Re: [galaxy-dev] An error occurred...
Hi Jeremy, Thanks for your effort, but when I cloned the dataset you shared with me and switched it as current history, I still got Error executing tool: 'hg19', after I tried to run Cufflinks on both Tophats, on single and pair end data. All best, Milos On Wed, Jan 18, 2012 at 1:47 AM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Milos, I successfully ran Cufflinks on your datasets; I've shared the history with you that has the results. Perhaps you ran into a transient error. Best, J. On Jan 17, 2012, at 8:13 AM, Milos Busarcevic wrote: Hi Jeremy, I have shared my history with you. Today, error that appears when I try to run cufflinks has changed into: Error executing tool: 'hg19'. Thanks, Milos On Mon, Jan 16, 2012 at 7:21 PM, Jeremy Goecks jeremy.goe...@emory.edu wrote: Milos, Can you share your history with me (Options - Share or Publish - share with a user -- my email address) and I'll take a look. Thanks, J. On Jan 16, 2012, at 12:46 PM, Milos Busarcevic wrote: Hi, I've got this message after trying to run Cufflinks on the Main instance: Server Error An error occurred. See the error logs for more information. (Turn debug on to display exception reports here) Is this a global problem and is there a way to fix it? Thanks, Milos ___ 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/ ___ 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/
Re: [galaxy-dev] problems with location of filter bar in trackster
Hans, A couple questions: (a) What browser/OS are you using when seeing this problem? (b) Can you replicate this behavior on our public server? A couple notes: depending on your Web server setup, it may be necessary to use the packed Trackster script rather than the full one. Also, we're planning to release a new distribution in the next couple days, so it may be worthwhile to put off debugging Trackster until then because there have been quite a few changes to Trackster since the last release and these may solve your issues. Thanks, J. On Jan 18, 2012, at 9:19 AM, Hans-Rudolf Hotz wrote: Hi I am still in the process of upgrading all our Galaxy servers to the current changeset (b258de1e6cea, Nov. 18) and now I am running into troubles with the visualization: Depending on the location of my mouse, the filter bar and the other extra buttons jump between two positions, which makes it impossible to use, see Screenshot_1.png and Screenshot_2.png I was looking for relevant code changes, which were committed after Nov. 18. I found changeset 856aac70b018 (Trackster: refactor action icon creation and initialization from Nov. 23) for ~/static/scripts/trackster.js Adding this change fixes the problem somehow, but I lose the original icons (for 'set display mode', 'Hide/Show track content', etc) and the bar is now below the track, see Screenshot_3.png Just using the ~/static/scripts/trackster.js from 'central' doesn't solve the problem either. Are there any extra steps I can do in addition to changeset 856aac70b018 in order to solve this problem (except for waiting/using for the next release) Thank you very much for your help Hans Screenshot_1.pngScreenshot_2.pngScreenshot_3.png___ 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/ ___ 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/
Re: [galaxy-dev] problems with location of filter bar in trackster
Hi Jeremy A couple questions: (a) What browser/OS are you using when seeing this problem? chrome and firefox on Linux as well as firefox on Mac (10.5.8) (b) Can you replicate this behavior on our public server? it works fine on the public server A couple notes: depending on your Web server setup, it may be necessary to use the packed Trackster script rather than the full one. what do you mean by packed Trackster script Also, we're planning to release a new distribution in the next couple days, so it may be worthwhile to put off debugging Trackster until then because there have been quite a few changes to Trackster since the last release and these may solve your issues. I am aware of the fact, that there will be an imminent release of a new distribution. However, I have reserved this week to do the upgrades in order to fit with in with other obligations I have Regards, Hans Thanks, J. On Jan 18, 2012, at 9:19 AM, Hans-Rudolf Hotz wrote: Hi I am still in the process of upgrading all our Galaxy servers to the current changeset (b258de1e6cea, Nov. 18) and now I am running into troubles with the visualization: Depending on the location of my mouse, the filter bar and the other extra buttons jump between two positions, which makes it impossible to use, see Screenshot_1.png and Screenshot_2.png I was looking for relevant code changes, which were committed after Nov. 18. I found changeset 856aac70b018 (Trackster: refactor action icon creation and initialization from Nov. 23) for ~/static/scripts/trackster.js Adding this change fixes the problem somehow, but I lose the original icons (for 'set display mode', 'Hide/Show track content', etc) and the bar is now below the track, see Screenshot_3.png Just using the ~/static/scripts/trackster.js from 'central' doesn't solve the problem either. Are there any extra steps I can do in addition to changeset 856aac70b018 in order to solve this problem (except for waiting/using for the next release) Thank you very much for your help Hans Screenshot_1.pngScreenshot_2.pngScreenshot_3.png___ 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/ ___ 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/
[galaxy-dev] Error download composite dataset from history
Hello! I'm running into an error when trying to download a composite dataset from the history with the floppy disk icon. Here is the error message in the logs: galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 285, in archive_composite_dataset os.rmdir( tmpd ) OSError: [Errno 39] Directory not empty: './database/tmp/tmpkRv28I' Then I tried replacing the os.rmdir by a shutil.rmtree to see if it would solve the issue, and here is what I got: galaxy.web.controllers.dataset ERROR 2012-01-18 16:34:30,239 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 286, in archive_composite_dataset shutil.rmtree( tmpd ) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 221, in rmtree onerror(os.remove, fullname, sys.exc_info()) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 219, in rmtree os.remove(fullname) OSError: [Errno 16] Device or resource busy: './database/tmp/tmpwpsShD/.nfs0289ccea0138' But when I check the contents of the direcory, there is no hidden .nfs-something file. Does anyone have an idea why this could occur? Both our testing instance and our production instance have the same issue, the first being on galaxy-central and the second on galaxy-dist. Thanks, L-A ___ 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/
Re: [galaxy-dev] Issues displaying/downloading datasets
I seem to be getting somewhere by monitoring the /var/log/httpd/error_log file (I don't know why I didn't think of that before). For each dataset I click I am seeing a corresponding message like this: *[Wed Jan 18 09:31:06 2012] [debug] mod_proxy_http.c(56): proxy: HTTP: canonicalising URL //localhost:8080/datasets/b23533e4ff1bb7ec/display/* * * *[Wed Jan 18 09:31:06 2012] [error] [client 172.26.14.93] (20023)The given path was above the root path: xsendfile: unable to find file: /panfs/galaxy_data/database/files/000/dataset_118.dat, referer: http://galaxy-dev.haib.org/galaxy/history* * * *[Wed Jan 18 09:31:06 2012] [debug] mod_proxy_http.c(1836): proxy: end body send* So it seems that there is some issue with the xsendfile module, or with apache serving up the dataset files, because '/panfs/galaxy_data/database/files/000/dataset_118.dat' is present. The only thing that I recall changing recently was to move the /panfs/galaxy_data/database/ directory from the local file system to an nfs share with the exact same path (mounted on /panfs). I'm not sure how that would make a difference though. I'm still looking into the xsendfile error lead though. -Josh On Tue, Jan 17, 2012 at 11:08 AM, Josh Nielsen jniel...@hudsonalpha.comwrote: Also, I just uploaded a 1.3GB FASTQ file and the small preview box in the history pane shows the first few lines, and when I click on the eye it actually displays in the window with the message This dataset is large and only the first megabyte is shown below. Show all | Save and it shows the first megabyte with no problems, but if I click 'Show all' or 'Save' I get the message The requested URL /galaxy/datasets/2faba7054d92b2df/display/ was not found on this server from apache. So I'm having a specific problem with displaying the whole dataset according to the URL it is trying to load. -Josh -- Forwarded message -- From: Josh Nielsen jniel...@hudsonalpha.com Date: Tue, Jan 17, 2012 at 10:22 AM Subject: Issues displaying/downloading datasets To: galaxy-dev@lists.bx.psu.edu Hello all, I recently have been having problems viewing/displaying datasets (with the eye icon) as well as downloading datasets in Galaxy which I have uploaded, although I can actually point to those datasets as input to other tools and they show up on the drop down menus and it runs perfectly. Every time that I click on the eye icon for a dataset in my history pane I get an apache error which displays in the window that says it cannot find /galaxy/datasets/X/display/?preview=True. I see a corresponding entry like this in paster.log (for example): *[17/Jan/2012:09:53:03 -0500] GET /galaxy/datasets/92b83968e0b52980/display/?preview=True