Re: [galaxy-user] Mapping does not start
Felix Hammer wrote: Hi, I am trying to map sequences with Bowtie. Have been waiting for a few hours now but it still says Job is waiting to run. A few days ago I didn't have this problem and the job started immediately. My guess is that the jobs are still stuck in a queue? How can I tell when the jobs will approximately start running? Is there a way to view the queue position? Hi Felix, Unfortunately, the cluster that serves these jobs is temporarily offline for emergency maintenance. Estimates are that it will be back up within a few hours. --nate thx, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/
Re: [galaxy-user] Upload via SCP?
Felix Hammer wrote: Hi, is it possible to use SCP to upload files instead of FTP? Hi Felix, At this time, no. --nate thxbye, Felix ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/ ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. 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/
Re: [galaxy-user] Bowtie Job doesn't start
Felix Hammer wrote: Hi, just trying to use Bowtie, but the job does not start. Is there somthing wrong with the server at the moment? Hi Felix, It looks like the reservation on the cluster which runs bowtie jobs isn't working at the moment and there's some contention for resources. I've reported the bug to the folks who maintain this cluster and hopefully it'll be resolved shortly. --nate Felix ___ 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/ ___ 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/
Re: [galaxy-user] Export data to filesystem
James Lindsay wrote: Hello, I was wondering if there was a way to export a dataset to the file system? Basically I think it would be advantageous if someone could copy a dataset to an export folder, they could then FTP this data away or work with it locally? Hi James, This doesn't exist currently, although various people have implemented it as a tool in their own environments, you may want to ask for copies of such tools over on the Development list. It's something we plan to implement more directly in the future. --nate Thanks for the help, James ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy down?
Felix Hammer wrote: Hi, is there currently a problem with the Galaxy Server? When will it be up again? Hi Felix, There were some problems caused by unusually high load which should now be resolved. Jobs are running now, albeit a bit slowly. Please let us know if there are any continuing problems. Thanks, --nate thx, Felix ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy server-FTP
Sher, Falak wrote: HI I would like to use Galaxy server to upload files via FTP. I seek help for, log in to the FTP server at main.g2.bx.psu.edu. I dont see ftp log in option there. help please ? Hi Falak, What software are you using to try to connect via FTP? --nate Falak ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy server-FTP
Sher, Falak wrote: Sorry I did not know there is some special software I need to use, could you help please ? Have you seen the instructions here?: https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP Those example screenshots use Cyberduck. FileZilla is also a popular cross-platform FTP client. --nate From: Nate Coraor [n...@bx.psu.edu] Sent: Thursday, March 31, 2011 11:36 PM To: Sher, Falak Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Galaxy server-FTP Sher, Falak wrote: HI I would like to use Galaxy server to upload files via FTP. I seek help for, log in to the FTP server at main.g2.bx.psu.edu. I dont see ftp log in option there. help please ? Hi Falak, What software are you using to try to connect via FTP? --nate Falak ___ 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/ ___ 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/
Re: [galaxy-user] Most Popular Linux flavour for Galaxy
Matloob Khushi wrote: Hello Galaxy Users We are anticipating setting up a local instance of Galaxy and wondering what is the most popular (or best) flavour of Linux people out there using. I wonder which OS on UseGalaxy.org has been used. Thanks for your help. Hi Matloob, The public Galaxy server runs Solaris 10. The tools run on two clusters, one running Debian Squeeze and the other running RHEL 5.6, both amd64. You might find that a specialized distribution like BioLinux or Scientific Linux may pre-package many of the tools you're interested in, which would make setup a bit easier. --nate Regards Matloob PhD Candidate ___ 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/ ___ 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/
Re: [galaxy-user] Loading files to local Galaxy
Paul-Michael Agapow wrote: From: Tilahun Abebe tilahun.ab...@uni.edu We are trying to load Illumina data to our local Galaxy instance. The files are between 700 MB and 2.2 GB. Files below 2 GB load in less than 5 minutes. Files larger than 2 GB don't upload at all. We installed Galaxy locally because we thought loading files will be faster than the server version. Any suggestions to solve this problem is highly appreciated. While (from others experience) Galaxy _should_ be able to upload files that large, we've had some problems with our local installation too. Investigation didn't reveal any cause, so we put it down to the quality of our network. You might what to look at the webserver or proxy that you have in front of Galaxy - from memory, both Apache and nginx can be configured to impose file size limits, so that _may_ be the problem. In any event, you might want to configure your server to handle uploads and downloads directly as per https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServe r. Finally you can pass an url to the upload dialog to get Galaxy to pull the file from an ftp server - for example - and that may prove more robust. Hi Paul, These failures may be due to the fact that many browsers will simply fail to upload files 2GB (although I know there are people out there have successfully done it). Tilahun, I'll echo Paul's suggestion to use the Production setup. There are also alternative options for getting data into Galaxy. For users, you can have an FTP server (or just a local directory on the server where they can place files for upload): https://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP Or you can use data libraries and load directly off filesystems accessible to the server: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles --nate Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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/ ___ 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/
Re: [galaxy-user] Loading files to local Galaxy
Tilahun Abebe wrote: Thank you Paul and Nate. We will try the options you suggested. One thing we found to work much faster (less than 5 minutes for most files) is to upload zipped data. Galaxy could upload and unzip the files without any problem. It doesn't seem any sequence data is lost. Has anyone tried this before? Yes, this is a standard feature. zip, gzip, and bzip2 are all supported. Only one file per archive at this time, however. --nate Thanks. Tilahun --- Nate Coraor wrote: Paul-Michael Agapow wrote: From: Tilahun Abebetilahun.ab...@uni.edu We are trying to load Illumina data to our local Galaxy instance. The files are between 700 MB and 2.2 GB. Files below 2 GB load in less than 5 minutes. Files larger than 2 GB don't upload at all. We installed Galaxy locally because we thought loading files will be faster than the server version. Any suggestions to solve this problem is highly appreciated. While (from others experience) Galaxy _should_ be able to upload files that large, we've had some problems with our local installation too. Investigation didn't reveal any cause, so we put it down to the quality of our network. You might what to look at the webserver or proxy that you have in front of Galaxy - from memory, both Apache and nginx can be configured to impose file size limits, so that _may_ be the problem. In any event, you might want to configure your server to handle uploads and downloads directly as per https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServe r. Finally you can pass an url to the upload dialog to get Galaxy to pull the file from an ftp server - for example - and that may prove more robust. Hi Paul, These failures may be due to the fact that many browsers will simply fail to upload files 2GB (although I know there are people out there have successfully done it). Tilahun, I'll echo Paul's suggestion to use the Production setup. There are also alternative options for getting data into Galaxy. For users, you can have an FTP server (or just a local directory on the server where they can place files for upload): https://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP Or you can use data libraries and load directly off filesystems accessible to the server: https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles --nate Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Centre for Infections, Health Protection Agency - ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk ** ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy tool error report from joh...@ibms.sinica.edu.tw
Hello, Please don't set your bug report address (error_email_to in universe_wsgi.ini) to the user mailing list. This should be set to a local address at your site. --nate galaxy-user@lists.bx.psu.edu wrote: GALAXY TOOL ERROR REPORT This error report was sent from the Galaxy instance hosted on the server 192.168.0.36:8080 - This is in reference to dataset id 377 from history id 2 - You should be able to view the history containing the related history item 176: Cuffcompare on data 175: transcript accuracy by logging in as a Galaxy admin user to the Galaxy instance referenced above and pointing your browser to the following link. 192.168.0.36:8080/history/view?id=f597429621d6eb2b - The user 'joh...@ibms.sinica.edu.tw' provided the following information: While executing cuffcompare, I encountered this error message: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' I was practicing RNA-seq analysis steps on newly installed galaxy to test if i could easily analyze my data. I could run cufflinks and cuffdiff through galaxy, but i'm unable to run cuffcompare. how should i solve this problem? thanks a lot! - job id: 126 tool id: cuffcompare - job command line: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py -s --ref_file=None --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data /home/galaxy/software/galaxy_dist/database/files/000/dataset_376.dat - job stderr: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' - job stdout: cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -s /home/galaxy/data/galaxy_data/sam_index/hg19.fa ./input1 - job info: None - job traceback: None - (This is an automated message). ___ 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/ ___ 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/
Re: [galaxy-user] uploading files via FTP
somy ork wrote: Hi, Am trying to configure galaxy to enable file upload via FTP. My server is configured with SFTP. and not FTP. Will this create a problem in galaxy? coz all my input files are above 2 GB. Should i change any settings in the universe_wsgi.ini file? Please guide me. Hi Somy, SFTP is fine for your local site, I really need to just generalize those configuration options and the wording so that is not specific to FTP. The same code can actually just be used to provide access to local directories that users can copy data into via whatever means is most appropriate for their own site. --nate Regards somy. ___ 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/ ___ 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/
Re: [galaxy-user] galaxy cluster setup
Robert Jackson wrote: Does anyone have practical info on galaxy setup on a cluster? Hi Robert, Please see the production server documentation at: http://usegalaxy.org/production --nate Robert C. Jackson Software Systems Specialist III The University of Texas Pan-American Computer Support Services Division of Information Technology Phone: 956-665-2455 Fax: 956-665-8777 ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy server issues?
