- galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Byte-range support for IGV ?
by Chebbi Mohamed Amine 11 Jul '12

11 Jul '12

HI Geert ! I did well : <Location "/"> XSendFile on XSendFilePath / </Location> and <Location "/"> # Compress all uncompressed content. SetOutputFilter DEFLATE SetEnvIfNoCase Request_URI \.(?:gif|jpe?g|png)$ no-gzip dont-vary SetEnvIfNoCase Request_URI \.(?:t?gz|zip|bz2)$ no-gzip dont-vary </Location> But it dosen't fix it. I think that il is may be a problem of server byte-range accepting? Thanks Amine 2012/7/4 Geert Vandeweyer <geert.vandeweyer2(a)ua.ac.be> > Hi, > > If I remember correctly, I solved this issue by enabling the xsendfile > module in apache and setting galaxy to use the proxy for file downloading. > > best regards, > > Geert > > > On 07/04/2012 11:15 AM, Chebbi Mohamed Amine wrote: > > HELLO ! > > I just updated our local galaxy instance and just wanted to try the new > IGV display application. When I try to display a BAM file whith the local > IGV, I encounter the following message : > > "HTTP and FTP access to BAM files require byte-range support" > > Has anyone encountred the same probleme? > > Thanks in advances > > Regards > Amine > > > > > ___________________________________________________________ > 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/ > > > > -- > > Geert Vandeweyer, Ph.D. > Department of Medical Genetics > University of Antwerp > Prins Boudewijnlaan 43 > 2650 Edegem > Belgium > Tel: +32 (0)3 275 97 56 > E-mail: geert.vandeweyer@ua.ac.behttp://ua.ac.be/cognitivegeneticshttp://www.linkedin.com/pub/geert-vandeweyer/26/457/726 > >

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Unable to queue job, resubmitting might help
by Geert Vandeweyer 11 Jul '12

11 Jul '12

Hi, Today I ran into a cluster error on our local instance using latest galaxy-dist and torque/pbs with the python-pbs binding. Under heavy load of the galaxy process, it appears that the handler processes failed to contact the pbs-server, although the pbs_server was still up and running. after that, a lot of the following statements kept appearing in the handler.log file: galaxy.jobs.runners.pbs DEBUG 2012-07-11 17:39:06,649 (11647/12788.pbs_master_address) Skipping state check because PBS server connection failed After restarting the galaxy process (run.sh), everything worked again, with no changes to the pbs_server. Would it be possible to setup some checks for this failure? Like: - contact system admin - restart galaxy - auto retry job submission after a while as to not crash workflows. best regards, Geert Vandeweyer

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Re: [galaxy-dev] pbs_python issues
by Iry Witham 11 Jul '12

