April 2014 - galaxy-dev - lists.galaxyproject.org

Re: [galaxy-dev] Job execution order mixed-up
by Jean-Francois Payotte 04 Jul '14

04 Jul '14

Hi John, Thank you for your answer and for trying to help. This is greatly appreciated! I didn't really made any progress in tracking down this error, and hopefully this weird behaviour will not happen anymore with the November 4th, distribution. But here are my answers to your questions, in case it would ring a bell: Has this behaviour been reported with any other workflow? It has been reported with 2 different workflows as of now. These 2 workflows doesn't have anything in common, except that they are huge (one of them has 37 steps, producing a total of about 110 datasets). Are you running Galaxy as a single process or multiple processes? If multiple processes, how many web, handler and manager processes do you have and are they all on the same machine? We are running Galaxy in multiple processes with 5 web servers, 3 job handlers and no manager (I believe the manager was rendered obsolete in one of the latest Galaxy distributions). All these processes are run on the same machine. Have you made any modifications to Galaxy that could result in this behaviour? No. What is the value of track_jobs_in_database in your universe_wsgi.ini configuration file? We never touched this part of the configuration file and the line still reads: "#track_jobs_in_database = None". After reading your answer, I've decided to modify this line to: "track_jobs_in_database = True" Unfortunately, running one of the faulty workflows several times (5x), I noticed that one of them was still showing this strange behaviour where some jobs were executed before their inputs were ready. Do you think this issue could be related to the fact that we are using Galaxy with the multiple processes configuration? We implemented this configuration some time ago because some of our users were complaining about the slow responsiveness of the web interface. Would you recommend using Galaxy without the multiple processes configuration? (Lets say if updating to November 4th distribution doesn't fix this issue) I guess you are probably using the multiple processes configuration as well on Galaxy main? Thanks again for your help! Jean-François ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Posted by John Chilton on Nov 09, 2013; 2:50pm Hello Jean-François, Have you made any progress tracking down this error? This appears very serious, but to tell you the truth I have no clue what could cause it. The distribution you are using is pretty old at this point I feel like if it was a bug the exhibited under relatively standard parameter combinations someone else would have reported it by now. Can you tell me some things: has this been reported with any other workflows? Is there anything special about this workflow? Can you rebuild the workflow and see if the error occurs again? Additional questions if the problem is not restricted to the workflow: are you running Galaxy as a single process or multiple processes? If multiple processes, how many web, handler, and manager processes do you have? Are they all on the same machine? Have you made any modifications to Galaxy that could result in this behavior? What is the value of track_jobs_in_database in your universe_wsgi.ini configuration file? -John On Thu, Nov 7, 2013 at 10:34 AM, Jean-Francois Payotte <[hidden email]> wrote: Dear Galaxy mailing-list, Once again I come seeking for your help. I hope someone already had this issue or will have an idea on where to look to solve it. :) One of our users reported having workflows failing because some steps were executed before all their inputs where ready. You can find a screenshot attached, where we can see that step (42) "Sort on data 39" has been executed while step (39) is still waiting to run (gray box). This behaviour has been reproduced with at least two different Galaxy tools (one custom, and the sort tool which comes standard with Galaxy). This behaviour seems to be a little bit random, as running two times a workflow where this issue occurs, only one time did some steps were executed in the wrong order. I could be wrong, but I don't think this issue is grid-related as, from my understanding, Galaxy is not using SGE job dependencies functionality. I believe all jobs stays in some internal queues (within Galaxy) until all input files are ready, and only then the job is submitted to the cluster. Any help or any hint on what to look at to solve this issue would be greatly appreciated. We have updated our Galaxy instance to August 12th distribution on October 1st, and I believe we never experienced this issue before the update. Many thanks for your help, Jean-François

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Sort error while running Cuffdiff
by TD 01 Jul '14

01 Jul '14

Hi All -- I'm a novice when it comes to all things programming, but I recently installed my own instance of Galaxy because I'm working with very large datasets. Everything seems to be running OK, but when I attempt to run Cuffdiff (w/ ref. annotation and bias correction from UCSC genome) on output from Tophat2, I get the following error: "*Error: sort order of reads in BAMs must be the same*." I'm perplexed, because I downloaded this output from Tophat2 that I ran on the public server, before putting it through Cuffdiff on my local instance. When I tried running the same files (prior to download) in Cuffdiff on the public server, they ran just fine. So, why do the files run properly when I run them publicly, but not locally? Am I missing some metadata? Is my install not complete? Does the ordering of bam files change when you download them? I've had a hard time finding solutions, so any tips are greatly appreciated. Cheers!

