galaxy-dev November 2013

galaxy-dev@lists.galaxyproject.org

83 participants
135 discussions

local_task_queue_workers
by Jorrit Boekel 07 Nov '13

07 Nov '13

Hi list, I would need a memory refresher about tasked jobs. When testing some larger analyses on a local installation, I thought the local_task_queue_workers setting in universe_wsgi.ini would be the limiting factor for how many tasks can be executed at the same time. In our setup, it is currently set to 2. However, 5 tasks are run simultaneously, leading to memory problems. Am I overlooking something that anyone knows of? cheers, jorrit boekel -- Scientific programmer Mass spec analysis support @ BILS Janne Lehtiö / Lukas Käll labs SciLifeLab Stockholm

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Trouble setting up a local instance of Galaxy
by Hazard, E. Starr 07 Nov '13

07 Nov '13

Hello, I am a new user of Galaxy. I have a Galaxy instance running (sort of) on a local research cluster. I issued the command "hg update stable” today and it retrieved no files. SO presume I am up-to-date on the stable release. I start the instance as a user named “galaxy”. Right now I am still running in “local” mode. I hope to migrate to DRMAA LSF eventually. I have tried to set up ProFTP to upload files but have not succeeded so I use Galaxy Web-upload. The upload was working nicely and I had added a couple of new tools and they were working with the uploaded files. Getting LSF/DRMAA to work was giving me fits and ultimately I deleted all my history files in an effort to start over. Presently, files being uploaded appear in history as say job 1 ( in a new history) The job status in the history panel of the web GUI changes from purple to yellow then then to red indicating some sort of error. There is no viewable error text captured, but I can click on the “eye” icon and see the first megabyte of the data (for tiny files I can see the entire content and it’s intact). In the Galaxy file system, however, these files appear but have a different number , say, dataset_399.dat On my system the uploaded files appear in /PATH/galaxy-dist/database/files/000 My first question is why is the data going into the “000” subdirectory and not one “owned’ by the user who is uploading? My second question is why is the dataset being labeled as dataset_399.dat and not dataset_001.dat? My third question is why do the uploaded files not appear as selectable options ( say I have paired-end fastq files and tool wants to have choices about filenames)? This problem is present for programs that seek one input file as well. I presume that Galaxy is confused because the numbering in history is not the same as the numbering in the file upload archive (e.g. /PATH/galaxy-dist/database/files/000 in my case) so my last question is how do I “reset” my system to get the dataset and history numbers to be the same? Here’s how I launch the Galaxy instance sh /shared/app/Galaxy/galaxy-dist/run.sh -v --daemon --pid-file=Nov6Localdaemon.pid.txt --log-file=Nov6Local1639daemon.log.txt Entering daemon mode Here are the last lines of the log Starting server in PID 26236. serving on 0.0.0.0:8089 view at http://127.0.0.1:8089 galaxy.tools.actions.upload_common DEBUG 2013-11-06 16:48:49,624 Changing ownership of /shared/app/Galaxy/galaxy-dist/database/tmp/upload_file_data_QZGHm4 with: /usr/bin/sudo -E scripts/external_chown_script.py /shared/app/Galaxy/galaxy-dist/database/tmp/upload_file_data_QZGHm4 hazards 502 galaxy.tools.actions.upload_common WARNING 2013-11-06 16:48:49,750 Changing ownership of uploaded file /shared/app/Galaxy/galaxy-dist/database/tmp/upload_file_data_QZGHm4 failed: sudo: no tty present and no askpass program specified galaxy.tools.actions.upload_common DEBUG 2013-11-06 16:48:49,751 Changing ownership of /shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO with: /usr/bin/sudo -E scripts/external_chown_script.py /shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO hazards 502 galaxy.tools.actions.upload_common WARNING 2013-11-06 16:48:49,775 Changing ownership of uploaded file /shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO failed: sudo: no tty present and no askpass program specified galaxy.tools.actions.upload_common INFO 2013-11-06 16:48:49,805 tool upload1 created job id 170 galaxy.jobs DEBUG 2013-11-06 16:48:50,678 (170) Persisting job destination (destination id: local) galaxy.jobs.handler INFO 2013-11-06 16:48:50,698 (170) Job dispatched galaxy.jobs.runners.local DEBUG 2013-11-06 16:48:50,994 (170) executing: python /shared/app/Galaxy/galaxy-dist/tools/data_source/upload.py /depot/shared/app/Galaxy/galaxy-dist /shared/app/Galaxy/galaxy-dist/database/tmp/tmpTq22ot /shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO 406:/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/dataset_406_files:/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/galaxy_dataset_406.dat