David K Crossman wrote: Hello! We uploaded 12 samples to Galaxy last night via FTP. This morning, I went to Get Data and clicked on all 12 that were under the FTP location, chose the type of file they were and reference genome and then clicked Excecute. The 12 moved over to the History panel and after a couple of minutes went from gray to yellow. As of this moment, all 12 are still in the yellow stage (still spinning). Is this normal for that many samples (each sample is about 8GB in size) or should they already have turned green? Any info would be greatly appreciated. Hi David, It's not unlikely for that many files of that size all at once. I've checked the PBS queue and your job is still running. --nate Thanks, David ___ 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/ ___ 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/
Re: [galaxy-user] cuffcompare error in galaxy
Hi Carlos, We're expecting to release a stable distribution this week, but you are always free to pull changes from the central repository. The suggested method would be to just pull all changesets up to the one you want, or up to the tip changeset. It's not trivial to pull single changesets, you have to export them from central, import them to your local repository, and then you'll have to merge when we release a new stable distribution. --nate Carlos Javier Borroto wrote: I see there is this changeset: https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389 As I have cufflinks 1.0.3, I wonder if this is the cause of the error. Maybe I should move to galaxy-central if I want to use cufflinks. Is there any clean way to backport a changeset from -central to -dist? Thanks, -- Carlos Borroto Baltimore, MD On Mon, Jun 20, 2011 at 2:01 PM, Carlos Javier Borroto carlos.borr...@gmail.com wrote: Hi John, I'm finding the exact same error while going through Jeremy's tutorial in a local instance of galaxy-dist. I was wonder if you found the solution. I see cuffcompare wrapper outputs these files: cc_output.combined.gtf cc_output.input1.refmap cc_output.input1.tmap cc_output.loci cc_output.stats cc_output.tracking and in the logs I'm seing this: galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combined.gtf to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as directed by from_work_dir Only cc_output.combined.gtf is correctly being moved, the rest aren't being call by the correct filenames. Thanks, -- Carlos Borroto Baltimore, MD 2011/6/10 吳正華 joh...@ibms.sinica.edu.tw: Dear galaxy team: I was testing local galaxy of our lab by analyzing RNA-seq data in Jeremy’s RNA-seq tutorial. http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise I could run TopHat, cufflinks, and cuffdiff and got results correctly, but when I executed cuffcompare through galaxy, the following error occurred: Tool execution generated the following error message: Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output' The tool produced the following additional output: cuffcompare v1.0.3 (2403) cuffcompare -o cc_output -s /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1 and error messages in log file (galaxy.log) are: galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py -s --ref_file=None --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished: python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py -s --ref_file=None --dbkey=hg19 --index_dir=/home/galaxy/software/galaxy_dist/tool-data /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output to /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.tmap to /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.refmap to /home/galaxy/software/galaxy_dist/database/files/000/dataset_401.dat as directed by from_work_dir galaxy.jobs DEBUG 2011-06-10 14:02:28,027 finish(): Moved /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output.combined.gtf to
Re: [galaxy-user] Unable to load FASTA files?
Hi, The cluster resource manager unexpectedly died. Everything should be working again after a restart. Please let us know if you're still experiencing any problems, and thanks for using Galaxy. --nate Nicola Nadeau wrote: I've been getting the same error when trying to run Picard, Mark Duplicat Reads. Maybe Galaxy is having memory issues? Nicola On 27/06/2011 13:09, Laura Elizabeth Spoor wrote: Is anyone else having trouble uploading FASTA files to the Galaxy server? I thought it was my files at first, but I have since tried to upload other FASTA files that I have previously had no trouble uploading and I get the same error reported in the info section when I click on the pen icon: Unable to queue job for execution. Resubmitting the job may succeed. (Unfortunately re-submitting the job does not succeed!). The file is 50 MB in size. Any help is greatly appreciated as I am unable to progress my work until this problem is corrected. Best Wishes, Laura -- Dr Nicola Nadeau Butterfly Genetics Group Department of Zoology University of Cambridge Downing Street Cambridge, CB2 3EJ Phone: 01223 336644 Email: nj...@cam.ac.uk Web: http://heliconius.zoo.cam.ac.uk/2009/nicola-nadeau/ ___ 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/ ___ 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/
Re: [galaxy-user] FTP and command line access in Galaxy
Peter Cock wrote: On Wed, Jun 22, 2011 at 6:47 AM, Robert Curtis Hendrickson curt...@uab.edu wrote: Nate, The Galaxy’s ability to pull files with user/password from FTP sites as a client is great. However, I need to pull data from an HTTP site at a sequencing center with user/password (already tried to get them to set up an FTP server, no luck). Any way to do this? Try asking the sequencing centre if the username and password can be provided as part of the HTTP URL, then give that URL to Galaxy. If it's using HTTP Authentication, the URL is the same as with ftp: http://user:h...@example.org/file.ext Other authentication systems which use forms and cookies or similar methods won't work. --nate Peter ___ 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/ ___ 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/
Re: [galaxy-user] temporary files
Christopher Schroeder wrote: Dear all, we extended the galaxy functionality with a couple of smaller custom scripts. Now we are in the need of some tmpFiles, since our data is getting bigger. As far as I understand galaxy by now there might be several options: - job_working_directory (all normal files generated by the job, deleted upon completion of job - safe?) - tmp-folder within the database folder (custom path in universe_wsgi.ini?) - system-tmp-folder (e.g. samtools-wraper - only very limited space on this harddisk) What is the best way to store temporary data in Galaxy (that can be deleted after job completion)? Hi Chris, It's really up to your personal preference. In the past we've used all three. In general, if the filesystem your job_working_directory resides in is suitable, it is probably the easiest choice since you get free cleanup on job completion. --nate Thank you in advance for your help! Chris ___ 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/ ___ 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/
Re: [galaxy-user] Galaxy Architecture Documentation
Oren, I do believe some folks have done this, I am a bit surprised none have replied. But yes, since Condor supports DRMAA, you should be able to point $DRMAA_LIBRARY_PATH at Condor's libdrmaa.so, enable the drmaa runner, and try it out. --nate Oren Livne wrote: Dear Dave, Victor, Is it possible to simply use the drmma job runner with the condor drmma lib.so? Thanks! Oren On 9/22/2011 3:21 PM, Victor Ruotti wrote: Hi Dave, That was me! I'm currently talking with the condor folks here in Madison WI. It would be great to get galaxy going with Condor since condor nows forms part of red hat. Besides the existing available docs that you listed below who do you think would be best as a contact for questions regarding this implementation? best, Victor On Sep 21, 2011, at 12:16 PM, Dave Clements wrote: Hi Oren, I had no idea so I went to the Galaxy mailing list archive @ Nabble (http://gmod.827538.n3.nabble.com/Galaxy-f829901.html) and searched for Condor (http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=search_pagenode=829901query=condor http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=search_pagenode=829901query=condor). It appears that Ravi Madduri @ Argonne has done some work with this. I was also at a meeting in March with someone from Wisconsin (where I think Condor is currently developed) and they indicated their might be interest in helping Galaxy work with Condor. I/you can pursue this option as well. Dave C. On Wed, Sep 21, 2011 at 9:38 AM, Oren Livne li...@uchicago.edu mailto:li...@uchicago.edu wrote: Dear Dave, This was very useful. Thank you so much. Specifically, I am trying to integrate Galaxy with Condor, which supports DRMAA. Is there an existing Condor job runner implementation, or any useful code for submitting Galaxy jobs to Condor? Thanks! Oren On 9/20/2011 12:21 PM, Dave Clements wrote: Hi Oren, This book chapter http://userwww.service.emory.edu/~eafgan/content/Galaxy_eScienceGateway.pdf http://userwww.service.emory.edu/%7Eeafgan/content/Galaxy_eScienceGateway.pdf, includes a high-level overview of Galaxy. (Note: that chapter will be copied to the wiki soon.) There is some API documentation. ~/scripts/api/README, ~/scripts/api/workflow_ execute.py and ~/scripts/api/example_watch_folder.py in the distribution http://wiki.g2.bx.psu.edu/News%20Briefs/2010_07_16#Initial_implementation_of_the_Galaxy_Web_API http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30#API http://wiki.g2.bx.psu.edu/Events/GCC2011 (/Galaxy Deployment and API/ presentation) http://wiki.g2.bx.psu.edu/Admin/Sample%20Tracking/Next%20Gen http://wiki.g2.bx.psu.edu/Events/GCC2011/Workflows%20and%20API Sometime in the next week I'll compile all this into a single wiki page. As far as I know there is no How to write a runner for Galaxy document. The closest we have is http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster and http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling Hope this helps, Dave C. On Mon, Sep 19, 2011 at 9:51 AM, Oren Livne li...@uchicago.edu mailto:li...@uchicago.edu wrote: Dear All, I am a software developer, new to Galaxy. Is there a detailed document about the Galaxy code architecture, API, what runners are, and how to write a runner? I am especially interested in integrating Galaxy with an external scheduler software (I am aware of Galaxy's scheduling capabilities). I'd like to intercept Galaxy workflows and send their object model to my scheduler. I could not find this information on the Galaxy Wiki. Thank you so much in advance, Oren Livne ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org http://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/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://galaxyproject.org/wiki/ ___ The Galaxy User list should be used for the discussion
