Re: [galaxy-dev] Galaxy not killing split cluster jobs
A suggested change will be coming down the pipe shortly, but it's good to hear that it will be useful! -Scott - Original Message - On Tue, May 1, 2012 at 3:46 PM, Dannon Baker dannonba...@me.com wrote: I'll take care of it. Thanks for reminding me about the TODO! This seems to have reached galaxy-central now: https://bitbucket.org/galaxy/galaxy-central/changeset/dc20a7b5b6ce i.e. When Galaxy creates sub-jobs from tools using the parallelism tag to split tasks over the cluster, if the user kills the parent job the child jobs should get kill too. That will be appreciated next time our cluster is heavily loaded :) 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/ ___ 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] egg distribution error when running galaxy-central
Clare- Have you resolved this yet? I had seen similar issues with respect to pycrypto before I used virtualenv, but I don't believe that I saw it afterwards. I'll take a look and see if I can reproduce it. I only have obvious things to recommend right now. For example, make sure that the environment has been loaded each time. Check http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server#Use_a_clean_environment , which I'm sure you've already done. -Scott - Original Message - On 1 August 2012 15:28, Clare Sloggett s...@unimelb.edu.au wrote: I can run galaxy-dist without problems and have been working with that (so its eggs are all installed already), but now I want to create a pull request so want to run galaxy-dist. oops, of course I mean 'so want to run galaxy-central.' -- Clare Sloggett Research Fellow / Bioinformatician Life Sciences Computation Centre Victorian Life Sciences Computation Initiative University of Melbourne, Parkville Campus 187 Grattan Street, Carlton, Melbourne Victoria 3010, Australia Ph: 03 903 53357 M: 0414 854 759 ___ 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] Local instance and storage space to provide
Hi Sarah- I'm sure others have experiences that could help, so I hope they will chime in. Nate put together some slides two years ago on production setups, including some architecture for the server main.g2.bx.psu.edu: http://wiki.g2.bx.psu.edu/Events/GDC2010?action=AttachFiledo=gettarget=GDC2010_building_scalable.pdf There is also a wiki page describing production environments: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server Again, I'm sure others have had different experiences with both more and less hardware on hand. Of course your mileage may vary based on the tools being used (which in your case I'm guessing is Tophat), the number of datasets that will need to be analyzed, and so on. I hope that helps! -Scott - Original Message - Dear all, To purchase equipment related to a local instance of Galaxy, I would like to have your feedback. Did you notice load problems when 10 to 20 users launch jobs at the same time and on a single instance of Galaxy, with mi-RNA or RNA seq data ? What do you recommend in terms of storage space, number of nodes, number of instances? Thank you in advance, Sarah Maman ___ 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] PBS Server Throwing Errors
Hi Dan- Thanks again for your great hospitality at UCI! It looks like you've done most of the sane things, and a quick check looks like the PBS egg is requesting protocol version 1 while the server supports protocol version 2. One possibility is that there is a protocol mismatch, which could be the result of using an old library. We can check if the egg is at fault first - try the following link for compiling the pbs_python.py egg yourself and try the example to see if the connection and a simple stats-gathering operation (the examples/pbsnodes-a.py script from pbs_python) works: https://subtrac.sara.nl/oss/pbs_python/wiki/TorqueInstallation -Scott - Original Message - Hi, Galaxy Community, Greetings from The University of Chicago; I hope all who attended the Galaxy conference enjoyed it as much as I did. I have searched the mailing list archives as well as Google to a resolve problem I am seeing, however I am somewhat at a loss as to the next course of action I should be taking to bring this issue to a close. I am hoping that one of the bright minds on this mailing list could help me shed some light on the solution to my problem, or at least help me identify a root cause. I have configured Galaxy to integrate with TORQUE (version 4.0.2) server, and successfully built the PBS python egg as specified in the Galaxy documentation. I am using Python version 2.6 and the latest build of Galaxy. Whenever I launch a job from the Galaxy UI, I get the following error message(s) on the PBS server: 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=AlternateUserAuthentication, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=QueueJob, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=Disconnect, from galaxy@ 07/30/2012 15:43:01;0002;PBS_Server;Svr;PBS_Server;Torque Server Version = 4.0.2, loglevel = 1 One thing I did notice, that suggests there might be a problem, is that there is no hostname after the galaxy@; most of the other messages in this log file have a host name appended to log entry, i.e.: 07/30/2012 15:43:38;0100;PBS_Server;Req;;Type StatusJob request received from root@sc01, sock=10 I have completed a tcpdump on the schedule node, and I can definitely see bi-directional traffic between the Galaxy server and the scheduler node on TCP port 15001. In addition to this, I have installed the TORQUE client tools on on the Galaxy server, and can spawn an interactive job with qsub -I, as well as check the status of queued jobs using qstat (from the Galaxy server). This suggests to me that there a potential problem with the PBS Egg, although I am not certain. Has anybody seen something like this before, or could somebody point me in the right direction? We do have a support contract with Adaptive Computing, and I am opening a ticket with them as well, however I wanted to reach out to the Galaxy community to cover all of my bases. Thank-you so much for taking the time to read my email. 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/ ___ 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] PBS Server Throwing Errors
I've been told by Galaxy folks to keep this on galaxy-dev. My apologies for any confusion. -Scott - Original Message - Hi Dan- Thanks again for your great hospitality at UCI! It looks like you've done most of the sane things, and a quick check looks like the PBS egg is requesting protocol version 1 while the server supports protocol version 2. One possibility is that there is a protocol mismatch, which could be the result of using an old library. We can check if the egg is at fault first - try the following link for compiling the pbs_python.py egg yourself and try the example to see if the connection and a simple stats-gathering operation (the examples/pbsnodes-a.py script from pbs_python) works: https://subtrac.sara.nl/oss/pbs_python/wiki/TorqueInstallation -Scott - Original Message - Hi, Galaxy Community, Greetings from The University of Chicago; I hope all who attended the Galaxy conference enjoyed it as much as I did. I have searched the mailing list archives as well as Google to a resolve problem I am seeing, however I am somewhat at a loss as to the next course of action I should be taking to bring this issue to a close. I am hoping that one of the bright minds on this mailing list could help me shed some light on the solution to my problem, or at least help me identify a root cause. I have configured Galaxy to integrate with TORQUE (version 4.0.2) server, and successfully built the PBS python egg as specified in the Galaxy documentation. I am using Python version 2.6 and the latest build of Galaxy. Whenever I launch a job from the Galaxy UI, I get the following error message(s) on the PBS server: 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=AlternateUserAuthentication, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=QueueJob, from galaxy@ 07/30/2012 15:42:48;0080;PBS_Server;Req;dis_request_read;conflicting version numbers, 1 detected, 2 expected 07/30/2012 15:42:48;0080;PBS_Server;Req;req_reject;Reject reply code=15058(Bad DIS based Request Protocol MSG=cannot decode message), aux=0, type=Disconnect, from galaxy@ 07/30/2012 15:43:01;0002;PBS_Server;Svr;PBS_Server;Torque Server Version = 4.0.2, loglevel = 1 One thing I did notice, that suggests there might be a problem, is that there is no hostname after the galaxy@; most of the other messages in this log file have a host name appended to log entry, i.e.: 07/30/2012 15:43:38;0100;PBS_Server;Req;;Type StatusJob request received from root@sc01, sock=10 I have completed a tcpdump on the schedule node, and I can definitely see bi-directional traffic between the Galaxy server and the scheduler node on TCP port 15001. In addition to this, I have installed the TORQUE client tools on on the Galaxy server, and can spawn an interactive job with qsub -I, as well as check the status of queued jobs using qstat (from the Galaxy server). This suggests to me that there a potential problem with the PBS Egg, although I am not certain. Has anybody seen something like this before, or could somebody point me in the right direction? We do have a support contract with Adaptive Computing, and I am opening a ticket with them as well, however I wanted to reach out to the Galaxy community to cover all of my bases. Thank-you so much for taking the time to read my email. 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/ ___ 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] egg distribution error when running galaxy-central
I haven't been able to reproduce this yet with the instructions you
gave, but I'm not using the same environment. Can you give me an idea
of what tools you're using outside of SciPy/NumPy/Enthought stuff?