HTTP/1.1 200 - http://galaxy-dev.haib.org/galaxy/history; Mozilla/5.0 (Macintosh; Intel Mac OS X 10.6; rv:8.0.1) Gecko/20100101 Firefox/8.0.1* For downloads I get the same error except that the requested URL is: *GET /galaxy/datasets/92b83968e0b52980/display?to_ext=txt* The alphanumeric code is of course different for each dataset but I am puzzled at how to even debug this because I cannot find anywhere on the file system or under the galaxy-dist directory any path that is named datasets and has a display subfolder (so I assume it is an internal url/path notation). I looked at the python code some and all I got was a headache. I see that it uses a fetch url method to grab a specific url for each dataset but I'm not sure what it is actually looking for on the file system, or if the url is just an alias to something else. I thought to check in the MySQL database but didn't see any corresponding values that matched datasets or the alphanumeric code (which I still can't tell where it is getting that from). Everything else in Galaxy works fine except for this. Could anyone please point me in the right direction about how to debug this? It would be much appreciated! Thanks, Josh ___ 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/
Re: [galaxy-dev] Issues displaying/downloading datasets
Ah, following the lead in the log paid off. I had to add the statement *XSendFilePath /panfs/galaxy_data *to /etc/httpd/conf/httpd.conf. Apparently ever since I had moved the dataset directory to /panfs/galaxy_data by setting the file_path variable in universe_wsgi.ini I have not attempted to view a dataset, and so I didn't even notice that the functionality broke when I moved it at first. I just needed to point XSendFilePath to the new directory and it worked. I hope this helps someone else if they encounter the same problem. Cheers, Josh ___ 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/
Re: [galaxy-dev] Status on importing BAM file into Library does not update
Nate - Is there a specific place in the Galaxy code that forks the samtools index on bam files on the cluster or the head node? I really need to track this down. On Fri, Jan 13, 2012 at 12:54 PM, Ryan Golhar ngsbioinformat...@gmail.comwrote: I re-uploaded 3 BAM files using the Upload system file paths. runner0.log shows: galaxy.jobs DEBUG 2012-01-13 12:50:08,442 dispatching job 76 to pbs runner galaxy.jobs INFO 2012-01-13 12:50:08,555 job 76 dispatched galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,697 (76) submitting file /home/galaxy/galaxy-dist-9/database/pbs/76.sh galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,697 (76) command is: python /home/galaxy/galaxy-dist-9/tools/data_source/upload.py /home/galaxy/galaxy-dist-9 /home/galaxy/galaxy-dist-9/datatypes_conf.xml /home/galaxy/galaxy-dist-9/database/tmp/tmpqrVYY7 208:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_208_files:None 209:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_209_files:None 210:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_210_files:None; cd /home/galaxy/galaxy-dist-9; /home/galaxy/galaxy-dist-9/set_metadata.sh ./database/files ./database/tmp . datatypes_conf.xml ./database/job_working_directory/76/galaxy.json galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:08,699 (76) queued in default queue as 114.localhost.localdomain galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:50:09,037 (76/114.localhost.localdomain) PBS job state changed from N to R galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:09,205 (76/114.localhost.localdomain) PBS job state changed from R to E galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:10,206 (76/114.localhost.localdomain) PBS job state changed from E to C galaxy.jobs.runners.pbs DEBUG 2012-01-13 12:51:10,206 (76/114.localhost.localdomain) PBS job has completed successfully 76.sh shows: [galaxy@bic pbs]$ more 76.sh #!/bin/sh GALAXY_LIB=/home/galaxy/galaxy-dist-9/lib if [ $GALAXY_LIB != None ]; then if [ -n $PYTHONPATH ]; then export PYTHONPATH=$GALAXY_LIB:$PYTHONPATH else export PYTHONPATH=$GALAXY_LIB fi fi cd /home/galaxy/galaxy-dist-9/database/job_working_directory/76 python /home/galaxy/galaxy-dist-9/tools/data_source/upload.py /home/galaxy/galaxy-dist-9 /home/galaxy/galaxy-dist-9/datatypes_conf.xml /home/galaxy /galaxy-dist-9/database/tmp/tmpqrVYY7 208:/home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_208_files:None 209:/ home/galaxy/galaxy-dist-9/database/job_working_directory/76/dataset_209_files:None 210:/home/galaxy/galaxy-dist-9/database/job_working_dire ctory/76/dataset_210_files:None; cd /home/galaxy/galaxy-dist-9; /home/galaxy/galaxy-dist-9/set_metadata.sh ./database/files ./database/tmp . dataty pes_conf.xml ./database/job_working_directory/76/galaxy.json Right as the job ended I check the job output files: [galaxy@bic pbs]$ ll total 4 -rw-rw-r-- 1 galaxy galaxy 950 Jan 13 12:50 76.sh [galaxy@bic pbs]$ ll total 4 -rw--- 1 galaxy galaxy 0 Jan 13 12:50 76.e -rw--- 1 galaxy galaxy 0 Jan 13 12:50 76.o -rw-rw-r-- 1 galaxy galaxy 950 Jan 13 12:50 76.sh samtools is now running on the head node. Where does Galaxy decide how to run samtools? Maybe I can add a check of some sort to see what's going on? On Fri, Jan 13, 2012 at 10:53 AM, Nate Coraor n...