galaxy.jobs DEBUG 2013-11-06 16:48:51,030 (170) Persisting job destination (destination id: local) galaxy.jobs.runners.local DEBUG 2013-11-06 16:48:53,335 execution finished: python /shared/app/Galaxy/galaxy-dist/tools/data_source/upload.py /depot/shared/app/Galaxy/galaxy-dist /shared/app/Galaxy/galaxy-dist/database/tmp/tmpTq22ot /shared/app/Galaxy/galaxy-dist/database/tmp/tmpEsyGfO 406:/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/dataset_406_files:/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/galaxy_dataset_406.dat galaxy.jobs.runners.local DEBUG 2013-11-06 16:48:53,463 executing external set_meta script for job 170: /depot/shared/app/Galaxy/galaxy-dist/set_metadata.sh /shared/app/Galaxy/galaxy-dist/database/files /shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170 . /depot/shared/app/Galaxy/galaxy-dist/universe_wsgi.ini /shared/app/Galaxy/galaxy-dist/database/tmp/tmpTq22ot /shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/galaxy.json /shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/metadata_in_HistoryDatasetAssociation_410_pUkPU9,/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/metadata_kwds_HistoryDatasetAssociation_410_iouZ6k,/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/metadata_out_HistoryDatasetAssociation_410_3c6Nj2,/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/metadata_results_HistoryDatasetAssociation_410_A6L2LO,/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/galaxy_dataset_406.dat,/shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/metadata_override_HistoryDatasetAssociation_410_8Wub22 galaxy.jobs.runners.local DEBUG 2013-11-06 16:48:54,789 execution of external set_meta for job 170 finished galaxy.jobs DEBUG 2013-11-06 16:48:54,815 (170) Changing ownership of working directory with: /usr/bin/sudo -E scripts/external_chown_script.py /shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170 galaxy 50982 galaxy.jobs ERROR 2013-11-06 16:48:54,839 (170) Failed to change ownership of /shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170, failing Traceback (most recent call last): File "/depot/shared/app/Galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 868, in finish self.reclaim_ownership() File "/depot/shared/app/Galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1452, in reclaim_ownership self._change_ownership( self.galaxy_system_pwent[0], str( self.galaxy_system_pwent[3] ) ) File "/depot/shared/app/Galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 1438, in _change_ownership assert p.returncode == 0 AssertionError galaxy.jobs DEBUG 2013-11-06 16:48:54,876 fail(): Moved /shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170/galaxy_dataset_406.dat to /shared/app/Galaxy/galaxy-dist/database/files/000/dataset_406.dat ls -ltr /shared/app/Galaxy/galaxy-dist/database/files/000 -rw------- 1 galaxy galaxy 93 Nov 6 16:48 dataset_406.dat >From http://dev.list.galaxyproject.org/Submitting-jobs-as-a-real-user-without-us… I tried this as sudo user scripts/external_chown_script.py /shared/app/Galaxy/galaxy-dist/database/job_working_directory/000/170 svcgalaxy 100000 Traceback (most recent call last): File "scripts/external_chown_script.py", line 16, in <module> import drmaa File "build/bdist.linux-x86_64/egg/drmaa/__init__.py", line 41, in <module> File "build/bdist.linux-x86_64/egg/drmaa/wrappers.py", line 43, in <module> RuntimeError: could not find drmaa library. Please specify its full path using the environment variable DRMAA_LIBRARY_PATH I have no idea why that refers to DRMAA anything because in this case I was running local In fact however I get that same error when I start galaxy with this ”job_conf.xml” cat job_conf.xml <?xml version="1.0"?> <job_conf> <plugins>  <plugin id="drmaa" type="runner" load="galaxy.jobs.runners.drmaa:DRMAAJobRunner" workers="8"/> </plugins> <handlers default="handlers">  <handler id="main" tags="handlers"/> </handlers> <destinations default="drmaa">  <destination id="drmaa" runner="drmaa" tags="hpcc3.musc.edu">  <param id="galaxy_external_runjob_script">scripts/drmaa_external_runner.py</param> <param id="galaxy_external_killjob_script">scripts/drmaa_external_killer.py</param> <param id="galaxy_external_chown_script">scripts/external_chown_script.py</param> </destination> </destinations> </job_conf> The other difference is that in the DRMAA case, the GUI upload job in the HISTORY panel goes “grey” and stays that way; nothing is ever uploaded. Summary: In local mode I can upload files but there are errors in HISTORY and I cannot get tools to see the uploaded files. In DMAA mode I cannot get the GUI upload to happen at all. BTW in user “galaxy”’s .bashrc file I have this line export DRMAA_LIBRARY_PATH=/opt/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so I’m baffled. Thanks Starr /shared/app/Galaxy/galaxy-dist/database/files

