Re: [galaxy-dev] Server stops itself
On Jan 11, 2013, at 4:49 AM, Rémy Dernat wrote: Hi Nate, Could you push these patch on the galaxy-dist repository ? Hi Rémy, Unfortunately, this change just missed the cutoff for today's galaxy-dist, so it will have to wait for the next one, which should be in two weeks. You are welcome to pull directly from galaxy-central, if you'd like. --nate Thanks, Regards 2013/1/11 Rémy Dernat remy...@gmail.com Hi Nate, Could you push these patch on the galaxy-dist repository ? Thanks, Regards ___ 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 runner weirdness
Hello, Can you please post the link to this patch? I do not see it in the mail thread and I too have noticed some issues with the DRMAA job running since updating to the Oct. 23rd distribution. I don't know if it is related yet but I'd like to try the patch to see. I have two local instances of Galaxy (prod and dev). On my dev instance (which is fully up to date), when I run the same job multiple times, sometimes it finishes and sometimes it dies, this is independent of which node it runs on. My prod instance is still at the Oct. 03 distribution and does not experience this problem. So I am afraid to update our production instance. Thanks in advance, Liisa From: Kyle Ellrott kellr...@soe.ucsc.edu To: Nate Coraor n...@bx.psu.edu Cc: galaxy-dev@lists.bx.psu.edu galaxy-dev@lists.bx.psu.edu Date: 10/01/2013 07:44 PM Subject:Re: [galaxy-dev] DRMAA runner weirdness Sent by:galaxy-dev-boun...@lists.bx.psu.edu I did a merge of galaxy-central that included the patch you posted today. The scheduling problem seems to have gone away. Although I'm still getting back 'Job output not returned from cluster' for errors. This seems odd, as the system previously would output stderr correctly. Kyle On Thu, Jan 10, 2013 at 8:30 AM, Nate Coraor n...@bx.psu.edu wrote: On Jan 9, 2013, at 12:18 AM, Kyle Ellrott wrote: I'm running a test Galaxy system on a cluster (merged galaxy-dist on Janurary 4th). And I've noticed some odd behavior from the DRMAA job runner. I'm running a multithread system, one web server, one job_manager, and three job_handlers. DRMAA is the default job runner (the command for tophat2 is drmaa://-V -l mem_total=7G -pe smp 2/), with SGE 6.2u5 being the engine underneath. My test involves trying to run three different Tophat2 jobs. The first two seem to start up (and get put on the SGE queue), but the third stays grey, with the job manager listing it in state 'new' with command line 'None'. It doesn't seem to leave this state. Both of the jobs that actually got onto the queue die (reasons unknown, but much to early, probably some tophat/bowtie problem), but one job is listed in error state with stderr as 'Job output not returned from cluster', while the other job (which is no longer in the SGE queue) is still listed as running. Hi Kyle, It sounds like there are bunch of issues here. Do you have any limits set as to the number of concurrent jobs allowed? If not, you may need to add a bit of debugging information to the manager or handler code to figure out why the 'new' job is not being dispatched for execution. For the 'error' job, more information about output collection should be available from the Galaxy server log. If you have general SGE problems this may not be Galaxy's fault. You do need to make sure that the stdout/stderr files are able to be properly copied back to the Galaxy server upon job completion. For the 'running' job, make sure you've got 'set_metadata_externally = True' in your Galaxy config. --nate Any ideas? Kyle ___ 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/
[galaxy-dev] macs error for chipseq data
Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: Hi Jen, Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out. It seems to me that MACS was installed What is the issue? Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer, Thanks for the information on MACS tools. Yes, I forgot to mention that I used bowtie mapped files as the input. Thank you very much, Kathryn ** *From:*Jennifer Jackson [mailto:j...@bx.psu.edu] *Sent:* Friday, January 11, 2013 3:48 AM *To:* Sun, Wenping [USA] *Cc:* galaxy-u...@bx.psu.edu *Subject:* [External] Re: [galaxy-user] macs error for chipseq data Hello Kathryn, This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 If you need more help with your local install, directing questions to the galaxy-...@bx.psu.edu mailto:galaxy-...@bx.psu.edu mailing list would be best, Thanks! Jen Galaxy team On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users, I've encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error An error occurred running this job: //bin/sh: macs: not found/ // Anybody can kindly provide some hints? Thanks, Kathryn ___ 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 Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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] macs error for chipseq data
There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon). For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance: sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default And that's it, no need to restart galaxy or anything. -Dannon On Jan 11, 2013, at 10:59 AM, Jennifer Jackson j...@bx.psu.edu wrote: Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: Hi Jen, Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out. It seems to me that MACS was installed…. What is the issue? Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer, Thanks for the information on MACS tools. Yes, I forgot to mention that I used bowtie mapped files as the input. Thank you very much, Kathryn From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-u...@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data Hello Kathryn, This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 If you need more help with your local install, directing questions to the galaxy-...@bx.psu.edu mailing list would be best, Thanks! Jen Galaxy team On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users, I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error An error occurred running this job: /bin/sh: macs: not found Anybody can kindly provide some hints? Thanks, Kathryn ___ 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 Hillman-Jackson Galaxy Support and Training http://galaxyproject.org -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Galaxy January 11, 2013 Distribution News Brief
*Galaxy January 11, 2013 Distribution News Brief* http://wiki.galaxyproject.org/News/2013_01_11_DistributionNewsBrief * Complete News Brief http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11* * Highlights:* * /*GCC2013 Training Day Topic Nomination closes TODAY!*/ Read more... http://wiki.galaxyproject.org/News/GCC2013TrainingDayNominations or see http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay * XML defined Tool shed repository dependencies http://wiki.galaxyproject.org/DefiningRepositoryDependencies introduced * Various enhancements http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11#Other_Tool_Shed to Tool Shed http://wiki.galaxyproject.org/Tool%20Shed containers, display of README files and SVG images, and the tool shed's functional test framework http://wiki.galaxyproject.org/HostingALocalToolShed#Functional_test_framework_for_the_tool_shed. * New genomes http://wiki.galaxyproject.org/DevNewsBriefs/2013_01_11#Data added to *Main http://wiki.galaxyproject.org/Main* Galaxy instance and rsync download. * Plus bug fixes and related enhancements for visualizations, histories, workflows, and tools. * http://getgalaxy.org* *http://bitbucket.org/galaxy/galaxy-dist* *http://galaxy-dist.readthedocs.org* new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist upgrade: $ hg pull -u -r a4113cc1cb5e / *Thanks for using Galaxy,* / The Galaxy Team http://wiki.galaxyproject.org/Galaxy%20Team -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/