Re: [galaxy-user] Injecting External File References
Oren Livne wrote: Dear All, We have a lot of sequencing data files whose locations and identifiers are managed by our home-grown webapp. We'd like to enable users to single-sign-on from our webapp into Galaxy (we will be using open ID on both systems for that). When the user opens a Galaxy window, we'd like them to be able to access the data files on our system which they have permissions to see. How should we go about that without copying or moving files? Should we make a new data library, or (preferably) create our identifier service and make it a remote data source/library that galaxy can see and that can be browsed like other data libraries? Is there an API we should write our service against, or wrap files with appropriate galaxy meta data, etc.? Hi Oren, Without knowing the full architecture it's a bit hard to say what the best solution is. However, Galaxy's API does allow for upload from locations on the filesystem or from an FTP/HTTP/HTTPS url to a data library, so you should be able to use this to do what you're talking about. Thanks, --nate Thank you so much, Oren ___ 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/
Re: [galaxy-user] Over disk quota
GANDRILLON OLIVIER wrote: Hello I just received the following message while using Galaxy through the web You are over your disk quota. Tool execution is on hold until your disk usage drops below your allocated quota. I deleted a couple of files but it didn't helped. I checked the FAQ and could not get the answer. Hi Olivier, The FAQ page is out of date and we'll be updating this as soon as possible. Please see the following for information about how to free up disk space: http://wiki.g2.bx.psu.edu/Main http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets Sorry for the inconvenience, and thanks for using Galaxy. --nate Thank's for your help Olivier ___ 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/ ___ 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/
Re: [galaxy-user] permanently delete problem
Richard Mark White wrote: hi, so i went to options--saved history--advanced--deleted datasets. then checked all of them, and then hit permanently delete. but nothign happened. they still show up as deleted, and they are taking up lots of my quota. how do i get rid of these? rich Hi Rich, I'm not sure what's going on here, I'm looking in to it. --nate ___ 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/
Re: [galaxy-user] permanently delete problem
Great, thanks for letting us know. Richard Mark White wrote: actually, i just waited a bit and now they are deletd. r From: Nate Coraor n...@bx.psu.edu To: Richard Mark White whit...@yahoo.com Cc: GANDRILLON OLIVIER olivier.gandril...@univ-lyon1.fr; galaxy-u...@bx.psu.edu galaxy-u...@bx.psu.edu Sent: Wednesday, October 26, 2011 12:55 PM Subject: Re: permanently delete problem Richard Mark White wrote: hi, so i went to options--saved history--advanced--deleted datasets. then checked all of them, and then hit permanently delete. but nothign happened. they still show up as deleted, and they are taking up lots of my quota. how do i get rid of these? rich Hi Rich, I'm not sure what's going on here, I'm looking in to it. --nate ___ 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/
Re: [galaxy-user] Data gets deleted from public server
On Nov 7, 2011, at 7:11 PM, shamsher jagat wrote: I uploaded two BAM files and was working with them but when I tried to use them again they are automatically deleted along with all the steps of analysis? Any reason or I am missing something. Hi Shamsher, Were you logged in when you performed this analysis? --nate Shamsher ___ 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/ ___ 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/
Re: [galaxy-user] Lastz
On Nov 11, 2011, at 9:21 AM, Andrew South wrote: Hello folks Anyone else having trouble with running Lastz to map? Jobs are being sent but not running. It stopped working for me two days ago after working perfectly, I've tried fiddling with the formats but no joy. Hi Andy, It looks like there's a problem with the cluster that runs our NGS jobs. I'm currently looking into it. Sorry for the inconvenience. --nate Thanks, Andy Dr A P South Centre for Oncology and Molecular Medicine University of Dundee Ninewells Hospital Medical School Dundee DD1 9SY Tel 01382 496432 Fax 01382 633952 a.p.so...@dundee.ac.uk Please consider the environment. Do you really need to print this email? The University of Dundee is a registered Scottish charity, No: SC015096 ___ 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/ ___ 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/
Re: [galaxy-user] Lastz
On Nov 11, 2011, at 10:01 AM, Andrew South wrote: Thanks Nate, hope it's a quick fix. Best wishes, Andy Hi Andy, All backlogged NGS jobs should now be running, new ones will likely queue until free slots are available. Please let us know if there's further trouble, and thanks for using Galaxy, --nate Please consider the environment. Do you really need to print this email? Nate Coraor n...@bx.psu.edu 11/11/2011 14:55 On Nov 11, 2011, at 9:21 AM, Andrew South wrote: Hello folks Anyone else having trouble with running Lastz to map? Jobs are being sent but not running. It stopped working for me two days ago after working perfectly, I've tried fiddling with the formats but no joy. Hi Andy, It looks like there's a problem with the cluster that runs our NGS jobs. I'm currently looking into it. Sorry for the inconvenience. --nate Thanks, Andy Dr A P South Centre for Oncology and Molecular Medicine University of Dundee Ninewells Hospital Medical School Dundee DD1 9SY Tel 01382 496432 Fax 01382 633952 a.p.so...@dundee.ac.uk Please consider the environment. Do you really need to print this email? The University of Dundee is a registered Scottish charity, No: SC015096 ___ 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/ The University of Dundee is a registered Scottish charity, No: SC015096 ___ 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/
Re: [galaxy-user] Lastz
On Nov 12, 2011, at 6:30 AM, Andrew South wrote: Dear Nate - It seems I may have upset the cluster again: I have 3 Lastz jobs running and cannot upload any more data. I had been uploading fine; started 3 lastz mapping jobs (Fasta (1 sequence) vs Fasta (~3000 sequences) output as SNP, when I realised I made a mistake, cancelled these jobs, uploaded the correct files and then ran the 3 comparisons (similar files) again and now these jobs have been running 1hr and I cannot upload any more data. Hi Andy, What are the details related to being unable to upload? Are the datasets sitting in a certain state (uploading, queued, etc.)? Did you have any other jobs running at the time? There are some concurrent job limits that could have been responsible. --nate Thanks in advance, Andy Please consider the environment. Do you really need to print this email? Nate Coraor n...@bx.psu.edu 11/11/2011 17:16 On Nov 11, 2011, at 10:01 AM, Andrew South wrote: Thanks Nate, hope it's a quick fix. Best wishes, Andy Hi Andy, All backlogged NGS jobs should now be running, new ones will likely queue until free slots are available. Please let us know if there's further trouble, and thanks for using Galaxy, --nate Please consider the environment. Do you really need to print this email? Nate Coraor n...@bx.psu.edu 11/11/2011 14:55 On Nov 11, 2011, at 9:21 AM, Andrew South wrote: Hello folks Anyone else having trouble with running Lastz to map? Jobs are being sent but not running. It stopped working for me two days ago after working perfectly, I've tried fiddling with the formats but no joy. Hi Andy, It looks like there's a problem with the cluster that runs our NGS jobs. I'm currently looking into it. Sorry for the inconvenience. --nate Thanks, Andy Dr A P South Centre for Oncology and Molecular Medicine University of Dundee Ninewells Hospital Medical School Dundee DD1 9SY Tel 01382 496432 Fax 01382 633952 a.p.so...@dundee.ac.uk Please consider the environment. Do you really need to print this email? The University of Dundee is a registered Scottish charity, No: SC015096 ___ 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/ The University of Dundee is a registered Scottish charity, No: SC015096 The University of Dundee is a registered Scottish charity, No: SC015096 ___ 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/
Re: [galaxy-user] disk quota not updating
On Nov 30, 2011, at 12:49 PM, Richard Mark White wrote: Hi, I was nearing my disk quota (at 97%), so I deleted a large number of datasets using delete permanently. But my usage did not go down at all. Is there a delay in this happening, or is there some way to purge the files? Hi Richard, It can take a bit if you delete a large amount of data at once. Did your usage eventually decrease? --nate richard ___ 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/ ___ 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/
Re: [galaxy-user] is public galaxy down?