There is the possibility that the virtualenv.py script isn't being
sourced correctly. We can check if it's actually using the correct
environment by calling echo $PATH and checking that the path is
pointing to the virtual environment. For example, I installed
virtualenv stuff under /home/smcmanus/clare/galaxy_env/bin, and
I got:
(galaxy_env)$ echo $PATH
/home/smcmanus/clare/galaxy_env/bin:/usr/local/bin:other stuff deleted
-Scott
- Original Message -
Hi all,
I'm trying to run galaxy-central on my laptop in order to play around
with some changes, and I'm having trouble getting it to run. I can
run
galaxy-dist without problems and have been working with that (so its
eggs are all installed already), but now I want to create a pull
request so want to run galaxy-dist. I'm not trying to install any
extra tools or data, just the code.
I'm running on OSX 10.7.4 and using virtualenv. I have Enthought
installed, and I assume I will be using its version of python by
default. The default python seems to be 2.7.3.
I'm using the same virtualenv environment for galaxy-dist and
galaxy-central (though it doesn't seem to matter if I give
galaxy-central its own environment, I see the same error). So the
steps were:
- create a virtualenv environment and activate it
- get galaxy-dist and call run.sh - it asked me to build quite a lot
of dependencies myself, which was just a matter of running the
requested commands, and then it worked with no problems.
- shut down galaxy-dist, and in another directory, get galaxy-central
and call run.sh. I think it asked me to build a couple of
dependencies, but then it gives up with the following:
(galaxy_env)Clares-MacBook-Pro:galaxy-central clare$ sh run.sh
--reload
Some eggs are out of date, attempting to fetch...
Warning: MarkupSafe (a dependent egg of Mako) cannot be fetched
Warning: pycrypto (a dependent egg of Fabric) cannot be fetched
Warning: simplejson (a dependent egg of WebHelpers) cannot be fetched
Fetched http://eggs.g2.bx.psu.edu/ssh/ssh-1.7.14-py2.7.egg
One of Galaxy's managed eggs depends on something which is missing,
this is almost certainly a bug in the egg distribution.
Dependency ssh requires pycrypto=2.1,!=2.4
Traceback (most recent call last):
File ./scripts/fetch_eggs.py, line 30, in module
c.resolve() # Only fetch eggs required by the config
File
/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py,
line 345, in resolve
egg.resolve()
File
/Users/clare/galaxy/galaxy-central/lib/galaxy/eggs/__init__.py,
line 168, in resolve
dists = pkg_resources.working_set.resolve( (
self.distribution.as_requirement(), ), env, self.fetch )
File
/Users/clare/galaxy/galaxy_env/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg/pkg_resources.py,
line 569, in resolve
raise VersionConflict(dist,req) # XXX put more info here
pkg_resources.VersionConflict: (ssh 1.7.14
(/Users/clare/galaxy/galaxy-central/eggs/ssh-1.7.14-py2.7.egg),
Requirement.parse('pycrypto=2.1,!=2.4'))
Fetch failed.
Any idea what is causing this?
Thanks,
Clare
--
Clare Sloggett
Research Fellow / Bioinformatician
Life Sciences Computation Centre
Victorian Life Sciences Computation Initiative
University of Melbourne, Parkville Campus
187 Grattan Street, Carlton, Melbourne
Victoria 3010, Australia
Ph: 03 903 53357 M: 0414 854 759
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Re: [galaxy-dev] [galaxy-user] Fwd: Local instance and storage space to provide
Sorry - I fouled up and should have kept this on galaxy-dev. -Scott - Original Message - I'm forwarding this to galaxy-user instead of galaxy-dev. -Scott - Forwarded Message - From: Scott McManus scottmcma...@gatech.edu To: Sarah Maman sarah.ma...@toulouse.inra.fr Cc: galaxy-dev@lists.bx.psu.edu Sent: Wednesday, August 1, 2012 4:18:29 PM Subject: Re: [galaxy-dev] Local instance and storage space to provide Hi Sarah- I'm sure others have experiences that could help, so I hope they will chime in. Nate put together some slides two years ago on production setups, including some architecture for the server main.g2.bx.psu.edu: http://wiki.g2.bx.psu.edu/Events/GDC2010?action=AttachFiledo=gettarget=GDC2010_building_scalable.pdf There is also a wiki page describing production environments: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server Again, I'm sure others have had different experiences with both more and less hardware on hand. Of course your mileage may vary based on the tools being used (which in your case I'm guessing is Tophat), the number of datasets that will need to be analyzed, and so on. I hope that helps! -Scott - Original Message - Dear all, To purchase equipment related to a local instance of Galaxy, I would like to have your feedback. Did you notice load problems when 10 to 20 users launch jobs at the same time and on a single instance of Galaxy, with mi-RNA or RNA seq data ? What do you recommend in terms of storage space, number of nodes, number of instances? Thank you in advance, Sarah Maman ___ 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/ ___ 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/ ___ 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] Strange Could not moveŠ. error
Ok - that makes sense. So the from_work_dir attribute is part of the tool's data element under outputs, and Jeremy fixed a timing issue. Thanks, Jeremy! -Scott - Original Message - Iry, This is probably an issue with using the from_work_dir attribute. Prior to changeset 524cfb8ca67d, the attribute didn't work when set_metadata_externally was True; 524cfb8ca67d modified the attribute implementation so that it works regardless of how metadata is set. This changeset is not in the most recent distribution, so you'll need to pull from -central if you want to use it immediately. Best, J. On Aug 2, 2012, at 12:24 PM, Iry Witham wrote: Hi Dev-Team, I am experiencing a strange error that I cannot replicate on two identical instances of my Galaxy server. I have a tool that runs fine on my test instance and fails on my development instance. The servers are identically configured and running the same build. The handler.log from the successful instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:31:07,881 (295) Working directory for job is: /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 galaxy.jobs.handler DEBUG 2012-08-02 11:31:07,881 dispatching job 295 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:31:08,083 (295) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) submitting file /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/pbs/295.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,382 (295) command is: perl /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1504.dat --ref /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1503.dat --genome-size 2716965481 --p-value 0.001 --bigger-window 1.5 --no-annotate --log2-threshold 0.6; cd /hpcdata/galaxy-test/galaxy-setup/galaxy-dist; /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/set_metadata.sh ./database/files /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295 . /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/universe_wsgi.ini /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/tmp/tmplTSKeF /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/galaxy.json /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_in_HistoryDatasetAssociation_689_Oh21hx,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_kwds_HistoryDatasetAssociation_689_xgxlZy,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_out_HistoryDatasetAssociation_689_H0claK,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_results_HistoryDatasetAssociation_689_rdQBs8,,/hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/metadata_override_HistoryDatasetAssociation_689_B0U0MV galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,395 (295) queued in default queue as 112605.scyld.localdomain galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:08,776 (295/112605.scyld.localdomain) PBS job state changed from N to R galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,117 (295/112605.scyld.localdomain) PBS job state changed from R to C galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:31:27,118 (295/112605.scyld.localdomain) PBS job has completed successfully galaxy.jobs DEBUG 2012-08-02 11:31:27,197 finish(): Moved /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/job_working_directory/000/295/cnv_seq_result.cnv to /hpcdata/galaxy-test/galaxy-setup/galaxy-dist/database/files/001/dataset_1555.dat as directed by from_work_dir galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,249 loading metadata from file for: HistoryDatasetAssociation 689 galaxy.jobs DEBUG 2012-08-02 11:31:27,382 job 295 ended galaxy.datatypes.metadata DEBUG 2012-08-02 11:31:27,382 Cleaning up external metadata files The same log from the failing instance shows the following: galaxy.jobs DEBUG 2012-08-02 11:54:29,234 (113) Working directory for job is: /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/job_working_directory/000/113 galaxy.jobs.handler DEBUG 2012-08-02 11:54:29,234 dispatching job 113 to pbs runner galaxy.jobs.handler INFO 2012-08-02 11:54:29,420 (113) Job dispatched galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) submitting file /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/database/pbs/113.sh galaxy.jobs.runners.pbs DEBUG 2012-08-02 11:54:29,669 (113) command is: perl /hpcdata/galaxy-dev/galaxy-setup/galaxy-dist/tools/jax_cnv/cnv-seq.pl --out-basename cnv_seq_result --test
Re: [galaxy-dev] Local Galaxy concept system: hardware spec questions
