[galaxy-dev] possible to resume failed workflow?
Hi, I've created a few workflows and have been having issues with some steps randomly failing. This would not be an issue if I could simply resume the workflow from the failed step, but it seems that this is not possible. Instead, I'm forced to restart the workflow from the beginning. Is this true or am I missing something? Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.org La Jolla Institute for Allergy and Immunology ___ 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] specifying nodes/processors with PBS
Hi, I've successfully configured a local galaxy instance to submit jobs to our local cluster, but have a question regarding setting PBS options such as the number of nodes and processors to use. I've followed the guide here: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster?highlight=%28pbs%29 Is there any way to do this in a tool-specific manner. For example, for running tophat to do a mapping run, I would want it to use 24 CPUs, but for simply converting a file type I would want only 1 CPU requested. Is there a way to specify this somewhere? Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.org La Jolla Institute for Allergy and Immunology ___ 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] upload from local filesysem
Thanks for the reply. Ideally, I would have a cron job run that would monitor a directory and automatically add the new files to a particular library. I do not want the end users to have to deal with this. Does anyone have a working solution or ideas for implementation? This is the main sticking point that is preventing us from using galaxy for our in-house next-gen sequencing pipeline. Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.org La Jolla Institute for Allergy and Immunology - Original Message - From: Alex Bossers alex.boss...@wur.nl To: J. Greenbaum jgb...@liai.org, galaxy-dev@lists.bx.psu.edu Sent: Wednesday, May 23, 2012 1:24:13 AM Subject: RE: [galaxy-dev] upload from local filesysem You can do so / allowing them to, by using the galaxy ftp solution. That way users can link or provide files in their email subdirs. You have to sort out how to set the users/rights properly on your linux box though. But see the galaxy ftp solution pages, it might be of help. Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] namens J. Greenbaum [jgb...@liai.org] Verzonden: woensdag 23 mei 2012 3:01 To: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] upload from local filesysem It seems that this topic has been covered at least several times and I've found this thread to be helpful: http://user.list.galaxyproject.org/Speed-up-uploading-into-local-Galaxy-terribly-slow-tp4429327p4436053.html However, as far as I understand, this will only allow the Admin to do the upload from a local disk. Has anyone had success allowing a regular user to upload from a local disk? This seems like a common issue, particularly with large sequencing files. It would be great to be able to add this as the first step in a workflow. Any info would be appreciated. Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.orgmailto:jgb...@liai.org La Jolla Institute for Allergy and Immunology ___ 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] specifying nodes/processors with PBS
Excellent! Thanks for the reply. -J -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.org La Jolla Institute for Allergy and Immunology - Original Message - From: Anthonius deBoer thondeb...@me.com To: J. Greenbaum jgb...@liai.org Cc: galaxy-dev@lists.bx.psu.edu Sent: Wednesday, May 23, 2012 2:03:18 PM Subject: Re: [galaxy-dev] specifying nodes/processors with PBS Yes, you can set these things for each tool independently. Check the file universe_wsgi.ini and check the section: [galaxy:tool_runners] There you can set the -pe options for GSUB in the same way you can do on the command line... Here's an example of my setup: gatk_variant_select = drmaa://-V -pe smp 1 gatk_validate_variants = drmaa://-V -pe smp 1 far = drmaa://-V -pe smp 1 velveth = drmaa://-V -pe mpi 4 velvetg = drmaa://-V -pe mpi 8 I set the -pe mpi option to 8 for VELVETH/G and to 1 for GATK for instance Thon On May 23, 2012, at 12:47 PM, J. Greenbaum jgb...@liai.org wrote: Hi, I've successfully configured a local galaxy instance to submit jobs to our local cluster, but have a question regarding setting PBS options such as the number of nodes and processors to use. I've followed the guide here: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster?highlight=%28pbs%29 Is there any way to do this in a tool-specific manner. For example, for running tophat to do a mapping run, I would want it to use 24 CPUs, but for simply converting a file type I would want only 1 CPU requested. Is there a way to specify this somewhere? Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.org La Jolla Institute for Allergy and Immunology ___ 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] Uploading problem
Thanks for the info. It's definitely browser-related as I was having the issue in Chrome, but FF seems to be working... -J -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.org La Jolla Institute for Allergy and Immunology - Original Message - From: Jorrit Boekel jorrit.boe...@scilifelab.se To: J. Greenbaum jgb...@liai.org, galaxy-dev@lists.bx.psu.edu Sent: Tuesday, May 22, 2012 7:04:26 AM Subject: Re: [galaxy-dev] Uploading problem Hi, Hanging uploads have been a problem before with small and large files: http://comments.gmane.org/gmane.science.biology.galaxy.devel/4583 I don't know if it's been fixed, but it seemed to depend on browser choice and on what server was running. I was recommended to use the nginx server IIRC. I still have the occasional problem though, but (I hope) less often. cheers, jorrit On 05/22/2012 03:50 PM, J. Greenbaum wrote: Hi Julie, All, I have a similar problem on a test environment with a postgres backend. The file that I'm uploading is a 50MB GTF file and it I'm getting the same behavior. Any help would be appreciated. Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.org La Jolla Institute for Allergy and Immunology - Original Message - From: julie dubois dubju...@gmail.com To: galaxy-dev@lists.bx.psu.edu Sent: Tuesday, May 22, 2012 12:12:06 AM Subject: [galaxy-dev] Uploading problem Hi, I test a production environnement of Galaxy with apache proxy and mysql database. It work, but when I upload a file (it's not very big : 460 Mo), Galaxy says that dataset is uploading and it has runned since yesterday and it's not finish! Where can the problem be ? Is it an installation problem or a material limitation : it's run in a machine with 8 Go RAM and 4 cores processor. Thank you Julie ___ 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] upload from local filesysem
It seems that this topic has been covered at least several times and I've found this thread to be helpful: http://user.list.galaxyproject.org/Speed-up-uploading-into-local-Galaxy-terribly-slow-tp4429327p4436053.html However, as far as I understand, this will only allow the Admin to do the upload from a local disk. Has anyone had success allowing a regular user to upload from a local disk? This seems like a common issue, particularly with large sequencing files. It would be great to be able to add this as the first step in a workflow. Any info would be appreciated. Thanks, Jason -- Jason Greenbaum, Ph.D. Manager, Bioinformatics Core | jgb...@liai.org La Jolla Institute for Allergy and Immunology ___ 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/