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Announcement: Galaxy Docker builds
by Björn Grüning 20 Jun '14

20 Jun '14

Dear Galaxy Devs and Users, I'm pleased to announce the Galaxy Docker Image project! The Galaxy Docker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features. One of the main goals is to make the access to entire tool suites as easy as possible. Usually, this includes the setup of a public available webservice that needs to be maintained, or that the Tool-user needs to either setup a Galaxy Server by its own or to have Admin access to a local Galaxy server. With docker, tool developers can create their own Image with all dependencies and the user only needs to run it within docker. Ideally suited to make your reviewers happy :) Currently, I have three test images to play with. The first one, bgruening/galaxy-stable is the main Image that will do all the heavy lifting of setting up PostgreSQL, Apache and Galaxy. bgruening/deepTools and bgruening/chemicaltoolbox are proof of concepts how easy it is to create an own Image build on top of the main Galaxy Image. https://index.docker.io/u/bgruening/galaxy-deeptools/ https://index.docker.io/u/bgruening/galaxy-chemicaltoolbox/ How to use it: docker run -d -p 8080:80 bgruening/galaxy-deeptools docker run -d -p 8080:80 -p 8000:8000 bgruening/galaxy-chemicaltoolbox For a more detailed description please read: https://github.com/bgruening/docker-recipes/tree/master/galaxy I would be very much interested in any kind of feedback. Especially, in two technical questions: I'm not sure if a "trusted build" from the docker index is the best way to go. Trusted Builds in docker are super convenient. It is a post-commit hook from github. Every time something is pushed, the image will be rebuild. The problem is that I can't tag my images with "trusted builds" and unless I have missed something, that forces me to create new repositories every time a new Galaxy release is out. A better way would be, one repository with different tags: galaxy-stable, galaxy-feb-2014 and so on. Every Galaxy release will be just a diff between the old and the new. But this is not possible with "trusted builds". One other trick I used is to remove the mercurial history, that saves 180MB. I'm not sure if this is wise, because it probably kills a few use cases. Currently, the aim of this project is a little bit different from being a developer environment. So I decided to remove it. Please ping me if this was a bad decision :) Thanks for reading! Bjoern

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Using Mesos to Enable distributed computing under Galaxy?
by Kyle Ellrott 17 Jun '14

17 Jun '14

I think one of the aspects where Galaxy is a bit soft is the ability to do distributed tasks. The current system of split/replicate/merge tasks based on file type is a bit limited and hard for tool developers to expand upon. Distributed computing is a non-trival thing to implement and I think it would be a better use of our time to use an already existing framework. And it would also mean one less API for tool writers to have to develop for. I was wondering if anybody has looked at Mesos ( http://mesos.apache.org/) You can see an overview of the Mesos architecture at https://github.com/apache/mesos/blob/master/docs/Mesos-Architecture.md The important thing about Mesos is that it provides an API for C/C++, Java/Scala and Python to write distributed frameworks. There are already implementations of frameworks for common parallel programming systems such as: - Hadoop (https://github.com/mesos/hadoop) - MPI ( https://github.com/apache/mesos/blob/master/docs/Running-torque-or-mpi-on-m… ) - Spark (http://spark-project.org) And you can find example Python framework at https://github.com/apache/mesos/tree/master/src/examples/python Integration with Galaxy would have three parts: 1) Add a system config variable to Galaxy called 'MESOS_URL' that is then passed to tool wrappers and allows them to contact the local mesos infrastructure (assuming the system has been configured) or pass a null if the system isn't available. 2) Write a tool runner that works as a mesos framework to executes single cpu jobs on the distributed system. 3) For instances where mesos is not available at a system wide level (say they only have access to an SGE based cluster), but the user wants to run distributed jobs, write a wrapper that can create a mesos cluster using the existing queueing system. For example, right now I run a Mesos system under the SGE queue system. I'm curious to see what other people think. Kyle

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Docker based tools
by Kyle Ellrott 07 Jun '14

07 Jun '14

I know a few people have talked about using docker to package and distribute Galaxy tools. The most recent version now runs on all major linux distributions, so it's a bit more inclusive now (but there probably won't ever be a windows or mac version). One strategy would be for tool configs to define an option Docker archive name and possibly an alternate command line to execute if the docker archive is being used. How far has that work gotten, and what are people thinking about it? Kyle

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Old Tool Shed URL http://community.g2.bx.psu.edu/ dead
by Peter Cock 28 May '14

28 May '14

Hello all, Either I made a typo in some old README files, or the old URL for the Tool Shed http://community.g2.bx.psu.edu/ has stopped working. Could this redirect to the current Tool Shed address http://toolshed.g2.bx.psu.edu/ please? Thanks, Peter