Hey Sebastian- It may help to consider other pieces aside from compute nodes that you will need, such as nodes for proxies and databases, networking gear (such as switches and cables), and so on. http://usegalaxy.org/production has some details, and there are high-level pieces explained at http://wiki.g2.bx.psu.edu/Events/GDC2010?action=AttachFiledo=gettarget=GDC2010_building_scalable.pdf You should also talk to your institution's IT folks about power requirements, how those costs passed on, off-site backup storage (though it sounds like you're counting on RAID 5/6), etc. It also may help if folks could share their experiences with benchmarking their own systems along with the tools that they've been using. The Galaxy Czars conference call could help - you could bring this up at the next meeting. I've answered inline, but in general I think that the bottleneck for your planned architecture will be I/O with respect to disk. The next bottleneck may be with respect to the network - if you have a disk farm with a 1 Gbps (125 MBps) connection, then it doesn't matter if your disks can write 400+ MBps. (Nate also included this in his presentation.) You may want to consider Infiniband over Ethernet - I think the Galaxy Czars call would be really helpful in this respect. 1. Using the described bioinformatics software: where are the potential system bottlenecks? (connections between CPUs, RAM, HDDs) One way to get a better idea is to start with existing resources, create a sample workflow or two, and measure performance. Again, the Galaxy czars call could be a good bet. 2. What is the expected relation of integer-based and floating point based calculations, which will be loading the CPU cores? This also depends on the tools being used. This might be more relevant if your architecture were to use more specialized hardware (such as GPUs or FPGAs), but this should be a secondary concern. 3. Regarding the architectural differences (strengths, weaknesses): Would an AMD- or an Intel-System be more suitable? I really can't answer which processor line is more suitable, but I think that having enough RAM per core is more important. Nate shows that main.g2.bx.psu.edu has 4 GB RAM per core. 4. How much I/O (read and write) can be expected at the memory controllers? Which tasks are most I/O intensive (regarding RAM and/or HDDs)? Workflows currently write all output to disk and read all input from disk. This gets back to previous questions on benchmarking. 5. Roughly separated in mapping and clustering jobs: which amounts of main memory can be expected to be required by a single job (given e.g. Illumina exome data, 50x coverage)? As far as I know mapping should be around 4 GB, clustering much more (may reach high double digits). Nate's presentation shows that main.g2.bx.psu.edu has 24 to 48 GB per 8 core reservation, and as before it shows that there is 4 GB per core. 6. HDD access (R/W) is mainly in bigger blocks instead of masses of short operations - correct? Again, this all depends on the tool being used and could help with some benchmarks. This question sounds like it's mostly related to choosing the filesystem - is that right? If so, then you may want to consider a compressing file system such as ZFS or BtrFS. You may also want to consider filesystems like Ceph or Gluster (now Red Hat). I know that Ceph can run on top of XFS and BtrFS, but you should look into BtrFS's churn rate - it might still be evolving quickly. Again, a ping to the Galaxy Czars call may help on any and possibly all of these questions. Good luck! -Scott ___ 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] code example for improved error handling
I'm writing documentation now - I'll have something this afternoon.
Sorry for the delay.
-Scott
- Original Message -
No, I call the executable directly from the xml. It kept failing
although it seemed to finish the job and I realized that on success
the executable prints a summary message to stderror, because it's
using stdout for the actual results so they can be pipped to another
command.
From the July news brief I understood that you can now add code to
the xml to check the stdout and std error for messages and I was
wondering if you have any documentation or sample code for that in
any published tool.
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete
Genomics, Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.com
From: John Patterson jmpa...@g.uky.edu
Date: Thursday, August 16, 2012 12:29 PM
To: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] code example for improved error handling
On 08/16/2012 03:02 PM, Birgit Crain wrote:
Hi
I'm writing a tools for an executable that writes results to stdout
and reports success message to stderr, so it really need the
improved error handling. Is there any sample code or documentation
available?
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist |
Complete
Genomics, Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.com
From: Nicole Rockweiler n.rockwei...@gmail.com
Date: Friday, July 20, 2012 10:53 AM
To: Brian Haas bh...@broadinstitute.org
Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] pipeline execution succeeds but galaxy
shows failure
Hi Brian,
A couple of days ago, smcmanus pushed the following change to the
repo:
Tools can now specify their own handling of stderr and stdout
regular
expressions as well as exit code ranges.
https://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to-use-return-codes-or-stderr-for-detecting-job
It looks like the documentation has yet to be written.
Hope this helps,
Nicole
On Fri, Jul 20, 2012 at 12:46 PM, Brad Chapman
chapm...@50mail.com
wrote:
Brian;
I wrote a pipeline (xml attached) that, from what I can gather,
succeeds, but galaxy shows it as an error and doesn't make the
output
file accessible as a new data set.
Is it possible the software is writing to standard error? Galaxy
doesn't
check status codes, but rather check for stderr and assumes that
output
indicates a problem. You can wrap the problematic programs with a
little
script to eat up stderr and check that everything is okay:
http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
Brad
From the server log, I can see that the command line is being
constructed correctly, and it even indicates that it's captured
the
output, but in the display of the web browser, it just shows up
in
the
error state. The script being run exits (0) on success. Any
ideas?
Here's what the output section of my xml file looks like:
outputs
data format=bam name=coordSortedBam label=${ tool.name }
on ${on_string}: coord-sorted read alignments
from_work_dir=alignment/alignment.coordSorted.bam/
/outputs
and here's what the server log states:
galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job
dispatched
galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453
executing:
alignReads.pl --target
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat
-o alignment --aligner bowtie --single
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat
--seqType fq
galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam
to
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat
as directed by from_work_dir
Again, as far as I can tell, everything worked - but the
browser
doesn't think so.
I've run the exact command above on the command-line, and it
exits(0)
indicating success.
Also, I've verified that when run through my galaxy instance,
the
galaxy-relocated output file is as expected.
Many thanks for your help. I'm still getting my feet wet with
galaxy, reading through all the documentation and searching the
mailing list for additional help.
best regards,
-brian
Re: [galaxy-dev] code example for improved error handling
Please see http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax .
There is a section for stdio, regex, and exit_code tag sets. The
documentation
applies to the latest galaxy-dist, though most of what's mentioned (aside from
updating
stdout and stderr with warning messages) is supported in galaxy-central.
(You can also use the fairly ugly URL
http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets
).
-Scott
- Original Message -
Hi
I'm writing a tools for an executable that writes results to stdout
and reports success message to stderr, so it really need the
improved error handling. Is there any sample code or documentation
available?
Thanks
Birgit Crain, Ph.D. | Sr. Professional Services Scientist | Complete
Genomics, Inc.
(650) 428-6023 office | (408) 605-3938 mobile
bcr...@completegenomics.com
From: Nicole Rockweiler n.rockwei...@gmail.com
Date: Friday, July 20, 2012 10:53 AM
To: Brian Haas bh...@broadinstitute.org
Cc: galaxy-...@bx.psu.edu galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] pipeline execution succeeds but galaxy
shows failure
Hi Brian,
A couple of days ago, smcmanus pushed the following change to the
repo:
Tools can now specify their own handling of stderr and stdout
regular
expressions as well as exit code ranges.
https://bitbucket.org/galaxy/galaxy-central/issue/325/allow-tool-authors-to-decide-whether-to-use-return-codes-or-stderr-for-detecting-job
It looks like the documentation has yet to be written.
Hope this helps,
Nicole
On Fri, Jul 20, 2012 at 12:46 PM, Brad Chapman chapm...@50mail.com
wrote:
Brian;
I wrote a pipeline (xml attached) that, from what I can gather,
succeeds, but galaxy shows it as an error and doesn't make the
output
file accessible as a new data set.
Is it possible the software is writing to standard error? Galaxy
doesn't
check status codes, but rather check for stderr and assumes that
output
indicates a problem. You can wrap the problematic programs with a
little
script to eat up stderr and check that everything is okay:
http://wiki.g2.bx.psu.edu/Future/Job%20Failure%20When%20stderr
Brad
From the server log, I can see that the command line is being
constructed correctly, and it even indicates that it's captured
the
output, but in the display of the web browser, it just shows up
in
the
error state. The script being run exits (0) on success. Any
ideas?