On Dec 17, 2011, at 8:34 AM, Richard Mark White wrote: I am unable to access for past several hours. Are others having the same issue? Hi Rich, Our core router has crashed, we're working on the problem and hope to have it fixed within the next few hours. Sorry for the inconvenience. --nate rich ___ 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/ ___ 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/
Re: [galaxy-user] Finding Galaxy version
On Dec 13, 2011, at 5:33 AM, Paul-Michael Agapow wrote: A perhaps obvious question: how do I work out what version of Galaxy an instance is? This has come up a few times because of apparent bugs and different behaviour across various development and production instances. Now if you’re installed straight from the repo, you can use “hg log” for the repo number. But that doesn’t work if it’s been installed in another way, say from a tarball or via another versioning system (we use git to synchronize tool development to a production server). Simple solution? Hi Paul, Since the hg changeset id is the Galaxy version, there's not a great way to determine the version without hg. I'd suggest making a note of the id when you fetch the tarball. --nate Paul Agapow (paul-michael.aga...@hpa.org.uk) Bioinformatics, Health Protection Agency ** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of the HPA, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses, but please re-sweep any attachments before opening or saving. HTTP://www.HPA.org.uk** ___ 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/ ___ 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/
Re: [galaxy-user] Tophat jobs not starting
On Dec 14, 2011, at 11:19 AM, Magdalena Strzelecka wrote: Hi, I have submitted some jobs to Tophat, but they have not started since yesterday (Dec 13th); i.e they were in a queue for 12 hrs. I have re-submitted everything again (2 jobs), but the same situation is happening. Is there some issue with Tophat at the moment? Hi Magdalena, This was due to a problem with the cluster Galaxy uses to run certain jobs. This was resolved early last week, although there may have been a few intermittent problems after that time. If tophat still has not run successfully, please let us know. Our sincere apologies for the inconvenience, Best, --nate Thanks. M. -- Magdalena Strzelecka, PhD Heald Lab University of California, Berkeley Department of Molecular Cell Biology 315 Life Sciences Addition # 3200 Berkeley, CA 94720-3200 phone: (510) 643-5002 fax: (510) 643-6791 e-mail: strzele...@berkeley.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/ ___ 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/
Re: [galaxy-user] Not able to get data from UCSC table browser
On Dec 22, 2011, at 5:35 PM, Sell, Christian wrote: Hi, I encountered similar problems today. I can’t open some histories, upload data or transfer data between histories. Regards Christian Hi, Due to extremely high load at the time, jobs were delayed. This has been resolved, so please let us know if you have any further problems with running jobs. Sorry for the inconvenience and thanks for using Galaxy. Thanks, --nate Von: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] Im Auftrag von Mike Dufault Gesendet: Donnerstag, 22. Dezember 2011 23:02 An: galaxy-user@lists.bx.psu.edu Betreff: Re: [galaxy-user] Not able to get data from UCSC table browser Hi Galaxy team, I also am having a similar problem. I uploaded data by ftp but when I try to load into a work history, it is stuck as Job waiting to run. Mike --- On Thu, 12/22/11, Peng Yu pengyu...@gmail.com wrote: From: Peng Yu pengyu...@gmail.com Subject: [galaxy-user] Not able to get data from UCSC table browser To: galaxy-user@lists.bx.psu.edu Date: Thursday, December 22, 2011, 12:06 AM Hi, I'm trying to get data from UCSC table browser. However, the browser always show Waiting for main.g2.bx.psu.edu Is there any problem with the galaxy server? -- Regards, Peng ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] ftp upload
On Dec 27, 2011, at 8:52 PM, Gabor Bartha wrote: I have tried to use ftp to upload files to main.g2.bx.psu.edu but the jobs have been failing with: 421 service not available, remote server has closed connection after about 1.5GB. Isn’t ftp the way you are supposed to upload large files? The file I am uploading is ~6GB in size. Hi Gabor, You can resume the upload if it's interrupted. I'll have a look at the logs to see if there is any indication why it's failed. --nate Gábor Bartha, Ph.D. Director of Information Sciences Synergenics, LLC 863 Mitten Rd., Suite 101 Burlingame, CA 94010 650-777-5202 ___ 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/ ___ 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/
Re: [galaxy-user] Error during data upload of fastq.gz
On Jan 30, 2012, at 11:37 AM, Stefan Kroeger wrote: Hi Jen, On 30.01.2012 16:12, Jennifer Jackson wrote: Are you still having this problem? One thought is that this file is some sort of README file in with the other data files from you source. Another is that the data is an annotation file, not a sequence file, with one or more columns of data in HTML format. yes I still have the problem, but to ensure it's not a file error I will check the original data from the lab. if the problem is still present I will come back to you. Some things to check: - have you opened/uncompressed the file locally to see if it contains any HTML? it's a complete lane so really hard to check by eye ;-) do you know any kind of command line fasta validation tool? - are you able to download, uncompress, and then load the file uncompressed or does that also give errors? Using upload from the desktop or FTP? tried both, no changes. Hi Stefan, Could you upload it to the FTP site and then send us the filename, without attempting to import it using the Upload File tool in the web interface? I'll grab a copy and take a look at it. --nate Thanks best regards Stefan [...] On 1/26/12 5:55 AM, Stefan Kroeger wrote: hi, Maybe anybody can give me a hint for the following problem... When I try to upload a fastq.gz file into galxy using url function the input os canceled with the following exception: An error occurred running this job: The uploaded file contains inappropriate HTML content I don't know where to start to have a look at. The upload of all other fastq.gz files from the same run works smooth. best stefan PS. Yes I know, the problem is really unspecific, sorry for that... ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] ftp
On Mar 20, 2012, at 8:13 AM, Richard Mark White wrote: Hi, Is anyone else having trouble connecting to main.g2.bx.psu.edu for FTP uploads? I cannot seem to connect since yesterday. Hi Rich, It's back up now. --nate Rich ___ 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/ ___ 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/
Re: [galaxy-user] Job is waiting to run
Hi Shisheng and Mónica, I see that jobs weren't dispatching on Galaxy Main, and have gotten them moving again. It'll take a bit to run through the backlog. Sorry for the inconvenience, and thanks for using Galaxy. --nate On Mar 22, 2012, at 5:30 AM, Mónica Pérez Alegre wrote: Hi Shisheng My partner and me have the same problem since yesterday. We would be very grateful for any help. regards -Mensaje original- De: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] En nombre de Shisheng Li Enviado el: miércoles, 21 de marzo de 2012 20:30 Para: galaxy-user@lists.bx.psu.edu Asunto: [galaxy-user] Job is waiting to run Dear Sir/Madam, I am a registered user of the public Galaxy Server (main). Any job I submitted today is labeled as Job is waiting to run forever. The total volume of my files is 249 mb, which is far below the quota limit of 250 gb, and I am trying to run less than 8 jobs. Could you please let me know the possible reasons? Sincerely, Shisheng ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] Problem using Galaxy