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user specific access/options
by Jennifer Jackson 19 May '14

19 May '14

Hi Petr, I am going to forward your email to the galaxy-dev list so that the development community can offer comments/suggestions. Best, Jen Galaxy team On 8/30/11 2:27 AM, Petr Novak wrote: > Hi everybody, > I am developing the application on Galaxy server. One of the requirement > is to create user specific list of options. Is it possible to access > somehow $__user_email__ in <options> tag or in <conditional> ?. I did > not found documentation how to used cheetah in galaxy tool xml files but > from files provided with galaxy, cheetah is used only in <command> and > <config> tag. Is that rigth? If it can be used in any part of xml > definition file it would make much easier to generate xml dynamicaly > based on the $__user_email__ > Does anybody have an idea how to manage this problem? > Petr Novak > > > ___________________________________________________________ > 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support

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Get the user credentials from the tool.
by Dmitry 19 May '14

19 May '14

Hello, Is there any way to provide a protected resource link to the external application? My tool is supposed to call a Web service via SSL which should access to the Galaxy resources. In ideal it would be something like ftp://user:password@mygalaxy.net/fasta.gz The Web service then downloads the resource and do the computation. Since user is already provided the login to galaxy, I do not want to ask the password again on a tool page. Sincerely, Dmitry

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Default value for data_column not working?
by Peter Cock 14 May '14

14 May '14

Hi all, I'm trying to write a new tool working with tabular data (specifically a Reciprocal Best Hits (RBH) tool using BLAST style tabular output). I want the user to be able to choose a column number (from one of the input files), but I have a default column in mind. However, Galaxy doesn't seem to obey the default column number: <inputs> <param name="a_vs_b" type="data" format="tabular" label="Hits from querying A against B" description="Tabular file, e.g. BLAST output" /> <param name="b_vs_a" type="data" format="tabular" label="Hits from querying B against A" description="Tabular file, e.g. BLAST output" /> <param name="id1" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="1" label="Column containing query ID" help="This is column 1 in standard BLAST tabular output" /> <param name="id2" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="2" label="Column containing match ID" help="This is column 2 in standard BLAST tabular output"/> <param name="score" type="data_column" data_ref="a_vs_b" multiple="False" numerical="False" value="12" label="Column containing containing score to rank on" help="The bitscore is column 12 in standard BLAST tabular output"/> </inputs> I've tried giving the default column value numerically (as shown), and also using value="c2" etc. Regardless, Galaxy just defaults to the first column. Is this a bug, or am I doing something wrong? Thanks, Peter

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history item status not updating
by Robert Baertsch 12 May '14

12 May '14

I submitted a workflow that in turn submits a drm job to sun grid engine. The queue had an error (probably due to a problem with automount). Traceback (most recent call last): File "/inside/depot4/galaxy/lib/galaxy/jobs/runners/__init__.py", line 60, in run_next method(arg) File "/inside/depot4/galaxy/lib/galaxy/jobs/runners/drmaa.py", line 169, in queue_job external_job_id = self.ds.runJob(jt) File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/__init__.py", line 331, in runJob _h.c(_w.drmaa_run_job, jid, _ct.sizeof(jid), jobTemplate) File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/helpers.py", line 213, in c return f(*(args + (error_buffer, sizeof(error_buffer)))) File "/inside/depot4/galaxy/eggs/drmaa-0.4b3-py2.7.egg/drmaa/errors.py", line 90, in error_check raise _ERRORS[code-1]("code %s: %s" % (code, error_buffer.value)) DeniedByDrmException: code 17: error: no suitable queues When the sysadmin cleared the error, the job started running normally after being in an error state for 10 minutes. The cool thing is that galaxy kept running without a problem. galaxy.jobs.runners.drmaa DEBUG 2013-06-27 14:51:22,968 (10481/4767487) state change: job is running galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:23,628 (10481/4767487) state change: job is queued and active galaxy.jobs.runners.drmaa DEBUG 2013-06-27 15:00:27,751 (10481/4767487) state change: job is running However in the history panel, the job shows as queued but not running, even if I refresh the history panel. Is this normal or should the status change to running? I'm using this version of straight galaxy: changeset: 10162:f295092476c7 branch: stable parent: 10160:2efb1083676b user: Dannon Baker <dannonbaker(a)me.com> date: Sat Jun 15 09:08:09 2013 -0400 summary: Fix reports import issue reported by Lance, https://trello.com/card/bug-in-reports-webapp-imports/506338ce32ae458f6d15e… -Robert Baertsch UC Santa Cruz

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