Here's what the output section of my xml file looks like:
outputs
data format=bam name=coordSortedBam label=${ tool.name }
on ${on_string}: coord-sorted read alignments
from_work_dir=alignment/alignment.coordSorted.bam/
/outputs
and here's what the server log states:
galaxy.jobs.handler INFO 2012-07-20 09:52:05,240 (30) Job
dispatched
galaxy.jobs.runners.local DEBUG 2012-07-20 09:52:05,453
executing:
alignReads.pl --target
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_26.dat
-o alignment --aligner bowtie --single
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_23.dat
--seqType fq
galaxy.jobs DEBUG 2012-07-20 09:52:16,673 finish(): Moved
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/job_working_directory/000/30/alignment/alignment.coordSorted.bam
to
/Users/bhaas/BioIfx/Galaxy/galaxy-dist/database/files/000/dataset_50.dat
as directed by from_work_dir
Again, as far as I can tell, everything worked - but the browser
doesn't think so.
I've run the exact command above on the command-line, and it
exits(0)
indicating success.
Also, I've verified that when run through my galaxy instance, the
galaxy-relocated output file is as expected.
Many thanks for your help. I'm still getting my feet wet with
galaxy, reading through all the documentation and searching the
mailing list for additional help.
best regards,
-brian
--
--
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
http://broad.mit.edu/~bhaas
tool id=alignreads name=alignReads version=0.0.1
descriptionalignReads: short read alignment tool
wrapper/description
requirements
requirement type=packagetrinity/requirement
/requirements
command
alignReads.pl --target $target -o alignment --aligner
$aligner_selection.aligner
## Inputs.
#if str($inputs.paired_or_single) == paired:
--left $inputs.left_input --right $inputs.right_input
#if $inputs.left_input.ext == 'fa':
--seqType fa
#else:
--seqType fq
#end if
#if str($inputs.library_type) != None:
--SS_lib_type $inputs.library_type
#end if
Re: [galaxy-dev] [galaxy-user] LimitInternalRecursion
It's the last rewrite rule that's causing the infinite recursion:
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
Check out this link:
http://httpd.apache.org/docs/current/mod/mod_rewrite.html#rewriterule
Look for the table of given rules and resulting substitutions - the proxying
appears to be supported for other hosts but not the same host.
-Scott
- Original Message -
Here is a copy of the whole VirtualHost section.
Thanks,
Adhemar
VirtualHost lbas046.cnptia.embrapa.br:443
ServerName lbas046.cnptia.embrapa.br
ErrorLog logs/galaxy_ssl_error_log
TransferLog logs/galaxy_ssl_access_log
LogLevel warn
SSLEngine on
SSLCertificateFile /etc/pki/tls/certs/lbas046.cnptia.embrapa.br.crt
SSLCertificateKeyFile
/etc/pki/tls/private/lbas046.cnptia.embrapa.br.key.insecure
SSLCACertificateFile /etc/pki/tls/certs/cacert.pem
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*)
/opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1
[L]
RewriteRule ^/galaxy/static/scripts/(.*)
/opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1
[L]
RewriteRule ^/galaxy/static/(.*)
/opt/bioinformatics/share/galaxy-central/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico
/opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt
/opt/bioinformatics/share/galaxy-central/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
Location /galaxy
AuthType Basic
AuthName Galaxy_pam
AuthPAM_Enabled on
Require valid-user
RewriteEngine On
RewriteCond %{LA-U:REMOTE_USER} (.+)
RewriteRule . - [E=RU:%1]
RequestHeader set REMOTE_USER %{RU}e env=RU
/Location
/VirtualHost
2012/8/22 Nate Coraor n...@bx.psu.edu
On Aug 21, 2012, at 4:44 PM, Adhemar wrote:
Hi,
There's this error message in my apache log:
[error] Request exceeded the limit of 10 subrequest nesting
levels
due to probable confguration error. Use 'LimitInternalRecursion'
to increase the limit if necessary. Use 'LogLevel debug' to get a
backtrace., referer: ...
When I turn the apache debug log on it also shows:
[debug] core.c(3072): r-uri = /galaxy/proxy:
http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/proxy:http://localhost:8080/root/history_item_updates
, referer: ...
It seems like mod_rewrite is somehow misconfigured, but I
couldb't
figure out what it is.
Here is my httpd.con mod_rewrite conf:
RewriteEngine on
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*)
/opt/bioinformatics/share/galaxy-central/static/june_2007_style/blue/$1
[L]
RewriteRule ^/galaxy/static/scripts/(.*)
/opt/bioinformatics/share/galaxy-central/static/scripts/packed/$1
[L]
RewriteRule ^/galaxy/static/(.*)
/opt/bioinformatics/share/galaxy-central/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico
/opt/bioinformatics/share/galaxy-central/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt
/opt/bioinformatics/share/galaxy-central/static/robots.txt [L]
RewriteRule ^/galaxy(.*) http://localhost:8080$1 [P]
Hi Adhemar,
I've moved this over to the galaxy-dev list since it's concerning a
local installation.
Are there any other RewriteRules defined? Are these directives
inside
another block, or just inside a VirtualHost? It would be useful
to
see your entire VirtualHost config.
--nate
Could you please help me to debug this?
Thank you,
Adhemar
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Re: [galaxy-dev] Galaxy with LSF scheduler
I haven't worked with an LSF cluster before, but it looks like it has DRMAA bindings. That means that you could try setting up a DRMAA galaxy runner : http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster -Scott - Original Message - Hello, Could you please tell me if it's possible to run Galaxy with an LSF scheduler, and if so, how? Thank you. ___ 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] Galaxy wiki is throwing errors during edit commit
I found that the problem happened if I used the UI for editing text. What I did instead was edit the wiki using the text-based mode instead. If you have set your preferences to use the UI for editing by default, then you will need to change it back to use the text-based editing instead; I found that, once I used the UI for editing text on the wiki, I couldn't save a set of changes. Let me know if that doesn't work. -Scott - Original Message - Hi Devs, The galaxy wiki is throwing error whenever I try to commit an edit change to it. I have attached a screenshot for your reference. Cheers Tomithy ___ 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] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)
I'll check it out. Thanks. - Original Message - Hi all (and in particular, Scott), I've just updated my development server and found the following error when running jobs on our SGE cluster via DRMMA: galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper finish method failed Traceback (most recent call last): File /mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py, line 371, in finish_job drm_job_state.job_wrapper.finish( stdout, stderr, exit_code ) File /mnt/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 1048, in finish if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): TypeError: check_tool_output() takes exactly 5 arguments (4 given) This looks to have been introduced in this commit: https://bitbucket.org/galaxy/galaxy-central/changeset/f557b7b05fdd701cbf99ee04f311bcadb1ae29c4#chg-lib/galaxy/jobs/__init__.py There should be an additional jobs argument, proposed fix: $ hg diff lib/galaxy/jobs/__init__.py diff -r 4007494e37e1 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Sep 18 09:40:19 2012 +0100 +++ b/lib/galaxy/jobs/__init__.py Tue Sep 18 10:06:44 2012 +0100 @@ -1045,7 +1045,8 @@ # Check what the tool returned. If the stdout or stderr matched # regular expressions that indicate errors, then set an error. # The same goes if the tool's exit code was in a given range. -if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): +job = self.get_job() +if ( self.check_tool_output( stdout, stderr, tool_exit_code, job ) ): task.state = task.states.OK else: task.state = task.states.ERROR (Let me know if you want this as a pull request - it seems a lot of effort for a tiny change.) Regards, 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/
Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)