Hi,
Please try starting with:
$ LC_ALL=C ./run.sh
--nate
On May 18, 2012, at 11:22 AM, Seyed Mehdi Jazayeri wrote:
Dear Sir/Madam,
I am a PhD student working on RNA-Seq as my dissertation. As a matter of fact
I want to do analyses of gene expressions for the sequences that I have and
for that I have tried to use Galaxy tools as it is one of the best platforms
in order to do analysis for RNA-Seq as well as others. I did all about
installation of Galaxy on my Mac OS 10.7 Lion but when I run the commands I
do not get any result from running any type of commands. And when I do run.sh
I will have nothing done. As a sample I send you the command I ran on my
system as follow
iMac-de-Biologia:galaxy-dist LabBioMol$ ./run.sh
Traceback (most recent call last):
File ./scripts/paster.py, line 34, in module
command.run()
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py,
line 84, in run
invoke(command, command_name, options, args[1:])
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py,
line 123, in invoke
exit_code = runner.run(args)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py,
line 218, in run
result = self.command()
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py,
line 276, in command
relative_to=base, global_conf=vars)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py,
line 313, in loadapp
**kw)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py,
line 204, in loadapp
return loadobj(APP, uri, name=name, **kw)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py,
line 224, in loadobj
global_conf=global_conf)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py,
line 248, in loadcontext
global_conf=global_conf)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py,
line 278, in _loadconfig
return loader.get_context(object_type, name, global_conf)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py,
line 413, in get_context
section)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py,
line 458, in _context_from_explicit
value = import_string(found_expr)
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py,
line 18, in import_string
return pkg_resources.EntryPoint.parse(x=+s).load(False)
File /Users/LabBioMol/galaxy-python/galaxy-dist/lib/pkg_resources.py,
line 1954, in load
entry = __import__(self.module_name, globals(),globals(), ['__name__'])
File
/Users/LabBioMol/galaxy-python/galaxy-dist/lib/galaxy/web/__init__.py, line
5, in module
from framework import expose, json, json_pretty, require_login,
require_admin, url_for, error, form, FormBuilder, expose_api
File
/Users/LabBioMol/galaxy-python/galaxy-dist/lib/galaxy/web/framework/__init__.py,
line 31, in module
from babel.support import Translations
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/support.py,
line 29, in module
from babel.dates import format_date, format_datetime, format_time, LC_TIME
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py,
line 34, in module
LC_TIME = default_locale('LC_TIME')
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/core.py,
line 642, in default_locale
return '_'.join(filter(None, parse_locale(locale)))
File
/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/core.py,
line 763, in parse_locale
raise ValueError('expected only letters, got %r' % lang)
ValueError: expected only letters, got 'utf-8'
iMac-de-Biologia:galaxy-dist LabBioMol$
Now I would appreciate if you could advise me what is the problem and how to
solve it.
Thanks for your attention in advance.
Best regards
SMJ
--
SMJ
Seyed Mehdi Jazayeri
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Re: [galaxy-user] Galaxy main not running jobs..
On Jun 16, 2012, at 7:38 PM, Jayaraman, Shyam wrote: Hi, My username is shyamsundar19...@gmail.com Galaxy main is not running jobs since today morning. They stay queued (gray) forever. I deleted and then re queued them twice. Still nothing.. Is the server down or is something wrong with my account?? Hi Shyam, There was a problem with our cluster scheduler that was resolved on Saturday night. Please let us know if you still have problems running jobs. --nate Kindly advice. Shyam S Jayaraman MD Staff Research Associate Division of Dermatology LABioMed Research Institute CA ___ 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/ ___ 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/
Re: [galaxy-user] jobs not running on main server
On Jun 16, 2012, at 7:31 PM, Jacob Musser wrote: Hello, I uploaded a couple small files via ftp to do some basic text manipulation on them in the main galaxy server. I have queued up several jobs (including just importing the files I uploaded into a history) but after two hours of waiting they are still gray and waiting to run. I have been using galaxy regularly lately and have never had to wait very long for a job to start running (usually a matter of seconds). I am not above my quota so this is not the problem. Is there something else I need to do or is there a problem with the servers that would explain why jobs aren't being run? Hi Jake, There was a problem with our cluster scheduler that was resolved on Saturday night. Please let us know if you still have problems running jobs. --nate All the best, Jake ___ 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/ ___ 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/
Re: [galaxy-user] Include a data folder into Galaxy
On Jun 25, 2012, at 2:49 AM, Björn Grüning wrote: Hi Norbert, please have a look at the FTP-Upload feature from galaxy. The idea is that every user gets an FTP folder in which he can upload data. If you create such a directory you can probably link your data in such directories and galaxy will offer them to the users in the upload tool. In addition to FTP uploads for users, you may find the Data Library upload options useful: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files --nate Hope that helps. Cheers, Bjoern Hello, hopefully this is a simple question: How can I include a folder into the Galaxy server? The backgroud is, that I installed Galaxy on one of out server, which has access to the data folders used everywhere at our institute. So, instead of uploading and copying serveral big files (and waisting space on servers) I want to make a link to the appropiate folder, so it can be used like as the data has been uploaded. I hope I explained enough details... The question is: is it possible? Thanks for help, Norbert ___ 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/ ___ 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/
Re: [galaxy-user] Job is waiting to run for two days..
On Jun 25, 2012, at 1:53 PM, Shanshan Pang wrote: Hi, I am in the step map with bowtie with a status of JOB IS WAITING TO RUN for two days. I tried to re-run it, but did not work. So any suggestions on it? Thanks! Hi Shanshan, The cluster used to run mapping and other NGS tools is very busy right now. Canceling and rerunning your job moves it to the bottom of the queue, so I would not suggest doing that. If your work is urgent, a cloud instance is the recommended alternative for large NGS jobs: http://getgalaxy.org/cloud --nate Shanshan ___ 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/ ___ 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/
Re: [galaxy-user] file upload renamed
Hi Neil,
You're looking for the option to link to data, which is explained here:
http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
--nate
On Aug 22, 2012, at 12:44 AM, neil.burd...@csiro.au wrote:
When uploading a file using “Get Data” it seems the file is renamed to
dataset_’id’.dat in ~/database/files/000/. Is it possible for the file to
keep its name rather than being renamed?
It seems this is being done because of the line
${output.dataset.dataset.id}:${output.files_path}:${file_name}
in the upload.xml file. But I don't know where in the code it gets
${file_name} from. Any ideas how i change this to get the correct name of the
file being uploaded?