11 Jul '12

I was successful in getting the bps_python egg to load finally. However, there is an issue that remains. When I submit a job it is sent to the local runner and not to pbs. Where should I start looking to change this work? Thanks, Iry On 7/10/12 12:00 PM, "galaxy-dev-request(a)lists.bx.psu.edu" <galaxy-dev-request(a)lists.bx.psu.edu> wrote: > >Message: 3 >Date: Mon, 9 Jul 2012 17:24:25 +0000 >From: Iry Witham <Iry.Witham(a)jax.org> >To: "Dorset, Daniel C" <daniel.dorset(a)Vanderbilt.Edu> >Cc: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >Subject: Re: [galaxy-dev] galaxy-dev Digest, Vol 73, Issue 10 >Message-ID: <CC207DDE.8F49%iry.witham(a)jax.org> >Content-Type: text/plain; charset="us-ascii" > >Hi Daniel, > > I did use -e previously. The ?e was a typo in my post. I ran it again >and it tries, but fails to generate the file(s) as shown: > >:galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist> >LIBTORQUE_DIR=/usr/local/lib/ python scripts/scramble.py -e pbs_python >fetch_one(): Trying to fetch: > http://eggs.g2.bx.psu.edu/pbs_python/pbs_python-4.1.0.tar.gz >fetch_one(): Fetched to: > >/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/archives/pbs >_ >python-4.1.0.tar.gz >unpack_source(): Unpacked to: > >/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6- >l >inux-x86_64-ucs4/pbs_python >copy_build_script(): Using build script >/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/scripts/pbs_ >p >ython.py >run_scramble_script(): Beginning build >run_scramble_script(): Executing in >/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6- >l >inux-x86_64-ucs4/pbs_python: > /usr/bin/python scramble.py > >-------------------------------------------------------------------------- >- >This script requires setuptools version 0.6c11 to run (even to display >help). I will attempt to download it for you (from >http://pypi.python.org/packages/2.6/s/setuptools/) but >you may need to enable firewall access for this script first. >I will start the download in 8 seconds. > >(Note: if this machine does not have network access, please obtain the >file > > >http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.e >g >g > >and place it in this directory before rerunning this script.) >-------------------------------------------------------------------------- >- >Downloading >http://pypi.python.org/packages/2.6/s/setuptools/setuptools-0.6c11-py2.6.e >g >g >checking for pbs-config... /usr/local/lib//../bin/pbs-config >Found torque version: 2.5.8 >checking for python... /usr/bin/python >checking for python version... 2.6 >checking for python platform... linux2 >checking for python script directory... >${prefix}/lib64/python2.6/site-packages >checking for python extension module directory... >${exec_prefix}/lib64/python2.6/site-packages >configure: creating ./config.status >config.status: creating Makefile >config.status: creating setup.py >scramble(): Patching setup.py >running egg_info >creating src/pbs_python.egg-info >writing src/pbs_python.egg-info/PKG-INFO >writing top-level names to src/pbs_python.egg-info/top_level.txt >writing dependency_links to src/pbs_python.egg-info/dependency_links.txt >writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' >reading manifest file 'src/pbs_python.egg-info/SOURCES.txt' >writing manifest file 'src/pbs_python.egg-info/SOURCES.txt' >running bdist_egg >installing library code to build/bdist.linux-x86_64/egg >running install_lib >running build_py >creating build >creating build/lib.linux-x86_64-2.6 >copying src/pbs.py -> build/lib.linux-x86_64-2.6 >copying src/PBSQuery.py -> build/lib.linux-x86_64-2.6 >running build_ext >building '_pbs' extension >creating build/temp.linux-x86_64-2.6 >creating build/temp.linux-x86_64-2.6/src >gcc -pthread -fno-strict-aliasing -DNDEBUG -fmessage-length=0 -O2 -Wall >-D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables >-fasynchronous-unwind-tables -g -fwrapv -fPIC -DTORQUE_2_4 >-I/usr/include/python2.6 -c src/pbs_wrap.c -o >build/temp.linux-x86_64-2.6/src/pbs_wrap.o >gcc -pthread -shared build/temp.linux-x86_64-2.6/src/pbs_wrap.o >-L/usr/local/lib -L/usr/lib64 -ltorque -lpython2.6 -o >build/lib.linux-x86_64-2.6/_pbs.so >creating build/bdist.linux-x86_64 >creating build/bdist.linux-x86_64/egg >copying build/lib.linux-x86_64-2.6/PBSQuery.py -> >build/bdist.linux-x86_64/egg >copying build/lib.linux-x86_64-2.6/pbs.py -> build/bdist.linux-x86_64/egg >copying build/lib.linux-x86_64-2.6/_pbs.so -> build/bdist.linux-x86_64/egg >byte-compiling build/bdist.linux-x86_64/egg/PBSQuery.py to PBSQuery.pyc >byte-compiling build/bdist.linux-x86_64/egg/pbs.py to pbs.pyc >creating stub loader for _pbs.so >byte-compiling build/bdist.linux-x86_64/egg/_pbs.py to _pbs.pyc >creating build/bdist.linux-x86_64/egg/EGG-INFO >copying src/pbs_python.egg-info/PKG-INFO -> >build/bdist.linux-x86_64/egg/EGG-INFO >copying src/pbs_python.egg-info/SOURCES.txt -> >build/bdist.linux-x86_64/egg/EGG-INFO >copying src/pbs_python.egg-info/dependency_links.txt -> >build/bdist.linux-x86_64/egg/EGG-INFO >copying src/pbs_python.egg-info/top_level.txt -> >build/bdist.linux-x86_64/egg/EGG-INFO >writing build/bdist.linux-x86_64/egg/EGG-INFO/native_libs.txt >zip_safe flag not set; analyzing archive contents... >creating dist >creating 'dist/pbs_python-4.1.0-py2.6-linux-x86_64.egg' and adding >'build/bdist.linux-x86_64/egg' to it >removing 'build/bdist.linux-x86_64/egg' (and everything under it) >Traceback (most recent call last): > File "scripts/scramble.py", line 50, in <module> > egg.scramble() > File >"/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/lib/galaxy/eggs/scramble.py" >, > line 60, in scramble > raise ScrambleFailure( self, "%s(): Egg build for %s did not appear to >fail, but no egg found to copy from expected path:\n %s" % ( >sys._getframe().f_code.co_name, self.name, new_egg ) ) >galaxy.eggs.scramble.ScrambleFailure: scramble(): Egg build for pbs_python >did not appear to fail, but no egg found to copy from expected path: > >/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/scripts/scramble/build/py2.6- >l >inux-x86_64-ucs4/pbs_python/dist/pbs_python-4.1.0-py2.6-linux-x86_64-ucs4. >e >gg" > >Iry > >On 7/7/12 3:10 PM, "Dorset, Daniel C" <daniel.dorset(a)Vanderbilt.Edu> >wrote: > >> >>________________________________________ >>From: galaxy-dev-bounces(a)lists.bx.psu.edu >>[galaxy-dev-bounces(a)lists.bx.psu.edu] On Behalf Of >>galaxy-dev-request(a)lists.bx.psu.edu [galaxy-dev-request(a)lists.bx.psu.edu] >>Sent: Saturday, July 07, 2012 11:00 AM >>To: galaxy-dev(a)lists.bx.psu.edu >>Subject: galaxy-dev Digest, Vol 73, Issue 10 >> >>Send galaxy-dev mailing list submissions to >> galaxy-dev(a)lists.bx.psu.edu >> >>To subscribe or unsubscribe via the World Wide Web, visit >> http://lists.bx.psu.edu/listinfo/galaxy-dev >>or, via email, send a message with subject or body 'help' to >> galaxy-dev-request(a)lists.bx.psu.edu >> >>You can reach the person managing the list at >> galaxy-dev-owner(a)lists.bx.psu.edu >> >>When replying, please edit your Subject line so it is more specific >>than "Re: Contents of galaxy-dev digest..." >> >> >>HEY! This is important! If you reply to a thread in a digest, please >>1. Change the subject of your response from "Galaxy-dev Digest Vol ..." >>to the original subject for the thread. >>2. Strip out everything else in the digest that is not part of the thread >>you are responding to. >> >>Why? >>1. This will keep the subject meaningful. People will have some idea >>from the subject line if they should read it or not. >>2. Not doing this greatly increases the number of emails that match >>search queries, but that aren't actually informative. >> >>Today's Topics: >> >> 1. pbs_python issues (Iry Witham) >> 2. Which css file does welcome.html use? (Dorset, Daniel C) >> 3. Re: Which css file does welcome.html use? (Jeremy Goecks) >> >> >>Hi Ira, >> >>I'm in charge of a Galaxy instance that's also deployed on a PBS Cluster, >>and I went through this process a couple of months ago. If I remember >>correctly, when you run your Python script, you're supposed to run it >>with "-e" not "?e" Assuming that you are pointing to the correct >>directory, it looks like everything else about your command is correct. >> >>Have you tried that? >> >>---------------------------------------------------------------------- >> >>Message: 1 >>Date: Fri, 6 Jul 2012 16:32:14 +0000 >>From: Iry Witham <Iry.Witham(a)jax.org> >>To: "galaxy-dev(a)lists.bx.psu.edu" <galaxy-dev(a)lists.bx.psu.edu> >>Subject: [galaxy-dev] pbs_python issues >>Message-ID: <CC1C8B4D.8EAD%iry.witham(a)jax.org> >>Content-Type: text/plain; charset="windows-1252" >> >>I am having an issue with pbs_python loading, but not submitting jobs to >>the cluster. >> >>The first issue is that when I ran 'LIBTORQUE_DIR=/usr/local/lib/ python >>scripts/scramble.py ?e pbs_python' it failed to generate the pbs_python >>egg in the /galaxy-dist/eggs/ directory. >> >>Secondly I copied the pbs_python-4.1.0-py2.6-linux-x86_64-ucs4.egg from >>my production galaxy server and restarted my test server. It appears to >>start, but when I attempt to run anything it uses the local runner and >>fails. The runner0.log shows the pbsjobrunner is loaded is below: >> >>galaxy.jobs.handler DEBUG 2012-07-06 10:08:45,681 Loaded job runner: >>galaxy.jobs.runners.pbs:PBSJobRunner >>galaxy.jobs.handler INFO 2012-07-06 10:08:45,682 job handler stop queue >>started >>galaxy.jobs.manager INFO 2012-07-06 10:08:45,687 job manager queue >>started >>galaxy.jobs.manager INFO 2012-07-06 10:08:45,688 job manager stop queue >>started >>galaxy.jobs.handler INFO 2012-07-06 10:08:45,692 job handler queue >>started >> >>I can't seem to get past this point since I upgraded. Can someone point >>me in the right direction? >> >>Thanks, >>Iry >> >> >>The information in this email, including attachments, may be confidential >>and is intended solely for the addressee(s). If you believe you received >>this email by mistake, please notify the sender by return email as soon >>as possible. >>