I have to admit that I'm a little confused as to why you would be getting this error at all - the job variable is introduced at line 298 in the same file, and it's used as the last variable to check_tool_output in the changeset you pointed to. (Also, thanks for pointing to it - that made investigating easier.) Is it possible that there was a merge problem when you pulled the latest set of code? For my own sanity, would you mind downloading a fresh copy of galaxy-central or galaxy-dist into a separate directory and see if the problem is still there? (I fully admit that there could be a bug that I left in, but all job runners should have stumbled across the same problem - the finish method should be called by all job runners.) Thanks again! -Scott - Original Message - I'll check it out. Thanks. - Original Message - Hi all (and in particular, Scott), I've just updated my development server and found the following error when running jobs on our SGE cluster via DRMMA: galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper finish method failed Traceback (most recent call last): File /mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py, line 371, in finish_job drm_job_state.job_wrapper.finish( stdout, stderr, exit_code ) File /mnt/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 1048, in finish if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): TypeError: check_tool_output() takes exactly 5 arguments (4 given) This looks to have been introduced in this commit: https://bitbucket.org/galaxy/galaxy-central/changeset/f557b7b05fdd701cbf99ee04f311bcadb1ae29c4#chg-lib/galaxy/jobs/__init__.py There should be an additional jobs argument, proposed fix: $ hg diff lib/galaxy/jobs/__init__.py diff -r 4007494e37e1 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Sep 18 09:40:19 2012 +0100 +++ b/lib/galaxy/jobs/__init__.py Tue Sep 18 10:06:44 2012 +0100 @@ -1045,7 +1045,8 @@ # Check what the tool returned. If the stdout or stderr matched # regular expressions that indicate errors, then set an error. # The same goes if the tool's exit code was in a given range. -if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): +job = self.get_job() +if ( self.check_tool_output( stdout, stderr, tool_exit_code, job ) ): task.state = task.states.OK else: task.state = task.states.ERROR (Let me know if you want this as a pull request - it seems a lot of effort for a tiny change.) Regards, 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/ ___ 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] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)
Thanks, Jorrit! That was a good catch. Yes, it's a problem with the TaskWrapper. I'll see what I can do about it. -Scott - Original Message - Is it possible that you are looking at different classes? TaskWrapper's finish method does not use the job variable in my recently merged code either (line ~1045), while JobWrapper's does around line 315. cheers, jorrit On 09/18/2012 03:55 PM, Scott McManus wrote: I have to admit that I'm a little confused as to why you would be getting this error at all - the job variable is introduced at line 298 in the same file, and it's used as the last variable to check_tool_output in the changeset you pointed to. (Also, thanks for pointing to it - that made investigating easier.) Is it possible that there was a merge problem when you pulled the latest set of code? For my own sanity, would you mind downloading a fresh copy of galaxy-central or galaxy-dist into a separate directory and see if the problem is still there? (I fully admit that there could be a bug that I left in, but all job runners should have stumbled across the same problem - the finish method should be called by all job runners.) Thanks again! -Scott - Original Message - I'll check it out. Thanks. - Original Message - Hi all (and in particular, Scott), I've just updated my development server and found the following error when running jobs on our SGE cluster via DRMMA: galaxy.jobs.runners.drmaa ERROR 2012-09-18 09:43:20,698 Job wrapper finish method failed Traceback (most recent call last): File /mnt/galaxy/galaxy-central/lib/galaxy/jobs/runners/drmaa.py, line 371, in finish_job drm_job_state.job_wrapper.finish( stdout, stderr, exit_code ) File /mnt/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py, line 1048, in finish if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): TypeError: check_tool_output() takes exactly 5 arguments (4 given) This looks to have been introduced in this commit: https://bitbucket.org/galaxy/galaxy-central/changeset/f557b7b05fdd701cbf99ee04f311bcadb1ae29c4#chg-lib/galaxy/jobs/__init__.py There should be an additional jobs argument, proposed fix: $ hg diff lib/galaxy/jobs/__init__.py diff -r 4007494e37e1 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Sep 18 09:40:19 2012 +0100 +++ b/lib/galaxy/jobs/__init__.py Tue Sep 18 10:06:44 2012 +0100 @@ -1045,7 +1045,8 @@ # Check what the tool returned. If the stdout or stderr matched # regular expressions that indicate errors, then set an error. # The same goes if the tool's exit code was in a given range. -if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ): +job = self.get_job() +if ( self.check_tool_output( stdout, stderr, tool_exit_code, job ) ): task.state = task.states.OK else: task.state = task.states.ERROR (Let me know if you want this as a pull request - it seems a lot of effort for a tiny change.) Regards, 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/ ___ 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] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)
Ok - that change was made. The difference is that the change is applied to the task instead of the job. It's in changeset 7713:bfd10aa67c78, and it ran successfully in my environments on local, pbs, and drmaa runners. Let me know if there are any problems. Thanks again for your patience. -Scott - Original Message - On Tue, Sep 18, 2012 at 3:09 PM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Is it possible that you are looking at different classes? TaskWrapper's finish method does not use the job variable in my recently merged code either (line ~1045), while JobWrapper's does around line 315. cheers, jorrit Yes exactly (as per my follow up email sent just before yours ;) ) 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/
Re: [galaxy-dev] DRMAA: TypeError: check_tool_output() takes exactly 5 arguments (4 given)
Sorry - that's changeset 7714:3f12146d6d81 -Scott - Original Message - Ok - that change was made. The difference is that the change is applied to the task instead of the job. It's in changeset 7713:bfd10aa67c78, and it ran successfully in my environments on local, pbs, and drmaa runners. Let me know if there are any problems. Thanks again for your patience. -Scott - Original Message - On Tue, Sep 18, 2012 at 3:09 PM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Is it possible that you are looking at different classes? TaskWrapper's finish method does not use the job variable in my recently merged code either (line ~1045), while JobWrapper's does around line 315. cheers, jorrit Yes exactly (as per my follow up email sent just before yours ;) ) 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/ ___ 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] Setting error levels in stdio
You should be able to use the following: stdio exit_code range=1: / exit_code range=:0 / /stdio Square brackets are not supported in the range. However, note that many shells will not return an exit code that is less than 0. Instead, the lowest 8 bits (i.e., value mod 256) will be returned. So returning -1 will give you -1 mod 256 = 255, returning -2 will give -2 mod 256 = 254, and so on. This should be true, as far as I know, for Linux and OS X. That means that you should only need one such range to support not equal to 0 semantics (though your mileage may vary): exit_code range=1: There is the issue of supporting negated ranges such as not equal to 2. Another possibility is a set of comma-delimited ranges. I wanted to keep the syntax as simple as possible (but no simpler), put the functionality out there and then add whatever makes it significantly easier to use. Supporting all exit codes could be done with a single range, so it didn't seem as useful to add those ranges at the time. -Scott - Original Message - Hi all, Regarding https://bitbucket.org/galaxy/galaxy-central/issue/325 and the new stdio tag is described on the wiki here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax The wiki text is unclear - it suggests square brackets might be needed, but the example lacks them: 1 stdio 2 exit_code range=2 level=fatal description=Out of Memory / 3 exit_code range=3:5 level=warning description=Low disk space / 4 exit_code range=6: level=fatal description=Bad input dataset / 5 /stdio In particular the less-than syntax might be being miss-rendered by the wiki. I've tried this as a way to say non-zero (i.e. more than one, or less than zero), but had an error in the Galaxy log from this: stdio exit_code range=1: / exit_code range=://0 / /stdio 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/
Re: [galaxy-dev] Setting error levels in stdio