Neil
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use the Galaxy Development list:
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please use the interface at:
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___
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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
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
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Re: [galaxy-user] interupted running jobs restart
On Aug 27, 2012, at 8:53 AM, petr wrote: We are running galaxy on pbs cluster. In out setting some jobs can take several weeks to finish and it is virtually impossible to wait for suitable moment when server can be restarted or turn down without interrupting running tasks. Is there an option on server setting which will enable jobs which were interrupted because of the server maintenance to run again after the cluster is back on? best regards. Petr Hi Petr, Galaxy automatically picks up jobs that were running via PBS when it's restarted. Only local jobs can't be recovered after a restart. Is this not working properly in your environment? --nate ___ 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/ ___ 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/
Re: [galaxy-user] Installing Galaxy on SGE Cluster - Questions
On Oct 2, 2012, at 12:45 PM, greg wrote: Hi guys, I'm following the instructions here to install Galaxy on our SGE cluster. http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster (I'm aiming for the unified install) Here are a couple of questions I'm hoping someone could clear up for me: How exactly do I use virtual env to make Galaxy install all the Python libraries there instead of on the system? How will Galaxy know to use the virtualenv to run and to use it for grid jobs? Hi Greg, You should start at the top level documentation for production servers: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server This includes instructions on how to set up a virtualenv. You can make this the default by setting the $PATH in the Galaxy user's ~/.bash_profile to include the virtualenv's bin directory (at the beginning of $PATH). Do I need to install all of the dependencies listed on this page: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies If so what's a good way to make sure they're contained in the galaxy-dist directory and make sure Galaxy and all of the jobs know to find these tools there? You only need to install the dependencies for the tools that you plan to use. Setting them up is explained in more detail here: http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies --nate Thanks, Greg ___ 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/ ___ 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/
Re: [galaxy-user] Fastq-groomer help
On Oct 3, 2012, at 2:02 PM, Kshama Aswath wrote: Hello: I have this 20GB data that I have uploaded onto my history and trying to get it run thr groomer. Just the first data set was uploaded yesterday and ran groomer on it and it was not done this morning. The message indicated taht it is still waiting to be run !!! I have 57 data sets to run and would appreciate if you could inform me about how long it may take to even get started or any other suggestion to get my job done will help. Thanks so much, user name :genenart Kshama. Hi Kshama, There were some problems dispatching jobs that have been resolved. Sorry for the inconvenience, and thanks for using Galaxy. --nate -- Kshama Aswath Graduate Student-(PhD) Bioinformatics and computational Biology Prince Williams Campus George Mason University Manasses,VA-20110 ___ 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/ ___ 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/
Re: [galaxy-user] Can't seem to stop or restart the Galaxy in server
On Oct 18, 2012, at 1:43 AM, Todd Oakley wrote: Yes, daemon/stop-daemon is the best way. However, to stop a process that was not started with --daemon, this is what I do: ps aux | grep galaxy Identify the process numbers for 3 Galaxy processes, which will change every time Galaxy is restarted. For example this line: galaxy 11638 0.0 0.0 63856 988 ?SNov10 0:00 /bin/sh ./run.sh --reload indicates the process has a number of 11638. The 3 processes look like: • /bin/sh ./run.sh --reload • python ./scripts/paster.py serve universe_wsgi.ini --reload • /home/galaxy/bin/python ./scripts/paster.py serve universe_wsgi.ini --reload Next, kill the three processes with this command: kill -9 ID1 ID2 ID3 Hi Todd, Are you unable to Ctrl+C when using --reload? Using --reload is actually my workaround for this problem. --nate On Oct 17, 2012, at 10:17 PM, Enis Afgan wrote: With a certain version of Python there's been an issue stopping Galaxy using ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the background and then 'sh run.sh --stop-damemon' to stop it. Hope this helps, Enis On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari sachit.techner...@gmail.com wrote: Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local machine, I need to close the terminal and restart the terminal again. However, in server I integrated several tools, now I need to restart the server to test it. I used ./run.sh --reload doesn't restart the server and I can't stop the server. How can I stop or restart Galaxy in the real working server? Thanks ___ 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/ ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Hi Greg, That's correct. If you're starting Galaxy with an init script, I'd put the export there. --nate Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote: Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.edu wrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ 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/ ___ 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/ ___ 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/ ___ 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/
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
On Nov 5, 2012, at 3:26 PM, greg wrote: Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script? thanks again, Yes, even when running behind Apache, you'll need an init script (or similar method) to start the Galaxy server. --nate Greg On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Hi Greg, That's correct. If you're starting Galaxy with an init script, I'd put the export there. --nate Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote: Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.edu wrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ 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/ ___ 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/ ___ 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/ ___ 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
Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg
On Nov 5, 2012, at 3:40 PM, greg wrote: Ok, that makes sense. Would you mind sharing how you set up your init script? What goes in it, where you place it? There are some sample init scripts in the contrib/ directory of the distribution. You should be able to place the export near the top, where other variables are set. --nate Thanks again, Greg On Mon, Nov 5, 2012 at 3:33 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:26 PM, greg wrote: Well, I want it to ultimately run under Apache. Does it still make sense to go in an init script? thanks again, Yes, even when running behind Apache, you'll need an init script (or similar method) to start the Galaxy server. --nate Greg On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor n...@bx.psu.edu wrote: On Nov 5, 2012, at 3:15 PM, greg wrote: And am I correct in the thinking that only the machine hosting the galaxy web interface and submitting jobs needs the export DRMAA_LIBRARY_PATH= variable? The normal nodes running jobs don't need this, right? Hi Greg, That's correct. If you're starting Galaxy with an init script, I'd put the export there. --nate Thanks, -Greg On Mon, Nov 5, 2012 at 3:12 PM, greg margeem...@gmail.com wrote: Thanks Scott. I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0 I guess that would be it. For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable permanent on the machine? -Greg On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus scottmcma...@gatech.edu wrote: I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need DRMAA_LIBRARY_PATH to point to the library being used. So in the example below, I had this: echo $DRMAA_LIBRARY_PATH /usr/lib/libdrmaa.so -Scott Have you installed SGE on the same machine? If so, then you should be able to do a locate libdrmaa.so, which should point to SGE's DRMAA library. For example, on a machine that I use, I see this: $ locate libdrmaa.so /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls /usr/lib/libdrmaa* /usr/lib/libdrmaa.so /usr/lib/libdrmaa.so.1.0 $ ls -la /usr/lib/libdrmaa.so lrwxrwxrwx 1 root root 15 Apr 18 2012 /usr/lib/libdrmaa.so - libdrmaa.so.1.0 You may also want to try updatedb (again, assuming you're using Linux) to index the files on your machine. Finally, if you can't find it, then you should check if you actually have SGE installed on that machine. I like to use dpkg on Ubuntu/Debian and yum on Centos to manipulate packages. -Scott I'm trying to install Galaxy on our SGE cluster (using the Unified method). I installed galaxy-dist, and now I'm on this section: drmaa egg The drmaa egg is provided by Galaxy, but you must tell it where your resource manager's DRMAA library is located, and this is done with the$DRMAA_LIBRARY_PATH environment variable: % export DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3 % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0 However I can't locate the the file libdrmaa.so.1.0.3 anywhere. In fact I don't have have an lsf nor sge directory within galaxy-dist. Thanks, Greg ___ 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/ ___ 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/ ___ 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
Re: [galaxy-user] [galaxy-dev] Account had be deleted ?