@bx.psu.edu wrote: On Jan 12, 2012, at 11:41 PM, Ryan Golhar wrote: Any ideas as to how to fix this? We are interested in using Galaxy to host all our NGS data. If indexing on the head node is going to happen, then this is going to be an extremely slow process. Could you post the contents of /home/galaxy/galaxy-dist-9/database/pbs/62.sh ? Although I have to admit this is really baffling. The presence of this line without an error: galaxy.datatypes.metadata DEBUG 2012-01-11 10:22:40,162 Cleaning up external metadata files Indicates that metadata was set externally and the relevant metadata files were present on disk. --nate ___ 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/
[galaxy-dev] Is it possible to pass runtime values to workflows through the API?
Hi, I was wondering if is possible to pass runtime values to workflows thought the API? I want to run the same workflow for several inputs, but there are values other than the inputs that I need to change for each run. Is it possible to leave these values as 'To be set at runtime' and set them through the API? Also, I see 'Step Actions' do not support the option of 'To be set at runtime', could this be included in a future release, in other words, can this be a feature request? Thanks, Carlos ___ 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/
Re: [galaxy-dev] problems with location of filter bar in trackster
it works fine on the public server Good, this narrows down the problem to installing the -central script on your instance b/c main's copy of the script is very similar to -central's. what do you mean by packed Trackster script All JavaScript files are compressed in size--comments/whitespace removed and variables renamed--to minimize their transfer time. These are available in /static/scripts/packed If you have directives in your proxy server config to use the packed scripts, you'll want to update the packed script from -central as well. The other thing to consider is browser caching: you may need to clear your browser cache to load the new Trackster script. Good luck, J. ___ 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/
Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException
excellent, thanks for the correction!
On Wed, Jan 18, 2012 at 8:59 AM, Shantanu Pavgi pa...@uab.edu wrote:
Ed,
I think you may want to add job with DrmCommunicationException error
back into the watched_jobs list.
{{{
except ( drmaa.DrmCommunicationException ), e:
# Catch drmaa communication exception, log a warning message and
# continue to monitor jobs.
log.warning((%s/%s) Couldn't communicate with the cluster scheduler to
check job status. %( galaxy_job_id, job_id ))
# keep old job state
new_watched.append( drm_job_state )
continue
}}}
Here is a patch and related discussion on it:
https://bitbucket.org/galaxy/galaxy-central/pull-request/23/catch-drmcommunication-exception
--
Shantanu
On Jan 13, 2012, at 2:11 PM, Edward Kirton wrote:
i had seen the job process die with this error:
if state != old_state:
UnboundLocalError: local variable 'state' referenced before assignment
since the DRM timeout is an intermittent error, i'm not absolutely
positive i have nailed it (a bit more time will tell -- i'm keeping an eye
on it with debug log messages), but it seems so. i intended to share this
as a patched clone when i became sure but when i read your email i just
sent what i had immediately. let us know if that seems to solve the
problem for you, so we'll have some confirmation.
glad to help,
ed
p.s. i have another patch for output not returned from cluster errors
that i'm also still validating, due to NFS race since we don't have inode
metadata caching turned off as the galaxy developers suggest.
On Fri, Jan 13, 2012 at 8:06 AM, Ann Black annbl...@eng.uiowa.edu wrote:
Thanks so much! I have applied the fix to our env.
In looking over the logic, there was an existing exception block that
would have caught the communication exception generically – but the job
moved (in this scenario erroneously) the job into a failure workflow. I
would like to understand what ended up hanging galaxy – so it must be
related to a valid job being moved into failure state ? Did you follow it
down the rabbit hole by any chance to see what caused the hang in your env
?