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Re: [galaxy-dev] Question regarding walltime exceeded not being correctly reported via the WebUI
by Daniel Patrick Sullivan 07 Nov '13

07 Nov '13

Hi, John, Thank you for taking the time to help me look into this issue. I have applied the patch you provided and confirmed that it appears to help remediate the problem (when a walltime is exceeded feedback is in fact provided via the Galaxy web UI; it no longer appears that jobs are running indefinitely). One thing I would like to note is that the error that is provided to the user is generic, i.e. the web UI reports "An error occurred with this dataset: Job cannot be completed due to a cluster error, please retry it later". So, the fact that a Walltime exceeded error actually occurred is not presented to the user (I am not sure if this is intentional or not). Again, I appreciate you taking the time to verify and patch this issue. I have attached a screenshot of the output for your review. I am probably going to be testing Galaxy with Torque 4.2.5 in the coming weeks, I will let you know if I identify any additional problems. Thank you so much have a wonderful day. Dan Sullivan On Tue, Nov 5, 2013 at 8:48 AM, John Chilton <chilton(a)msi.umn.edu> wrote: > Hey Daniel, > > Thanks so much for the details problem report, it was very helpful. > Reviewing the code there appears to be a bug in the PBS job runner - > in some cases pbs_job_state.stop_job is never set but is attempted to > be read. I don't have torque so I don't have a great test setup for > this problem, any chance you can make the following changes for me and > let me know if they work? > > Between the following two lines: > > log.error( '(%s/%s) PBS job failed: %s' % ( > galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ), > 'Unknown error: %s' % status.exit_status ) ) ) > self.work_queue.put( ( self.fail_job, pbs_job_state ) ) > > log.error( '(%s/%s) PBS job failed: %s' % ( > galaxy_job_id, job_id, JOB_EXIT_STATUS.get( int( status.exit_status ), > 'Unknown error: %s' % status.exit_status ) ) ) > pbs_job_state.stop_job = False > self.work_queue.put( ( self.fail_job, pbs_job_state ) ) > > And at the top of the file can you add a -11 option to the > JOB_EXIT_STATUS to indicate a job timeout. > > I have attached a patch that would apply against the latest stable - > it will probably will work against your branch as well. > > If you would rather not act as my QC layer, I can try to come up with > a way to do some testing on my end :). > > Thanks again, > -John > > > On Mon, Nov 4, 2013 at 10:10 AM, Daniel Patrick Sullivan > <dansullivan(a)gmail.com> wrote: > > Hi, Galaxy Developers, > > > > I have what I hops is somewhat of a basic question regarding Galaxy's > > interaction with a pbs job cluster and information reported via the > webUI. > > Basically, in certain situations, the walltime of a specific job is > > exceeded. This is of course to be expected and all fine and > > understandeable. > > > > My problem is that the information is not being relayed back to the end > user > > via the Galaxy web UI, which causes confusion in our Galaxy user > community. > > Basically the Torque scheduler generates the following message when a > > walltime is exceeded: > > > > 11/04/2013 > > 08:39:45;000d;PBS_Server.30621;Job;163.sctest.cri.uchicago.edu;preparing > to > > send 'a' mail for job 163.sctest.cri.uchicago.edu to > > s.cri.galaxy(a)crigalaxy-test.uchicago.edu (Job exceeded its walltime > limit. > > Job was aborted > > 11/04/2013 > > 08:39:45;0009;PBS_Server.30621;Job;163.sctest.cri.uchicago.edu;job exit > > status -11 handled > > > > Now, my problem is that this status -11 return code is not being > correctly > > handled by Galaxy. What happens is that Galaxy throws an exception, > > specificially: > > > > 10.135.217.178 - - [04/Nov/2013:08:39:42 -0500] "GET > > /api/histories/90240358ebde1489 HTTP/1.1" 200 - > > "https://crigalaxy-test.uchicago.edu/history" "Mozilla/5.0 (X11; Linux > > x86_64; rv:23.0) Gecko/20100101 Firefox/23.0" > > galaxy.jobs.runners.pbs DEBUG 2013-11-04 08:39:46,137 > > (2150/163.sctest.cri.uchicago.edu) PBS job state changed from R to C > > galaxy.jobs.runners.pbs ERROR 2013-11-04 08:39:46,139 > > (2150/163.sctest.cri.uchicago.edu) PBS job failed: Unknown error: -11 > > galaxy.jobs.runners ERROR 2013-11-04 08:39:46,139 (unknown) Unhandled > > exception calling fail_job > > Traceback (most recent call last): > > File > "/group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", > > line 60, in run_next > > method(arg) > > File "/group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", > line > > 561, in fail_job > > if pbs_job_state.stop_job: > > AttributeError: 'AsynchronousJobState' object has no attribute 'stop_job' > > > > After this exception occurs, the Galaxy job status via the Web UI is > still > > reported as "Job is currently running". It appears that the job will > remain > > in this state (from the end users perspective) indefinitely. Has anybody > > seen this issue before? > > > > I noticed that return code -11 does not exist in > > /group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/pbs.py under the > > JOB_EXIT_STATUS dictionary. I tried adding an entry for this, however > > when I do the exception changes to: > > > > galaxy.jobs.runners.pbs ERROR 2013-11-04 10:02:17,274 > > (2151/164.sctest.cri.uchicago.edu) PBS job failed: job walltime exceeded > > galaxy.jobs.runners ERROR 2013-11-04 10:02:17,275 (unknown) Unhandled > > exception calling fail_job > > Traceback (most recent call last): > > File > "/group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", > > line 60, in run_next > > method(arg) > > File "/group/galaxy_test/galaxy-dist/lib/galaxy/jobs/runners/pbs.py", > line > > 562, in fail_job > > if pbs_job_state.stop_job: > > AttributeError: 'AsynchronousJobState' object has no attribute 'stop_job' > > > > I am wondering if this is a bug or if it is just because I am using a > newer > > version of TORQUE (I am using TORQUE 4.2.2). > > > > In terms of Galaxy, I am using: > > > > [s.cri.galaxy@crigalaxy-test galaxy-dist]$ hg parents > > changeset: 10408:6822f41bc9bb > > branch: stable > > parent: 10393:d05bf67aefa6 > > user: Dave Bouvier <dave(a)bx.psu.edu> > > date: Mon Aug 19 13:06:17 2013 -0400 > > summary: Fix for case where running functional tests might overwrite > > certain files in database/files. > > > > [s.cri.galaxy@crigalaxy-test galaxy-dist]$ > > > > Does anybody know how I could fix this such that walltime exceeded > messages > > are correctly reporeted via the Galaxy web UI for TORQUE 4.2.2? Thank > you > > so much for your input and guidance, and for the ongoing development of > > Galaxy. > > > > Dan Sullivan > > > > ___________________________________________________________ > > 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/ >