On Nov 7, 2012, at 5:47 AM, Diam Hsu wrote: Dear Sir or Madam, I used to use Galaxy to analyze NGS data, but these two days I could't login my Galaxy account, it also told me that my account has been marked deleted, and asked me to contact the Galaxy administrator to restore my account. Could you help me restore my accounts because I have to use Galaxy to finish my thesis. Hi, Your account was disabled because we discovered that you were using more than one account. The Galaxy Main server is a public resource and we implemented quotas to give everyone fair access to our (limited) resources. If you need more resources than we are able to make available on Galaxy Main, your needs might be best suited to a cloud or local instance of Galaxy. For more information on these, see: http://wiki.g2.bx.psu.edu/Big%20Picture/Choices If you'd like to use one of your existing accounts, please let me know which one and I'll re-enable it. --nate Thank you very much for your help!!! Best regards, Dima Hsu Graduate student, Graduate Institute of Biomedical Informatics Taipei Medical University, Taipei, Taiwan Email:b1984...@gmail.com ___ 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/
Re: [galaxy-user] Local Install - Understanding Upload File Concept
On Nov 16, 2012, at 10:41 AM, greg wrote: On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 9:14 AM, greg wrote: Are you running the upload tool on a cluster? --nate Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't verified that it's doing that yet. I wanted to upload a file to test on first. Here are the changes I made to universe_wsgi.ini after copying the sample: #upload1 = local:/// I'm guessing that it's working, you can verify by having a look in your Galaxy server output/log file. new_file_path will need to be set to something that is accessible on the cluster. --nate -Greg ___ 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/
Re: [galaxy-user] Local Install - Understanding Upload File Concept
On Nov 16, 2012, at 12:22 PM, greg wrote: I guess I'm still confused about new_file_path. The upload tool uses that directory to store files temporariliy until the upload completes? And then moves it? (Will it clean up anything placed in the new_file_path directory?) Yes, the parameters of the upload tool are written to a temp file in this directory. It is cleaned up upon completion. A lot of other things use new_file_path, and not all of them clean themselves up, so it's a good idea to use an automated process to clean the directory. --nate Thanks, Greg On Fri, Nov 16, 2012 at 10:56 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 10:41 AM, greg wrote: On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 9:14 AM, greg wrote: Are you running the upload tool on a cluster? --nate Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't verified that it's doing that yet. I wanted to upload a file to test on first. Here are the changes I made to universe_wsgi.ini after copying the sample: #upload1 = local:/// I'm guessing that it's working, you can verify by having a look in your Galaxy server output/log file. new_file_path will need to be set to something that is accessible on the cluster. --nate -Greg ___ 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/
Re: [galaxy-user] Local Install - Understanding Upload File Concept
On Nov 16, 2012, at 12:24 PM, greg wrote: Also what would I look for in the log file to know if it's issuing jobs? I started a new upload, but I don't see anything from the galaxy user when I run qstat. If you follow the log, you should see messages from galaxy.jobs, and specifically, galaxy.jobs.runners.drmaa. --nate Thanks again. Greg On Fri, Nov 16, 2012 at 12:22 PM, greg margeem...@gmail.com wrote: I guess I'm still confused about new_file_path. The upload tool uses that directory to store files temporariliy until the upload completes? And then moves it? (Will it clean up anything placed in the new_file_path directory?) Thanks, Greg On Fri, Nov 16, 2012 at 10:56 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 10:41 AM, greg wrote: On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor n...@bx.psu.edu wrote: On Nov 16, 2012, at 9:14 AM, greg wrote: Are you running the upload tool on a cluster? --nate Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't verified that it's doing that yet. I wanted to upload a file to test on first. Here are the changes I made to universe_wsgi.ini after copying the sample: #upload1 = local:/// I'm guessing that it's working, you can verify by having a look in your Galaxy server output/log file. new_file_path will need to be set to something that is accessible on the cluster. --nate -Greg ___ 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/
Re: [galaxy-user] Problems with large gzipped fasta files
Hi Jim, Could you send me a URL to the dataset so I can grab a copy and try to reproduce this problem? Sorry for the trouble you've been having with the upload functionality and the delay in getting back to you. --nate On Feb 5, 2013, at 8:48 AM, Jim Robinson wrote: Hi, I am having a lot of difficulty uploading some large gzipped fastqs (~ 10GB) to the public server. I have tried both ftp and pulling by http URL. The upload succeeds, however I get an error as it tries to gunzip it.I have tried more than 10 times now and succeeded once. These files are correct and complete, and gunzip properly locally. The error shown is usually this empty format: txt, database: ? Problem decompressing gzipped data However on 2 occasions (both ftp uploads) I got the traceback below. Am I missing some obvious trick? I searched the archives and see references to problems with large gzipped files but no solutions. Thanks Jim Traceback (most recent call last): File /galaxy/home/g2main/galaxy_main/tools/data_source/upload.py, line 384, in module __main__() File /galaxy/home/g2main/galaxy_main/tools/data_source/upload.py, line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File /galaxy/home/g2main/galaxy_main/tools/data_source/upload.py, line 270, in add_file line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) File /galaxy/home/g2main/galaxy_main/lib/galaxy/datatypes/sniff.py, line 106, in convert_newlines shutil.move( temp_name, fname ) File /usr/lib/python2.7/shutil.py, line 299, in move copy2(src, real_dst) File /usr/lib/python2.7/shutil.py, line 128, in copy2 copyfile(src, dst) File /usr/lib/python2.7/shutil.py, line 84, in copyfile copyfileobj(fsrc, fdst) File /usr/lib/python2.7/shutil.py, line 49, in copyfileobj buf = fsrc.read(length) IOError: [Errno 5] Input/output error ___ 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/ ___ 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/
Re: [galaxy-user] Problems with large gzipped fasta files
On Feb 13, 2013, at 12:25 PM, Jim Robinson wrote: Sorry Nate, I misunderstood at first, you want a URL to the dataset here on my server? I can definitely copy one up to an http server, I still have Ricardo's files on a hard disk. I'll start the copy now and let you know when its ready. Yeah, that's it exactly. Thanks! --nate Jim Hi Jim, Could you send me a URL to the dataset so I can grab a copy and try to reproduce this problem? Sorry for the trouble you've been having with the upload functionality and the delay in getting back to you. --nate On Feb 5, 2013, at 8:48 AM, Jim Robinson wrote: ___ 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/
Re: [galaxy-user] Problem Loading History Pane
On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote: To whom it may concern: The History panel on the right side of the Galaxy page is taking a very very long time to load. Also, when it does load, I have tired to save my .bam files and the transmissions gets truncated to ~7000kb - 8000kb of data. All of my .bam files are several GB. Some times, when I retry tor download the data, it succeeds and other times it is again truncated. The size of the truncation may be different for the same file on the retry attempt. Is there a problem with Galaxy? Hi Mike, There are some performance problems with the Main site that we are currently investigating. Thanks for the information and we apologize for the problems. --nate Thanks, Mike ___ 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/ ___ 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/
Re: [galaxy-user] wrong disk usage figure reported on galaxy main
On Mar 7, 2013, at 4:46 AM, pbour...@agilent.com pbour...@agilent.com wrote: Hi, I noticed since yesterday that my “disk usage” % (top-right) has jumped from ~20% to ~ 80 % for no apparent reason. The added size of all my current histories is now only 29 Gb, which should be ~11%, and I looked in my deleted histories but all of them are 0 bytes in size and with status “deleted permanently”, there are no histories currently shared with me by other users. Is there something else I can check or look into in order to get my disk usage back to where it should be ? Many thanks in advance for your help ! Hi Pierre, There was an error in calculating your disk usage - it has been recalculated and the correct number should now be displayed. Sorry for the inconvenience. --nate Pierre ___ 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/ ___ 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/
Re: [galaxy-user] problem with registration
On May 28, 2013, at 5:40 AM, Patel, Bella wrote: Hi I have tried to register for Galaxy but apparantly a user with my email address already exists! Very strange as I have never registered for this software. Can you advise? Bella Patel Hi Bella, It's possible that your account creation request was accidentally submitted twice, which would have displayed the error message you received. If you are unable to log in to the account using the password you specified, please use the password reset feature to gain access to your account. --nate ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Egg build failed for numpy 1.6.0