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DRMAA.NoActiveSessionError
by Johannes Eichner 11 Jul '12

11 Jul '12

Dear Galaxy-Dev-Team, I just restarted our local Galaxy instance at the University of Tuebingen, Germany, and obtained a DRMAA.NoActiveSessionError. You can find an excerpt from my shell below. The error can be avoided by disabling the SGE support in the universe.wsgi.ini. However, as our galaxy instance runs on a virtual machine, which requires the cluster environment for proper job processing, I would very much appreciate your help on this issue. Kind regards, Johannes Traceback (most recent call last): File "/rahome/webservices/galaxy/lib/galaxy/web/buildapp.py", line 82, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/rahome/webservices/galaxy/lib/galaxy/app.py", line 124, in __init__ self.job_manager = jobs.JobManager( self ) File "/rahome/webservices/galaxy/lib/galaxy/jobs/__init__.py", line 44, in __init__ self.dispatcher = DefaultJobDispatcher( app ) File "/rahome/webservices/galaxy/lib/galaxy/jobs/__init__.py", line 1190, in __init__ self._load_plugin( name ) File "/rahome/webservices/galaxy/lib/galaxy/jobs/__init__.py", line 1207, in _load_plugin self.job_runners[name] = runner( self.app ) File "/rahome/webservices/galaxy/lib/galaxy/jobs/runners/sge.py", line 96, in __init__ self.ds.init( self.default_cell ) File "build/bdist.linux-x86_64/egg/DRMAA.py", line 186, in init errParse(eno, estr) File "build/bdist.linux-x86_64/egg/DRMAA.py", line 167, in errParse else: raise _errindex[errno-_errMin](errstring) InternalError: cl_com_setup_commlib failed: timeout while waiting for thread start Exception DRMAA.NoActiveSessionError: NoActiveSessionError('',) in <bound method Session.__del__ of <DRMAA.Session object at 0x4ecfb50>> ignored -- Dipl.-Inf. (Bioinf.) Johannes Eichner Univ. Tuebingen, WSI-RA, Sand 1, D-72076 Tuebingen, Germany Phone: (+49/0) 7071 / 29 78970 Fax: (+49/0) 7071 / 29 5091