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Dynamic tool configuration
by Biobix Galaxy 06 Nov '13

06 Nov '13

Hi all, We are working on a galaxy tool suite for data analysis. We use a sqlite db to keep result data centralised between the different tools. At one point the tool configuration options of a tool should be dependent on the rows within a table of the sqlite db that is the output of the previous step. In other words, we would like to be able to set selectable parameters based on an underlying sql statement. If sql is not possible, an alternative would be to output the table content into a txt file and subsequently parse the txt file instead of the sqlite_db within the xml configuration file. When looking through the galaxy wiki and mailing lists I came across the <code> tag which would be ideal, we could run a python script in the background to fetch date from the sqlite table, however that function is deprecated. Does anybody know of other ways to achieve this? Thanks! Jeroen Ir. Jeroen Crappé, PhD Student Lab of Bioinformatics and Computational Genomics (Biobix) FBW - Ghent University

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Re: [galaxy-dev] Galaxy dropping jobs?
by Nikolai Vazov 06 Nov '13

06 Nov '13

Hi again, The loop (as explained below), did the job :) Nikolay Thank you very much, Nate, 1. I have put a fix : a loop running the JobStatus check 5 times every 60 secs and only then throwing an exception as the one below. It happened that all connect failures happen at the same time - at slurm log rotation time at 3 am. Hopefully it helps :) 2. Our slurm conf keeps the info about each job for 5 min. But looking at the code, it seems that in in the case you describe below, there will be an "Invalid job exception" leading to "Job finished" state. Am I wrong? Anyway, I'll let you know if the loop does the job. Thanks again, Nikolay On 2013-11-04 15:57, Nate Coraor wrote: > Hi Nikolay, > With slurm, the following change that I backed out should fix the > problem: > > https://bitbucket.org/galaxy/galaxy-central/diff/lib/galaxy/jobs/runners/dr… > Although I do believe that if Galaxy doesn't read the completion > state before slurm "forgets" about the job (MinJobAge in slurm.conf), > this change could result in the job becoming permanently stuck in the > running state. > I should have some enhancements to the DRMAA runner for slurm coming > soon that would prevent this. > --nate > On Oct 31, 2013, at 5:27 AM, Nikolai Vazov wrote: > >> Hi, >> >> I discovered a weird issue in the job behaviour : Galaxy is running a >> long job on a cluster (more than 24h), about 15 hours later it misses >> the connection with SLURM on the cluster and throws the following >> message : >> [root@galaxy-prod01 galaxy-dist]# grep 3715200 paster.log >> galaxy.jobs.runners.drmaa INFO 2013-10-30 10:51:54,149 (555) queued >> as 3715200 >> galaxy.jobs.runners.drmaa DEBUG 2013-10-30 10:51:55,149 (555/3715200) >> state change: job is queued and active >> galaxy.jobs.runners.drmaa DEBUG 2013-10-30 10:52:13,516 (555/3715200) >> state change: job is running >> galaxy.jobs.runners.drmaa INFO 2013-10-31 03:29:33,090 (555/3715200) >> job left DRM queue with following message: code 1: slurm_load_jobs >> error: Unable to contact slurm controller (connect failure),job_id: >> 3715200 >> Is there a timeout in Galaxy for contacting slurm? Yet, the job is >> still running properly on the cluster ... >> Thanks for help, it's really urgent :) >> Nikolay >> >> -- >> Nikolay Vazov, PhD >> Research Computing Centre - http://hpc.uio.no >> USIT, University of Oslo >> ___________________________________________________________ >> 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/ -- Nikolay Vazov, PhD Research Computing Centre - http://hpc.uio.no USIT, University of Oslo