The wiki markup was also fixed. The // is not supported. -Scott - Original Message - My apologies: stdio exit_code range=1: / exit_code range=:-1 / /stdio Again, note that the second range will not be useful as OS X and Linux (or at least the distros I've used) will never return a value less than 0. Sorry. -Scott - Original Message - You should be able to use the following: stdio exit_code range=1: / exit_code range=:0 / /stdio Square brackets are not supported in the range. However, note that many shells will not return an exit code that is less than 0. Instead, the lowest 8 bits (i.e., value mod 256) will be returned. So returning -1 will give you -1 mod 256 = 255, returning -2 will give -2 mod 256 = 254, and so on. This should be true, as far as I know, for Linux and OS X. That means that you should only need one such range to support not equal to 0 semantics (though your mileage may vary): exit_code range=1: There is the issue of supporting negated ranges such as not equal to 2. Another possibility is a set of comma-delimited ranges. I wanted to keep the syntax as simple as possible (but no simpler), put the functionality out there and then add whatever makes it significantly easier to use. Supporting all exit codes could be done with a single range, so it didn't seem as useful to add those ranges at the time. -Scott - Original Message - Hi all, Regarding https://bitbucket.org/galaxy/galaxy-central/issue/325 and the new stdio tag is described on the wiki here: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax The wiki text is unclear - it suggests square brackets might be needed, but the example lacks them: 1 stdio 2 exit_code range=2 level=fatal description=Out of Memory / 3 exit_code range=3:5 level=warning description=Low disk space / 4 exit_code range=6: level=fatal description=Bad input dataset / 5 /stdio In particular the less-than syntax might be being miss-rendered by the wiki. I've tried this as a way to say non-zero (i.e. more than one, or less than zero), but had an error in the Galaxy log from this: stdio exit_code range=1: / exit_code range=://0 / /stdio 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/ ___ 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] Improved error logging in TaskWrapper
Thanks, Peter! Those are good suggestions. I'll look into it soon. -Scott - Original Message - Hi all, I've been running into some sporadic errors on our Cluster while using the latest development Galaxy, and the error handling has made this quite difficult to diagnose. For a user perspective, the jobs seem to run, get submitted to the cluster, and finish, and the data looks OK via the 'eye' view icon, but is red in the history with: 0 bytes An error occurred running this job: info unavailable Furthermore, the stdout and stderr via the 'info' icon are blank. For watching the log (and adding more diagnosis lines), what is happening is the job is being split and sent out to the cluster fine, and starts running. If one of the tasks fails (and this seems to be happening due to some sort of file system error on our cluster), Galaxy spots this, and kills the rest of the jobs. That's good. The problem is it fails to record any record of why the job died. This is my suggestion for now - it would be nice to go further and fill the info text show in the history peep as well?: $ hg diff diff -r 4de1d566e9f8 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Fri Sep 21 11:02:50 2012 +0100 +++ b/lib/galaxy/jobs/__init__.py Fri Sep 21 11:59:27 2012 +0100 @@ -1061,6 +1061,14 @@ log.error( stderr for job %d is greater than 32K, only first part will be logged to database % task.id ) task.stderr = stderr[:32768] task.command_line = self.command_line + +if task.state == task.states.ERROR: +# If failed, will kill the other tasks in this job. Record this +# task's stdout/stderr as should be useful to explain the failure: +job = self.get_job() +job.stdout = ((From one sub-task:)\n +task.stdout)[:32768] +job.stderr = ((From one sub-task:)\n +task.stderr)[:32768] + self.sa_session.flush() log.debug( 'task %d ended' % self.task_id ) Regards, 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/
Re: [galaxy-dev] Galaxy not recording return codes (error levels)
Just to be clear, whenever a tool's stdio rules are triggered there should be messages prepended to stdout and/or stderr. If a tool defines a stdio regular expression and the regular expression matches on stdout, a message should be prepended to stdout. However, these will be empty if tools without stdio sections fail (which is true for most tools at this time). What you're asking for is to include the return code in the history panel. It might make more sense to include this kind of information in the View Details (which you get by clicking on the job name and then clicking the i button). That way there's less clutter and it's still easy to get to failures (which hopefully aren't happening very often). What do you think? -Scott - Original Message - Dear all, Is there a plan to record the return code (error level) in the Galaxy Job history, along with the stdout and stderr strings? I would find this very useful - especially for situations where a job is killed (e.g. by the OS) and there is no indication of why it died (stderr is empty). 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/ ___ 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] Using an unique database for tow differents versions of Galaxy
Maybe a better question is why you would want two separate versions of galaxy running to begin with. There could be another way to solve your problem. -Scott - Original Message - The main problem with different versions of galaxy is that the database schema that they expect (as applied by versioned migrations from the galaxy codebase) is different. So you could end up working with a database that has fields and keys you aren't expecting, which would be bad. -Dannon On Sep 21, 2012, at 3:54 PM, Promita Bose boseprom...@gmail.com wrote: Perhaps I missed it but why 'Definitely not' ? If storage is a limiting factor/constraint, then may be worth attempting ... ? Promita On Fri, Sep 21, 2012 at 3:13 PM, James Taylor ja...@jamestaylor.org wrote: Definitely not. And please keep replies on the list. -- jt On Fri, Sep 21, 2012 at 1:50 PM, Chebbi Mohamed Amine chebbimam...@gmail.com wrote: Yes the two instances are of two different versions. So if I understand well there is no mean to do it like this ? Thanks 2012/9/21 James Taylor ja...@jamestaylor.org If the two different Galaxy instances are different *versions* of Galaxy, this is unlikely to work out well. -- jt On Fri, Sep 21, 2012 at 11:59 AM, Chebbi Mohamed Amine chebbimam...@gmail.com wrote: Hello Galaxy-team! I installed recently two differents versions of Galaxy and I would like to use the same database for the two instances without loosing data (histories, workflows etc..). Thank you in advance 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/ ___ 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/ -- MSc Promita Bose 404-408-9060 ___ 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/ ___ 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 not recording return codes (error levels)
Good - after taking a step back I thought it seemed better to leave everything null rather than guess at an exit code. Does anyone have any objections to adding an exit code column with null values for previously-executed jobs? -Scott - Original Message - Or allow the error code field to be null in the database (shown as blank or not available in the web interface). 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/
Re: [galaxy-dev] No module named controllers.library_common error on fresh Galaxy install from 4-Oct-2012
That's been fixed in a galaxy-central commit last night; the webapps were moved around, and this didn't point to the new webapps directory. See changeset 210c39f4bf7f or later. In particular, the problem you're seeing had to do with the templates/library/common/library_common.mako pointing to galaxy.web.controllers.library_common instead of galaxy.webapps.galaxy.controllers.library_common . A few other files had also been affected. -Scott - Original Message - I gave up on figuring out why jobs don't get started for 15 minutes and started a new instance of galaxy, but when I tried to create a new data library, I got this error... Error attempting to display contents of library (TEST DATA): No module named controllers.library_common. Any ideas? Thon ___ 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] Fwd: 'UsesFormDefinitions' is not defined