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Re: [galaxy-dev] No action for /admin_toolshed/prepare_for_install
by Greg Von Kuster 10 Jul '12

10 Jul '12

Hi Peter, In your Galaxy install directory there will be a .hg subdirectory, and in that subdirectory there will be a file name hgrc. Yours probably looks something like this if you are tracking galaxy-dist. [paths] default = https://,your username.(a)bitbucket.org/galaxy/galaxy-dist Just change the value of the path to track galaxy central: [paths] default = https://,your user name.(a)bitbucket.org/galaxy/galaxy-central When you pull and update, you'll get the latest from galaxy central. On Jul 10, 2012, at 6:13 PM, Peter van Heusden wrote: > Hi Greg > > Is there any way to migrate from galaxy-dist to galaxy-central, or is a > re-installation necessary? > > On 07/10/2012 11:56 PM, Greg Von Kuster wrote: >> Hello Peter, >> >> To use the public Galaxy tool sheds, your local Galaxy instance must be running the tip from Galaxy central, not Galaxy dist. You need to be running at least 7368:3e6ab1cf0c2e, as this is the revision running on the public tool sheds. The public tool sheds always track the Galaxy central repository. >> >> Greg Von Kuster >> >> >> On Jul 10, 2012, at 5:45 PM, Peter van Heusden wrote: >> >>> I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed >>> using the Admin interface to Galaxy. Unfortunately, each time I do this >>> I get an error page with the message: >>> >>> No action for /admin_toolshed/prepare_for_install >>> >>> My Galaxy installation is galaxy-dist, revision 7148:17d57db9a7c0. >>> >>> Does anyone know why this might be happening? >>> >>> Thanks, >>> 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/ > >

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No action for /admin_toolshed/prepare_for_install
by Peter van Heusden 10 Jul '12

10 Jul '12

I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed using the Admin interface to Galaxy. Unfortunately, each time I do this I get an error page with the message: No action for /admin_toolshed/prepare_for_install My Galaxy installation is galaxy-dist, revision 7148:17d57db9a7c0. Does anyone know why this might be happening? Thanks, Peter

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Galaxy not killing split cluster jobs
by Peter Cock 10 Jul '12

10 Jul '12

Hi all, We're running our Galaxy with an SGE cluster, using the DRMAA support in Galaxy, and job splitting. I've noticed if the user cancels a job (that was running or queued on the cluster) while the job is shows as deleted in Galaxy, looking at the queue on the cluster with qstat shows it persists. I've not seen anything similar reported except for this PBS issue: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003633.html When I don't use job splitting, cancelling jobs seems to work: galaxy.jobs.handler DEBUG 2012-05-01 14:46:47,755 stopping job 57 in drmaa runner galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:47,756 (57/26504) Being killed... galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:47,757 (57/26504) Removed from DRM queue at user's request galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:48,441 (57/26504) state change: job finished, but failed galaxy.jobs.runners.drmaa DEBUG 2012-05-01 14:46:48,441 Job output not returned from cluster When I am using job splitting, cancelling jobs fails: galaxy.jobs.handler DEBUG 2012-05-01 14:28:30,364 stopping job 56 in tasks runner galaxy.jobs.runners.tasks WARNING 2012-05-01 14:28:30,386 stop_job(): 56: no PID in database for job, unable to stop That warning comes from lib/galaxy/jobs/runners/tasks.py which starts: def stop_job( self, job ): # DBTODO Call stop on all of the tasks. #if our local job has JobExternalOutputMetadata associated, then our primary job has to have already finished if job.external_output_metadata: pid = job.external_output_metadata[0].job_runner_external_pid #every JobExternalOutputMetadata has a pid set, we just need to take from one of them else: pid = job.job_runner_external_id if pid in [ None, '' ]: log.warning( "stop_job(): %s: no PID in database for job, unable to stop" % job.id ) return pid = int( pid ) ... I'm a little confused about tasks.py vs drmaa.py but that TODO comment looks pertinent. Is that the problem here? Regards, Peter

