed, possibly as a side effect of updating packages or >> > removing packages that were causing conflicts with the Galaxy eggs. Numpy >> > and biopython should now install successfully, as they do in my local >> > environment. >> > >> >--Dave B. >> >> Thanks Dave, fingers crossed for tonight's test run :) >> >> Bjoern - it looks like we can leave the NumPy definition as is... > > Ah sorry, totally forgot about it :( > Progress, Fortran is working and lapack seems to have installed, but: e.g. http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename Installation errors - no functional tests were run for any tools in this changeset revision Tool dependencies TypeNameVersion biopython package 1.62 Error running install Numerical Python (NumPy) is not installed. This package is required for many Biopython features. Please install it before you install Biopython. You can install Biopython anyway, but anything dependent on NumPy will not work. If you do this, and later install NumPy, you should then re-install Biopython. You can find NumPy at http://numpy.scipy.org TypeNameVersion numpy package 1.7.1 Error Running from numpy source directory. /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmp3kNwuR/tmp-toolshed-mtdGJ0d5H/numpy-1.7.1/numpy/distutils/system_info.py:1494: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) /var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmp3kNwuR/tmp-toolshed-mtdGJ0d5H/numpy-1.7.1/numpy/distutils/system_info.py:1408: UserWarning: Atlas (http://math-atlas.sourceforge.net/) libraries not found. Directories to search for the libraries can be specified in the numpy/distutils/site.cfg file (section [atlas]) or by setting the ATLAS environment variable. warnings.warn(AtlasNotFoundError.__doc__) error: Command "/usr/bin/gfortran -Wall -Wall -shared build/temp.linux-x86_64-2.7/numpy/linalg/lapack_litemodule.o build/temp.linux-x86_64-2.7/numpy/linalg/python_xerbla.o -L/ToolDependencies/lapack/3.4.2/iuc/package_lapack_3_4/60957bd68fe2/lapack/lib -Lbuild/temp.linux-x86_64-2.7 -llapack -lblas -lgfortran -o build/lib.linux-x86_64-2.7/numpy/linalg/lapack_lite.so" failed with exit status 1 Most of that is warnings about not using ATLAS (which we expect) but I'm not quite sure why it fails... Peter ___ 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/