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Supporting file sets for running a tool with multiple input files
by Lukasse, Pieter 06 Nov '13

06 Nov '13

Hi, Is there any news regarding support for the following scenario in Galaxy: - User has N files which he would like to process with a Galaxy tool using the same parameters - User uploads a (.tar or .zip ?) file to Galaxy and selects this as the input file for the tool - Tool produces an output .zip file with the N result files I know Galaxy-P had a workaround for this some time ago. But has this been solved in the main Galaxy code base? Or are there any feasible workarounds that I can add to my Toolshed package to ensure my .zip file does not get unzipped at upload (default Galaxy behaviour)? Thanks and regards, Pieter Lukasse Wageningen UR, Plant Research International Departments of Bioscience and Bioinformatics Wageningen Campus, Building 107, Droevendaalsesteeg 1, 6708 PB, Wageningen, the Netherlands +31-317480891; skype: pieter.lukasse.wur http://www.pri.wur.nl<http://www.pri.wur.nl/>

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Re: [galaxy-dev] latest galaxy-central version
by James Taylor 06 Nov '13

06 Nov '13

Robert, I'm not sure what is going on here, other than that the javascript that converts buttons into dropdown menus has not fired. Are there any javascript errors? Marten is working on rewriting libraries, and we will be eliminating the progressive loading popupmenus for something much more efficient, but this also might indicate a bug so let us know if there is anything odd in the console. -- James Taylor, Associate Professor, Biology/CS, Emory University On Mon, Nov 4, 2013 at 1:58 PM, Robert Baertsch <baertsch(a)soe.ucsc.edu>wrote: > HI James, > I just pulled in the latest code to see how you changed from iframe to > divs. Very exciting update. > > > I tried importing a bam file into the library using the admin tool that > reads the file directly from a path on the server. > > During the copy operation, the screen gets into a weird state. > ps -ef shows these two processes running: > python /data/galaxy-central/tools/data_source/upload.py > /data/galaxy-central /data/galaxy-central/database/tmp/tmpywxnFE > /data/galaxy-central/database/tmp/tmpXkEvSY > 8876:/data/galaxy-central/database/job_working_directory/004/4547/dataset_8876_files:/data/galaxy-central/database/files/008/dataset_8876.dat > samtools sort /data/galaxy-central/database/files/008/dataset_8876.dat > /tmp/tmpNbcggh/sorted > > Do you finish rendering the screen after the copy operation is complete? > > -Robert > >

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errors after updating galaxy distribution
by Dan Tenenbaum 06 Nov '13