Thanks again,
Ann
From: Edward Kirton eskir...@lbl.gov
Date: Thu, 12 Jan 2012 13:00:27 -0800
To: Ann Black annbl...@eng.uiowa.edu
Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException
sometimes the scheduler can't keep up with all the work in it's 15sec
cycle, so it doesn't respond to some messages. here's a fix i've been
trying that seems to work.
in lib/galaxy/jobs/runners/drmaa.py:
def check_watched_items( self ):
Called by the monitor thread to look at each watched job and deal
with state changes.
new_watched = []
for drm_job_state in self.watched:
job_id = drm_job_state.job_id
galaxy_job_id = drm_job_state.job_wrapper.job_id
old_state = drm_job_state.old_state
try:
state = self.ds.jobStatus( job_id )
# InternalException was reported to be necessary on some
DRMs, but
# this could cause failures to be detected as completion!
Please
# report if you experience problems with this.
except ( drmaa.InvalidJobException, drmaa.InternalException
), e:
# we should only get here if an orphaned job was put into
the queue at app star
tup
log.debug((%s/%s) job left DRM queue with following
message: %s % ( galaxy_jo
b_id, job_id, e ) )
self.work_queue.put( ( 'finish', drm_job_state ) )
continue
# BEGIN DRM TIMEOUT: Don't fail on scheduler communication
error (probably just too busy)
except ( drmaa.DrmCommunicationException ), e:
log.warning((%s/%s) DRM Communication Exception % (
galaxy_job_id, job_id
))
continue
# END DRM TIMEOUT
On Wed, Jan 11, 2012 at 9:18 AM, Ann Black annbl...@eng.uiowa.eduwrote:
Good Morning galaxy group!
I was hoping that someone might have some ideas on a problem we have
experienced a handful of times running galaxy on our local cluster.
Occasionally we experience some communication timeouts between out
cluster head node and a compute node which will self heal. However, this in
turn will hang galaxy. Below you will see output from our galaxy log file.
When the ERROR happens (which is not often) it consistently seems to hang
galaxy. We have to kill it off and restart it. We are running galaxy as a
single PID at this time (we are still just testing it out, etc) and it is
running on our head node (which we plan to move off of in the future).
galaxy.jobs.runners.drmaa DEBUG 2012-01-10 19:19:58,800 (1654/698075)
state change: job is running
galaxy.jobs.runners.drmaa ERROR 2012-01-10 20:57:47,021 (1654/698075)
Unable to
Re: [galaxy-dev] Is it possible to pass runtime values to workflows through the API?
Hi Dannon, On Wed, Jan 18, 2012 at 3:32 PM, Dannon Baker dannonba...@me.com wrote: On Jan 18, 2012, at 12:20 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi, I was wondering if is possible to pass runtime values to workflows thought the API? I want to run the same workflow for several inputs, but there are values other than the inputs that I need to change for each run. Is it possible to leave these values as 'To be set at runtime' and set them through the API? Not yet, though this is something I've wanted to add for a while now. Great, I'll be looking forward this functionality. Also, I see 'Step Actions' do not support the option of 'To be set at runtime', could this be included in a future release, in other words, can this be a feature request? Which step actions would this be appropriate for? The rename action can accept a workflow parameter which would provide runtime naming functionality. If I recall correctly during a recent email exchange[1], you commented this is only something that it is in the wish list. Maybe I confused the feature in my previous email. Is it possible to use workflows parameter in the rename action? If so, please could you comment on how can I do it?. And yes, you are correct, I can't think of any cases where using a workflow parameter wouldn't solve my needs for a renaming edit action, still exposing these values to the API via runtime functionality, I think it would gives even more freedom. Not a priority for sure. Either way, exposing runtime values to the API with edit actions using workflows parameters or both workflows parameters and edit actions being able to be set at runtime with these values exposed to API, would solves my current needs. [1]http://galaxy-development-list-archive.2308389.n4.nabble.com/How-to-set-output-name-programmatically-in-workflows-using-the-API-td4285907.html Thanks a lot for all your effort, Carlos ___ 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/
Re: [galaxy-dev] Error download composite dataset from history