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Installation on HPC and file upload
by Lee Hazelwood 10 Jul '12

10 Jul '12

Dear developers, I'm wondering if you might be able to help us with an issue with have at Leeds. We have installed the galaxy platform on our HPC cluster at Leeds. One issue we have is uploading files > 2 GB through the internet browser. We have tried the URL route also without success. Are there any solutions to this problem? One idea we had was whether it is possible to change the upload to look at the filesystem local to galaxy rather than the users own computer. Many thanks Lee -- Dr Lee Hazelwood BHRC Bioinformatics Technology Group Leader Biomedical and Health Research Centre Faculty of Biological Sciences and Leeds Institute of Molecular Medicine University of Leeds, Leeds, LS2 9JT, UK. E-mail: L.D.Hazelwood(a)leeds.ac.uk<mailto:L.D.Hazelwood@leeds.ac.uk> http://www.bhrc.ac.uk/initiatives/technology-groups/bioinformatics-technolo…

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Re: [galaxy-dev] Job output not returned from Cluster
by Sascha Kastens 10 Jul '12

10 Jul '12

Hi Hemant, thanks for your help. I have set the value to 100, but this did not fix the problem. I am now trying to get a NFS mounted with -noac. Cheers, Sascha Original Message processed by CONSOLIDATE Subject: RE: [galaxy-dev] Job output not returned from Cluster Sent: Montag, 9. Juli 2012 17:38 From: Kelkar, Hemant (hkelkar(a)unc.edu) Hi Sascha, I am not sure if the error you are seeing is like one I had posted in this thread? http://dev.list.galaxyproject.org/Problem-related-to-a-job-that-quot-failed… --Hemant From: galaxy-dev-bounces(a)lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Sascha Kastens Sent: Monday, July 09, 2012 11:26 AM To: galaxy-dev(a)lists.bx.psu.edu Subject: Re: [galaxy-dev] Job output not returned from Cluster Hi! Unfortunately I was not able to fix this problem yet. Is anybody out there who had a similar problem while using Galaxy with SGE or has the knowledge about the things I can look at? Thanks in advance! Cheers, Sascha

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Automating customized setup of cloudman galaxy
by Dave Lin 09 Jul '12

09 Jul '12

Dear Galaxy Dev Team- I'm looking to automate the complete setup/build of a customized galaxy cluster from the command line. I'm looking for help/suggestions on several steps (labeled MANUAL) where it currently requires manual ui-input 1) [Automated] Have a script that uses cloudman + ec2-api-tools to create new galaxy cluster on Amazon from scratch. 2) [MANUAL] open browser to the new instance, enter volume size and start a new cluster. (Looking to be invoke this via command-line) 3) [MANUAL] Create standard users via the galaxy ui. (looking to be able to create a few standard users via command-line, not UI) 4) [MANUAL] Update galaxy to galaxy-dev tip using the galaxy-ui. (Can I just run hg pull/update? There doesn't seem to be the mercurial metadata in the galaxy-central directory.) 5) [Automated] Pull custom code from personal bitbucket, apply changes, create missing directories, install tools, etc. Copy over various configs (toos_conf.xml , universe_wsgi,etc) 6) [MANUAL] Import each workflow using the galaxy UI. (Have several workflows, and currently have to manually import them via the UI. I'm looking to make some type of command-line/api call that can pass the workflow to galaxy) I could go into the code and figure out how to call these functions or possibly just insert rows into the database. However, I'm looking to approach this using more official/supported API's. Would be happy to try to contribute/document this process once I have it working if others are interested. Thanks in advance, Dave

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