06 Nov '13

Hi, I updated my galaxy distribution with hg pull -u Then tried to re-run galaxy and got an error: $ ./run.sh Traceback (most recent call last): File "./scripts/paster.py", line 33, in <module> serve.run() File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1049, in run invoke(command, command_name, options, args[1:]) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 1055, in invoke exit_code = runner.run(args) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 220, in run result = self.command() File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py", line 643, in command app = loadapp( app_spec, name=app_name, relative_to=base, global_conf=vars) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 350, in loadapp return loadobj(APP, uri, name=name, **kw) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 374, in loadobj global_conf=global_conf) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 399, in loadcontext global_conf=global_conf) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 423, in _loadconfig return loader.get_context(object_type, name, global_conf) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 561, in get_context section) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 620, in _context_from_explicit value = import_string(found_expr) File "/home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/loadwsgi.py", line 125, in import_string return pkg_resources.EntryPoint.parse("x=" + s).load(False) File "/home/microbeco/galaxy-dist/lib/pkg_resources.py", line 1954, in load entry = __import__(self.module_name, globals(),globals(), ['__name__']) File "/home/microbeco/galaxy-dist/lib/galaxy/web/buildapp.py", line 3, in <module> from galaxy.webapps.galaxy.buildapp import app_factory File "/home/microbeco/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 16, in <module> import galaxy.model.mapping File "/home/microbeco/galaxy-dist/lib/galaxy/model/mapping.py", line 14, in <module> from sqlalchemy.types import BigInteger ImportError: cannot import name BigInteger I also tried to update my database but got a different error: $ sh manage_db.sh upgrade 114 -> 115... Traceback (most recent call last): File "./scripts/manage_db.py", line 62, in <module> main( repository=repo, url=db_url ) File "/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/shell.py", line 150, in main ret = command_func(**kwargs) File "/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py", line 221, in upgrade return _migrate(url, repository, version, upgrade=True, err=err, **opts) File "/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/api.py", line 349, in _migrate schema.runchange(ver, change, changeset.step) File "/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/schema.py", line 184, in runchange change.run(self.engine, step) File "/home/microbeco/galaxy-dist/eggs/sqlalchemy_migrate-0.5.4-py2.7.egg/migrate/versioning/script/py.py", line 101, in run func() TypeError: upgrade() takes exactly 1 argument (0 given) How can I fix this? Thanks, Dan

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Egg distribution issue
by Iry Witham 06 Nov '13

06 Nov '13

Hi Dev Team, I have run into an egg distribution issue. I had performed an upgrade late last month and am experiencing issues fetching eggs. I am getting the following error message: galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist> python ./scripts/fetch_eggs.py Fetched http://eggs.galaxyproject.org/sqlalchemy_migrate/sqlalchemy_migrate-0.7.2-p… One of Galaxy's managed eggs depends on something which is missing, this is almost certainly a bug in the egg distribution. Dependency "sqlalchemy-migrate" requires "setuptools" Traceback (most recent call last): File "./scripts/fetch_eggs.py", line 37, in <module> c.resolve() # Only fetch eggs required by the config File "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/lib/galaxy/eggs/__init__.py", line 345, in resolve egg.resolve() File "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/lib/galaxy/eggs/__init__.py", line 168, in resolve dists = pkg_resources.working_set.resolve( ( self.distribution.as_requirement(), ), env, self.fetch ) File "/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist-jax/galaxy-dist-jax/lib/pkg_resources.py", line 569, in resolve raise VersionConflict(dist,req) # XXX put more info here pkg_resources.VersionConflict: (sqlalchemy-migrate 0.7.2 (/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg), Requirement.parse('setuptools')) Could someone point me in the right direction? Thanks, Iry __________________________________ Iry T. Witham Scientific Applications Administrator Scientific Computing Group Computational Sciences Dept. The Jackson Laboratory 600 Main Street Bar Harbor, ME 04609 Phone: 207-288-6744 email: iry.witham(a)jax.org [cid:3302E28C-F24A-4AF1-97B8-A33A6CD618F6] 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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Deleting history entries not working, javascript void link?
by Peter Cock 05 Nov '13

05 Nov '13

Hi all, I've just updated our main Galaxy to release_2013.11.04 but also see the following problem on galaxy-central, and on https://usegalaxy.org/ as well. (1) Go to any history with deleted files (2) Cog icon, tick "Include Deleted datasets" (3) Look at a deleted dataset in your history column, note the yellow "Warning" box with text: This dataset has been deleted. Click *here* to undelete it or *here* to immediately remove it from disk (4) Notice the first *here* link (undelete) has a sensible URL, e.g. as shown via your browser's status bar or right click to copy the URL. (5) Notice the second *here* (remove) has this as the URL: javascript:void(0) Unsurprisingly, the remove link has no effect as it is a JavaScript command to do nothing, and the user cannot therefore purge the file from their history. I've confirmed this on multiple browsers on multiple machines. Regards, Peter

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galaxy-dev November 2013