This was fixed in galaxy-central last week and should be part of galaxy-dist. What happened is that controllers were migrated and a couple of modules were left out. See changeset 210c39f4bf7f or later, which I believe was fixed on October 4th. In particular, the problem you're seeing had to do with the templates/library/common/library_common.mako pointing to galaxy.web.controllers.library_common instead of galaxy.webapps.galaxy.controllers.library_common. A few other files had also been affected. -Scott - Original Message - Hi Alex I am in the same situation, updating our galaxy servers to the Oct 5th release (changeset: 7824:b5bda7a5c345), and I have encountered the same problem. I guess, there are actually two problems: First problem - this happens with a fresh install: == I can't create a library at all, I get the following error message: Error attempting to display contents of library (foo): No module named controllers.library_common. There have been a few commits on library_common.py over the last few days, which might solve this problem.? Second problem - this happens after upgrading an existing installation == Like the situation you reported earlier this morning, I get: Error attempting to display contents of library (haruhotz): name 'UsesFormDefinitions' is not defined. I manage to track down the problem to the fact that in the old version, we've had ~/lib/galaxy/web/controllers/ which apparently has been replaced by ~/lib/galaxy/webapps/galaxy/controllers/ if I remove ~/lib/galaxy/web/controllers/ I get a new error: Error attempting to display contents of library (haruhotz): No module named library_common. which is very similar to the error you get with a fresh install Obviously, old stuff (ie ~/lib/galaxy/web/controllers/) is still used after the upgrade. Sorry, no solution yet, but maybe it helps the developers to track down the problem and help us getting the servers running again. Regards Hans-Rudolf On 10/18/2012 10:48 AM, Alexander Graf wrote: Hi, yesterday I updated Galaxy to the latest revision and now it is not possible to access any Data Libraries or to create a new one. Galaxy shows me a read box with following error message: *Error attempting to display contents of library (100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not defined.* The log file message is: /GET /galaxy/library_common/browse_library?sort=namewebapp=galaxyf-description=Allf-name=Allpage=1cntrller=libraryshow_item_checkboxes=falseasync=falseoperation=browseid=9d04ee723dc2cac7 HTTP/1.1 302 - http://x.x.x.x/galaxy/library/browse_libraries?status=erroruse_panels=Falsemessage=Error+attempting+to+display+contents+of+library+%100326_HWUSI-EAS632R_0002%29%3A+name+__sq__UsesFormDefinitions__sq__+is+not+defined.; Mozilla/5.0 (X11; Linux x86_64) / Any ideas how to solve this problem or were to start troubleshooting? Thank you in advance Alex ___ 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/ ___ 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] Fwd: 'UsesFormDefinitions' is not defined
Excuse me - I meant to say that this will part of the upcoming galaxy-dist. -Scott - Original Message - This was fixed in galaxy-central last week and should be part of galaxy-dist. What happened is that controllers were migrated and a couple of modules were left out. See changeset 210c39f4bf7f or later, which I believe was fixed on October 4th. In particular, the problem you're seeing had to do with the templates/library/common/library_common.mako pointing to galaxy.web.controllers.library_common instead of galaxy.webapps.galaxy.controllers.library_common. A few other files had also been affected. -Scott - Original Message - Hi Alex I am in the same situation, updating our galaxy servers to the Oct 5th release (changeset: 7824:b5bda7a5c345), and I have encountered the same problem. I guess, there are actually two problems: First problem - this happens with a fresh install: == I can't create a library at all, I get the following error message: Error attempting to display contents of library (foo): No module named controllers.library_common. There have been a few commits on library_common.py over the last few days, which might solve this problem.? Second problem - this happens after upgrading an existing installation == Like the situation you reported earlier this morning, I get: Error attempting to display contents of library (haruhotz): name 'UsesFormDefinitions' is not defined. I manage to track down the problem to the fact that in the old version, we've had ~/lib/galaxy/web/controllers/ which apparently has been replaced by ~/lib/galaxy/webapps/galaxy/controllers/ if I remove ~/lib/galaxy/web/controllers/ I get a new error: Error attempting to display contents of library (haruhotz): No module named library_common. which is very similar to the error you get with a fresh install Obviously, old stuff (ie ~/lib/galaxy/web/controllers/) is still used after the upgrade. Sorry, no solution yet, but maybe it helps the developers to track down the problem and help us getting the servers running again. Regards Hans-Rudolf On 10/18/2012 10:48 AM, Alexander Graf wrote: Hi, yesterday I updated Galaxy to the latest revision and now it is not possible to access any Data Libraries or to create a new one. Galaxy shows me a read box with following error message: *Error attempting to display contents of library (100326_HWUSI-EAS632R_0002): name 'UsesFormDefinitions' is not defined.* The log file message is: /GET /galaxy/library_common/browse_library?sort=namewebapp=galaxyf-description=Allf-name=Allpage=1cntrller=libraryshow_item_checkboxes=falseasync=falseoperation=browseid=9d04ee723dc2cac7 HTTP/1.1 302 - http://x.x.x.x/galaxy/library/browse_libraries?status=erroruse_panels=Falsemessage=Error+attempting+to+display+contents+of+library+%100326_HWUSI-EAS632R_0002%29%3A+name+__sq__UsesFormDefinitions__sq__+is+not+defined.; Mozilla/5.0 (X11; Linux x86_64) / Any ideas how to solve this problem or were to start troubleshooting? Thank you in advance Alex ___ 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/ ___ 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] Corner case in task splitter - merging zero files
Hey Peter-
Thanks - I'll look into it. If you're able to reproduce the problem easily
and wouldn't mind crafting a pull request, then it would be much
appreciated. Otherwise I'll put this on my to-do list to be done soon.
I or someone else may want to revisit the exception handling to prevent
that from happening.
Thanks!
-Scott
- Original Message -
Hi Scott,
Following some failing hard drives, I'm rebuilding our Galaxy server.
Something isn't quite right with our cluster integration yet, but it
has
exposed a problem in Galaxy's handling of task splitting - it can
sometimes attempt to merge zero files.
Here is my fix for the BLAST XML format (now in the ToolShed),
https://bitbucket.org/peterjc/galaxy-central/changeset/5cb6411bad19802ba4001a083164366b42850a48
Here's an example using the text format:
galaxy.jobs.splitters.multi ERROR 2012-10-18 16:26:21,330 Error
merging files
Traceback (most recent call last):
File
/mnt/galaxy/galaxy-central/lib/galaxy/jobs/splitters/multi.py,
line 133, in do_merge
output_type.merge(output_files, output_file_name)
File /mnt/galaxy/galaxy-central/lib/galaxy/datatypes/data.py,
line
545, in merge
raise Exception('Result %s from %s' % (result, cmd))
Exception: Result 2 from cat
/mnt/galaxy/galaxy-central/database/files/000/dataset_304.dat
The problem obviously is that while cat file1 ... fileN merged
will
work fine for one or more files, with no files it sits waiting for
stdin
(and from a user perspective stalls).
This logic error is in lib/galaxy/datatypes/data.py method merge,
which could either treat zero files as an error, or a no-op:
if len(split_files) == 1:
cmd = 'mv -f %s %s' % ( split_files[0], output_file )
else:
cmd = 'cat %s %s' % ( ' '.join(split_files),
output_file )
result = os.system(cmd)
I think this should be something like this:
if not split_files:
raise Exception('Asked to merge zero files')
elif len(split_files) == 1:
cmd = 'mv -f %s %s' % ( split_files[0], output_file )
else:
cmd = 'cat %s %s' % ( ' '.join(split_files),
output_file )
result = os.system(cmd)
It might also make sense to check for zero files in the code which
calls the merge, i.e. lib/galaxy/jobs/splitters/multi.py function
do_merge
I'm still investigating upstream how this comes about, one clue:
galaxy.jobs.runners.drmaa DEBUG 2012-10-18 16:25:01,930 (273/510)
state change: job is running
galaxy.jobs.runners.drmaa DEBUG 2012-10-18 16:25:03,040 (273/510)
state change: job finished, but failed
galaxy.jobs.runners.drmaa DEBUG 2012-10-18 16:25:03,074 Job output
not
returned from cluster
galaxy.jobs DEBUG 2012-10-18 16:25:03,074 task 641 for job 273 ended;
exit code: 0
galaxy.jobs DEBUG 2012-10-18 16:25:03,148 task 641 ended
galaxy.jobs.runners.tasks DEBUG 2012-10-18 16:25:05,169 execution
finished - beginning merge: tblastx -query
/mnt/galaxy/galaxy-central/database/files/000/dataset_127.dat -db
/var/local/blast/ncbi/nt -query_gencode 2 -evalue 0.001 -out
/mnt/galaxy/galaxy-central/database/files/000/dataset_304.dat
-outfmt 0 -num_threads 8
galaxy.jobs.splitters.multi DEBUG 2012-10-18 16:25:05,181 files []
If you would prefer that small suggestion as a pull request, let me
know.