Hi, L-A Thanks for reporting this - I just pushed a fix in galaxy-central 6556:ab1a5ab063ce Please let us know if that resolves the problem? 2012/1/19 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hello! I'm running into an error when trying to download a composite dataset from the history with the floppy disk icon. Here is the error message in the logs: galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 285, in archive_composite_dataset os.rmdir( tmpd ) OSError: [Errno 39] Directory not empty: './database/tmp/tmpkRv28I' Then I tried replacing the os.rmdir by a shutil.rmtree to see if it would solve the issue, and here is what I got: galaxy.web.controllers.dataset ERROR 2012-01-18 16:34:30,239 Unable to remove temporary library download archive and directory Traceback (most recent call last): File /g/funcgen/galaxy-dev/lib/galaxy/web/controllers/dataset.py, line 286, in archive_composite_dataset shutil.rmtree( tmpd ) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 221, in rmtree onerror(os.remove, fullname, sys.exc_info()) File /g/steinmetz/collaboration/software/CentOS5/opt/Python-2.6.5/lib/python2.6/shutil.py, line 219, in rmtree os.remove(fullname) OSError: [Errno 16] Device or resource busy: './database/tmp/tmpwpsShD/.nfs0289ccea0138' But when I check the contents of the direcory, there is no hidden .nfs-something file. Does anyone have an idea why this could occur? Both our testing instance and our production instance have the same issue, the first being on galaxy-central and the second on galaxy-dist. Thanks, L-A ___ 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/ -- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444; ___ 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/
Re: [galaxy-dev] running functional tests on a galaxy server
Greg, That seems to work mainly for running tests from the sample universe/tool config files, so it uses the local job runner. What I would like to do is run tests using the actual Galaxy server configuration (which might use PBS/DRMAA and a cluster). The method I mention from that page seemed to be for that purpose, but again it seems possibly out-of-date... chris On Jan 18, 2012, at 4:20 PM, Greg Von Kuster wrote: Hello Chris, You should be able to run functional tests from the Galaxy install directory using the following from the command line. %sh run_functional_tests.sh There are several options you can use as well. Greg On Jan 18, 2012, at 4:38 PM, Fields, Christopher J wrote: I have been following the basic protocol for running remote tests on a Galaxy server (in this case, our local one) using: http://wiki.g2.bx.psu.edu/Admin/Running%20Tests From reading this, I assume the tests are to be run from the galaxy root directory, like so: GALAXY_TEST_EXTERNAL=1 GALAXY_TEST_HOST=my.local.galaxy.url GALAXY_TEST_PORT=8080 \ ./nosetests.sh However, no 'nosetests.sh' script exists there. Should we be using ./scripts/nosetests.py? ./scripts/functional_tests.py? Any clarification on this would be very helpful, we're just searching for a way to run tests in as automated a way as possible using the server configuration. chris Chris Fields Senior Research Scientist National Center for Supercomputing Applications Institute for Genomic Biology University of Illinois at Urbana-Champaign ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/
Re: [galaxy-dev] running functional tests on a galaxy server
Just to add for the list, nate mentioned on IRC that running tests on an external server likely doesn't work at the moment but that ./scripts/functional_tests.py may have something to work with via environment variables. chris On Jan 18, 2012, at 8:03 PM, Fields, Christopher J wrote: Greg, That seems to work mainly for running tests from the sample universe/tool config files, so it uses the local job runner. What I would like to do is run tests using the actual Galaxy server configuration (which might use PBS/DRMAA and a cluster). The method I mention from that page seemed to be for that purpose, but again it seems possibly out-of-date... chris On Jan 18, 2012, at 4:20 PM, Greg Von Kuster wrote: Hello Chris, You should be able to run functional tests from the Galaxy install directory using the following from the command line. %sh run_functional_tests.sh There are several options you can use as well. Greg On Jan 18, 2012, at 4:38 PM, Fields, Christopher J wrote: I have been following the basic protocol for running remote tests on a Galaxy server (in this case, our local one) using: http://wiki.g2.bx.psu.edu/Admin/Running%20Tests From reading this, I assume the tests are to be run from the galaxy root directory, like so: GALAXY_TEST_EXTERNAL=1 GALAXY_TEST_HOST=my.local.galaxy.url GALAXY_TEST_PORT=8080 \ ./nosetests.sh However, no 'nosetests.sh' script exists there. Should we be using ./scripts/nosetests.py? ./scripts/functional_tests.py? Any clarification on this would be very helpful, we're just searching for a way to run tests in as automated a way as possible using the server configuration. chris Chris Fields Senior Research Scientist National Center for Supercomputing Applications Institute for Genomic Biology University of Illinois at Urbana-Champaign ___ 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/ Greg Von Kuster Galaxy Development Team g...@bx.psu.edu ___ 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/ ___ 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/
