Re: [galaxy-dev] Job output not returned from Cluster
Hi Hemant, thanks for your help. I have set the value to 100, but this did not fix the problem. I am now trying to get a NFS mounted with -noac. Cheers, Sascha Original Message processed by CONSOLIDATE Subject: RE: [galaxy-dev] Job output not returned from Cluster Sent: Montag, 9. Juli 2012 17:38 From: Kelkar, Hemant (hkel...@unc.edu) Hi Sascha, I am not sure if the error you are seeing is like one I had posted in this thread? http://dev.list.galaxyproject.org/Problem-related-to-a-job-that-quot-failed-quot-td4627406.html#a4632168 --Hemant From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Sascha Kastens Sent: Monday, July 09, 2012 11:26 AM To: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Job output not returned from Cluster Hi! Unfortunately I was not able to fix this problem yet. Is anybody out there who had a similar problem while using Galaxy with SGE or has the knowledge about the things I can look at? Thanks in advance! Cheers, Sascha ___ 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 killing split cluster jobs
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/
[galaxy-dev] Tophat and bowtie jobs failed!
Hi, I have submitted tophat to run on two datasets yesterday morning. The jobs waited in the queue whole yesterday and the statues now show the output files being deleted. Not knowing the architecture that these services are running on, we also tried to submit couple of alignments for smaller datasets which both had the same faith. Now thinking there might be something wrong on the server. My user name is Avazeh and tophat jobs are still visible in the history, 52-55 and 60-63. Thanks for all the help, Avazeh ___ 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] Installation on HPC and file upload
Dear developers, I'm wondering if you might be able to help us with an issue with have at Leeds. We have installed the galaxy platform on our HPC cluster at Leeds. One issue we have is uploading files 2 GB through the internet browser. We have tried the URL route also without success. Are there any solutions to this problem? One idea we had was whether it is possible to change the upload to look at the filesystem local to galaxy rather than the users own computer. Many thanks Lee -- Dr Lee Hazelwood BHRC Bioinformatics Technology Group Leader Biomedical and Health Research Centre Faculty of Biological Sciences and Leeds Institute of Molecular Medicine University of Leeds, Leeds, LS2 9JT, UK. E-mail: l.d.hazelw...@leeds.ac.ukmailto:l.d.hazelw...@leeds.ac.uk http://www.bhrc.ac.uk/initiatives/technology-groups/bioinformatics-technology-group/ ___ 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 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/
[galaxy-dev] No action for /admin_toolshed/prepare_for_install
I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed using the Admin interface to Galaxy. Unfortunately, each time I do this I get an error page with the message: No action for /admin_toolshed/prepare_for_install My Galaxy installation is galaxy-dist, revision 7148:17d57db9a7c0. Does anyone know why this might be happening? 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] No action for /admin_toolshed/prepare_for_install
Hello Peter, To use the public Galaxy tool sheds, your local Galaxy instance must be running the tip from Galaxy central, not Galaxy dist. You need to be running at least 7368:3e6ab1cf0c2e, as this is the revision running on the public tool sheds. The public tool sheds always track the Galaxy central repository. Greg Von Kuster On Jul 10, 2012, at 5:45 PM, Peter van Heusden wrote: I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed using the Admin interface to Galaxy. Unfortunately, each time I do this I get an error page with the message: No action for /admin_toolshed/prepare_for_install My Galaxy installation is galaxy-dist, revision 7148:17d57db9a7c0. Does anyone know why this might be happening? 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] No action for /admin_toolshed/prepare_for_install
Hi Peter, In your Galaxy install directory there will be a .hg subdirectory, and in that subdirectory there will be a file name hgrc. Yours probably looks something like this if you are tracking galaxy-dist. [paths] default = https://,your userna...@bitbucket.org/galaxy/galaxy-dist Just change the value of the path to track galaxy central: [paths] default = https://,your user na...@bitbucket.org/galaxy/galaxy-central When you pull and update, you'll get the latest from galaxy central. On Jul 10, 2012, at 6:13 PM, Peter van Heusden wrote: Hi Greg Is there any way to migrate from galaxy-dist to galaxy-central, or is a re-installation necessary? On 07/10/2012 11:56 PM, Greg Von Kuster wrote: Hello Peter, To use the public Galaxy tool sheds, your local Galaxy instance must be running the tip from Galaxy central, not Galaxy dist. You need to be running at least 7368:3e6ab1cf0c2e, as this is the revision running on the public tool sheds. The public tool sheds always track the Galaxy central repository. Greg Von Kuster On Jul 10, 2012, at 5:45 PM, Peter van Heusden wrote: I am trying to install a tool (tmap_wrapper) from the Galaxy toolshed using the Admin interface to Galaxy. Unfortunately, each time I do this I get an error page with the message: No action for /admin_toolshed/prepare_for_install My Galaxy installation is galaxy-dist, revision 7148:17d57db9a7c0. Does anyone know why this might be happening? 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/