Regards,
Peter
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Re: [galaxy-dev] Corner case in task splitter - merging zero files
Ok -it's in. Thanks again! I will add a to-do item to put output-merge messages into stdout so that they're more visible. -Scott - Original Message - Thanks, Peter! I'll get to it this afternoon EDT. -Scott - Original Message - On Thu, Oct 18, 2012 at 5:19 PM, Scott McManus scottmcma...@gatech.edu wrote: Hey Peter- Thanks - I'll look into it. If you're able to reproduce the problem easily and wouldn't mind crafting a pull request, then it would be much appreciated. Otherwise I'll put this on my to-do list to be done soon. I or someone else may want to revisit the exception handling to prevent that from happening. Thanks! -Scott OK then: https://bitbucket.org/galaxy/galaxy-central/pull-request/78/avoid-stall-when-merging-zero-files-fao/diff I can explain what was happening: We had a mount problem. The Galaxy server could talk to SGE and submit jobs, but when the jobs came to run the mount providing their home directory and the Galaxy file system was down, so they failed. Naturally this meant Galaxy got no output files back. Reading the code, you deliberately attempt to merge any files present (e.g. if 9 out of 10 come back). That does make sense as it could be instructive (as long as it is flagged as an error, which doesn't seem to be happening). I think getting zero files back from the split-jobs ought to be an error condition. In fact, failing to get all the expected sub-files back should also be an error condition (although it is still nice to do the merge so the user can see the partial output). I think a little re-factoring might be needed to treat these explicitly as errors. Regards, 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/ ___ 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] Failed to run display.py
Hi Tom- Are you still having this problem? If so, then could you try your request again and return what you're seeing from the console's logging output for that request? If not, then anything that you may have done to get around this problem would be appreciated. -Scott - Original Message - Hi Dannon, Thanks for the reply. Galaxy is running - I just typed http://localhost:8080 on the browser and I get the galaxy with the line: Hello world! It's running... Tom. On Sun, Oct 21, 2012 at 3:55 PM, Dannon Baker dannonba...@me.com wrote: On Oct 21, 2012, at 6:11 AM, Tom Hait sth...@gmail.com wrote: so I tried to change the URL to: http://localhost:8080 , http://127.0.0.1:8080 ... It also didn't work. Any Ideas about could go wrong? First thing I'd check would be to verify that your galaxy server is currently running, and on localhost:8080. -Dannon ___ 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] Think I found a bug
That sounds perfectly reasonable. I'll make the change. Thanks, Juan! -Scott - Original Message - Hi galaxy devs, We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step Traceback (most recent call last): File /usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py, line 298, in monitor self.monitor_step() File /usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py, line 341, in monitor_step self.dispatcher.stop( job ) File /usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py, line 438, in stop self.job_runners[runner_name].stop_job( job ) File /usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 180, in stop_job if job.get_external_output_metadata(): AttributeError: 'Job' object has no attribute 'get_external_output_metadata' By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added: class Job( object ): ... def get_external_output_metadata( self ): return None ... In this file: https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f6a8ba122d253/lib/galaxy/__init__.py?at=default Do you think this fix is correct, or is it a potential problem? Also, sorry I sent you through this channel, I couldn't find the way of reporting this on BitBucket. Regards, -- Juan González-Vallinas PhD Student Regulatory Genomics Group Research Unit in Biomedical Informatics (GRIB) Universitat Pompeu Fabra (UPF) Barcelona Spain (Currently @ UPenn) ___ 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] Syntax error (!) in latest pull?!
Well, lib/galaxy/datatypes/registry.py hasn't changed in over two months. Out of curiousity, I tried downloading a fresh copy of galaxy-central (without any initial configuration or database, either) and didn't encounter the same problem. I even tried messing with that line of code and didn't have any luck reproducing the same traceback. What version of python are you using? -Scott - Original Message - Got this in the latest pull of galaxy central... Ideas? Traceback (most recent call last): File ./scripts/set_metadata.py, line 24, in ? import galaxy.model.mapping #need to load this before we unpickle, in order to setup properties assigned by the mappers File /mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/model/__init__.py, line 13, in ? import galaxy.datatypes.registry File /mnt/ngs/analysis/svcgalaxy/galaxy-central/lib/galaxy/datatypes/registry.py, line 145 finally: ^ SyntaxError: invalid syntax ___ 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] Think I found a bug
It should have been fixed yesterday - if a job is running locally and the user cancels it, then the job will be stopped immediately. Thanks, Juan! -Scott - Original Message - Ok, thanks for the response! On 6 November 2012 12:50, Dannon Baker dannonba...@me.com wrote: Hi Juan, Thanks for reporting this, it is indeed a bug. The fix below isn't quite correct (if there is an external metadata job, we do actually want to terminate it) but I'll take care of it. For reporting bugs in the future, certainly feel free to message this list or you can also file an issue using http://galaxyproject.org/trello Thanks! -Dannon On Nov 6, 2012, at 11:54 AM, Juan González-Vallinas juanramongvalli...@gmail.com wrote: Hi galaxy devs, We are in the final stages of deploying a new Galaxy instance. We downloaded the galaxy-dist version a month ago aprox. We realized that, when launching a job and deleting it in the middle of the execution (hitting the Delete button in the history bar) will output the following error in the logger: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 Stopping job 45: galaxy.jobs.handler DEBUG 2012-11-05 15:56:33,537 stopping job 45 in local runner galaxy.jobs.handler ERROR 2012-11-05 15:56:33,538 Exception in monitor_step Traceback (most recent call last): File /usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py, line 298, in monitor self.monitor_step() File /usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py, line 341, in monitor_step self.dispatcher.stop( job ) File /usr/local/www/galaxy-dist/lib/galaxy/jobs/handler.py, line 438, in stop self.job_runners[runner_name].stop_job( job ) File /usr/local/www/galaxy-dist/lib/galaxy/jobs/runners/local.py, line 180, in stop_job if job.get_external_output_metadata(): AttributeError: 'Job' object has no attribute 'get_external_output_metadata' By copying the definition of get_external_output_data from the Task class into the Job class, we fixed the problem and now the jobs are terminated successfully. This is the code I added: class Job( object ): ... def get_external_output_metadata( self ): return None ... In this file: https://bitbucket.org/galaxy/galaxy-central/src/9d6a61f060d359a0289b3163990f6a8ba122d253/lib/galaxy/__init__.py?at=default Do you think this fix is correct, or is it a potential problem? Also, sorry I sent you through this channel, I couldn't find the way of reporting this on BitBucket. Regards, -- Juan González-Vallinas PhD Student Regulatory Genomics Group Research Unit in Biomedical Informatics (GRIB) Universitat Pompeu Fabra (UPF) Barcelona Spain (Currently @ UPenn) ___ 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/___ 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] Can't edit galaxy workflow
Make sure that you are pulling from galaxy-central and not galaxy-dist. I believe something like: hg pull -r rev# -u http://bitbucket.org/galaxy/galaxy-central should work. The problem may be that you are pointing to galaxy-dist by default, which will not know about that revision (yet). -Scott - Original Message - Thanks a lot Dannon, for your reply. But hg keeps saying following when I try to pull: abort: unknown revision '5013377e0bf7'! Is there any other way of manually getting it? (Sorry, I'm not an expert on those new SCMs) Sanjar. On 11/13/2012 06:33 PM, Dannon Baker wrote: Sanjar, This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time. -Dannon On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote: I tried to reply to similar posts, but couldn't figure out how to do it. So posting again: Galaxy giving this error when editing workflow, just after creating workflow from existing history: URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e_=1352817462148 Module weberror.evalexception.middleware:364 in respond app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:258 in get_tooltip return self.tool.help.render( static_path=static_path ) AttributeError: 'NoneType' object has no attribute 'render' Could anyone help me to solve this problem? Thanks, Sanjar. ___ 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/ ___ 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] Can't edit galaxy workflow
Bitbucket will only show the first 7 characters when browsing through commits. Try this: https://bitbucket.org/galaxy/galaxy-central/changeset/5013377e0bf7a656ea593098f1d1b38f3d6928c6 -Scott - Original Message - Hi, Can you please send the entire link to access this changeset? I keep searching for 5013377e0bf7 but can not find it. Thanks in advance, Liisa From: Dannon Baker dannonba...@me.com To: Sanjarbek Hudaiberdiev hudai...@icgeb.org Cc: galaxy-...@bx.psu.edu Date: 13/11/2012 12:34 PM Subject: Re: [galaxy-dev] Can't edit galaxy workflow Sent by: galaxy-dev-boun...@lists.bx.psu.edu Sanjar, This is fixed as of 5013377e0bf7. This may not be in the next distribution, but will be in the one after that. Of course, you can manually pull the change from galaxy-central at any time. -Dannon On Nov 13, 2012, at 9:45 AM, Sanjarbek Hudaiberdiev hudai...@icgeb.org wrote: I tried to reply to similar posts, but couldn't figure out how to do it. So posting again: Galaxy giving this error when editing workflow, just after creating workflow from existing history: URL: http://localhost/galaxy/workflow/load_workflow?id=df7a1f0c02a5b08e_=1352817462148 Module weberror.evalexception.middleware:364 in respond app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ environ, self.app) Module paste.wsgilib:539 in intercept_output app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ body = method( trans, **kwargs ) Module galaxy.web.framework:73 in decorator return simplejson.dumps( func( self, trans, *args, **kwargs ) ) Module galaxy.webapps.galaxy.controllers.workflow:733 in load_workflow 'tooltip': module.get_tooltip( static_path=url_for( '/static' ) ), Module galaxy.workflow.modules:258 in get_tooltip return self.tool.help.render( static_path=static_path ) AttributeError: 'NoneType' object has no attribute 'render' Could anyone help me to solve this problem? Thanks, Sanjar. ___ 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/ ___ 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/