Hi, Almost all of the Galaxy development team uses Macs, so it should certainly work. The problems with eggs, as you have both found, typically come with using non-standard versions of Python. Your best bet is to use the version that shipped with your version of OS X, which can be found in /System/Library/Frameworks/Python.framework. You can ensure that this version is always used by putting it first on $PATH or setting up a virtualenv with it, e.g.: % virtualenv --python=/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python genv --nate On Aug 5, 2013, at 8:12 AM, Fabrice BESNARD wrote: Hi, I am preferentially using the main server. But recently I have also tried to build a local Galaxy server. I also have a mac (Mac Pro OSx 10.6.8). Since I am not a specialist at all, I asked some kind of expert people from my institute. They told me that installing Galaxy on Mac can really be nightmare because there are some conflicts in the versions of python... This could explain the problem you are encountering with the egg dependencies. So they advised me to install an Ubuntu (12.04) operating system in a virtual machine using Virtual box. This is supposed to be much easier to install Galaxy and indeed, the installation of my local galaxy server ran fast and well. However, I don't know whether the tip is good or not, because I am now facing big problems with the virtual machine: the Ubuntu virtual machine is very unstable and often crashes while running big datas on Galaxy... The problem does not come from Galaxy, but from either Ubuntu guest system, the virtual machine or the communication with the mac host system and I haven't found out how to fix it yet. But since your version of Mac is different, you can try this solution, it might work better in your configuration. Hope that helps, Fabrice But at the moment, I have lots of problem with the Hi, I am trying to install a local version of galaxy on my mac book (x86_64, OSx 10.8.4). I seem to be having a lot of trouble with fetching and installing specific egg dependencies. Initially pysam was giving me trouble, but once I ran scramble.py -e pysam, the problem was fixed. Now I have trouble with the numpy egg dependency. Does anyone have any idea why a egg would fail to build. I am assuming it is because I have a more recent numpy version (1.7.1) installed already. What should I do, short of uninstalling the newer version of numpy ? Any help on the matter would be greatly appreciated. Thank you. L -- === Dr. Lahcen Campbell Contact: lahcencampb...@gmail.com http://bioinf.may.ie/index.html === ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +33-1-44-32-39-44 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at:
Re: [galaxy-user] error message from Filezilla
On Sep 11, 2013, at 7:48 AM, Amit Pande wrote: Hi, I am getting the following error from the server : Command:USER genebus...@googlemail.com Response:331 Password required for genebus...@googlemail.com Command:PASS *** Response:530 Sorry, the maximum number of clients (3) for this user are already connected. Error:Critical error Error:Could not connect to server. Can you please help. Hi Amit, Please give it a try now, I've restarted the FTP server (I believe this is due to a bug in the server). --nate warm regards, Amit. ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] cannot download data to Galaxy
On Sep 11, 2013, at 9:56 AM, Elwood Linney wrote: Hello, My connection with Galaxy online shutoff last night while I was transferring data to it. When I tried to connect again with Fetch this morning I was not allowed and a message like Sorry the maximum number of clients for this user are already connected. I have had what appears to be the bad habit of not logging off to Galaxy. I am working on the same data sets with three different computers, I only have one login to Galaxy, so yes, I was logged in on 3 different computers. When I logged off of them, and tried to transfer data, I still got the same message. I realize people might be trying to get around the 250gb limit by having multiple logins--I am not one of them, I am the only user on the three computers I am using. If not logging off when I leave the computer is a problem to Galaxy, I will religiously log off each time I am not using the computer (the computers are in three different rooms in my lab and my lab consists of just me and a tech--I am the only one who knows the computer login for both the computers and for Galaxy). If I have created a problem by being lazy, I apologize, but I have grown dependent upon using Galaxy online and some new data just came in. Hi Elwood, This is not due to staying logged in to the web interface, I believe it's a bug in the FTP server that we're using. I've restarted the server, could you let us know if you're still getting the maximum clients message if you try to connect? --nate Sincerely, Elwood Linney Professor of Molecular Genetics and Microbiology Duke University Medical Center ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Online galaxy turning everything red on RNAseq steps
The problem with cuffdiff should be fixed. Still looking at the tophat failures. Thanks for your patience, and for sticking with us as we iron this out. --nate On Oct 9, 2013, at 7:52 PM, Jennifer Jackson wrote: Hi Elwood, As I emailed to your direct question, we are looking at your bug reports in detail and will get back to you there. Thanks for submitting the problems that way. For anyone else reading, if you find problems right now on the upgraded server, we are most definitely interested in learning about them. Please submit bug reports for anything odd, even if it seems small, and put in the comments additional observations if you have time. We appreciate the feedback, and your patience, as always! Jen Galaxy team On 10/9/13 1:04 PM, Elwood Linney wrote: Hello, I have been waiting a few weeks to process some RNA seq datasets but woke up this morning with lots of steps red. I thought it just might be because of the movement of the system but I processed steps for some histories and everything has turned red. I also noticed that online Galaxy now has RNAseq steps separated into two sections--does this have something to do with the problems? el linney Duke University Medical Center ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Issues on RNAseq since the changeover
On Oct 18, 2013, at 12:48 PM, Elwood Linney wrote: My histories seem to be stopping their processing around the Tophat-cuffmerge steps since the change over of Galaxy online. Sometimes a red box appears over my history name but disappears in a minute or less. I am wondering, given the way the Toolshed now looks different for RNAseq work, if some changes have been made that are disallowing the procedures I used previously. For example: I run larger Fastq files (100 million to 200 million 50bp single-ended reads per sample). I have been grooming my illumina fastq's, using Tophat (not Tophat2) for alignment, then Cuffmerge, then Cuffdiff. This worked in the past but my history are just getting thru Tophat or Cuffmerge and stalling. Should I be doing this in a different manner? This has been my second time around with these datasets after it was suggested that I delete and start all over again. Elwood Linney Hi Elwood, The wait is unfortunately due to two limits on large multicore jobs like cuffmerge and tophat: - Only 1 job per user could previously be placed into the cluster queue for multicore jobs - as of this morning we've increased it to 2 - All of the nodes available for running multicore jobs are currently allocated, so there is some wait, even once your job is allowed to be added to the queue You had a tophat job running prior to increasing the limit to 2, so no other jobs would have even been eligible to complete until that job finished. After the increase you still have the same tophat job running but another one has been queued, and it is waiting for available nodes. I hope you'll find that the wait time for these is shorter than on the old Galaxy Main. We are also expecting to add additional hardware to this pool soon. --nate ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] problems in transitioning from Tophat to Cuffdiff
This is great news, thanks for letting us know. --nate On Oct 22, 2013, at 2:34 PM, Elwood Linney wrote: thank you all, its clearly working now and that is coming just in time, the results of two of these datasets will help us plan our next experiments for capping up a manuscript or two el linney On Tue, Oct 22, 2013 at 12:03 PM, Nate Coraor n...@bx.psu.edu wrote: Hi Elwood, Jeremy and I took at a look at this. The failures in your history with this message: Error: number of labels must match number of conditions ...are due to a regression in the cuffdiff tool which Jeremy has just fixed. Some characters such as spaces in the condition name were valid prior to the move, but after the move they became invalid. They should now be valid once again. You've got one tophat job running and a cuffdiff job queued, and the rest of your grey datasets are waiting for those two jobs to be finished before they'll be queued (we'll be working on creating a visual distinction for this). I fixed the queued cuffdiff job, which I believe should allow it to run without error (or at least, not the same error). --nate On Oct 22, 2013, at 9:56 AM, Jennifer Jackson wrote: Elwood, Would you please share: 1. an original history that worked (if possible) 2. the workflow you are using and let me know how you generated (did you extract it recently (last week or so)? 3. problem history There are a few known issues in here, some mitigated, one that has to do with extracted workflows from existing older histories that is Cuffdiff specific (actually, a few problems, found another last night). I want to rule those out or at least try to provide feedback. I am at a conference over next several days, so let's use galaxy-bugs as a cc whenever we communicate so nothing is left lingering, plus I know Nate was looking into some of your data. Jeremy may jump also in at any time and help - he is the author of the wrapper. So, in your reply, remove galaxy-u...@bx.psu.edu and add galaxy-b...@bx.psu.edu Jen Galaxy team On 10/22/13 5:42 AM, Elwood Linney wrote: After successfully using RNAseq software in Galaxy online for about 10 different datasets to just get gene expression differences between replicates from control versus exposed zebrafish embryos, I am having no luck getting cuffdiff to work with the moved Galaxy. I had this problem with histories developed before the move and histories developed after the move. I have had this problem using an order cuffmerge gtf file that worked in the past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the files and by just using a ref file gtf from UCSC. I don't know if this is just some interface problem with a different version of the software that was included with the move, or a reference genome that does not interface with Cuffdiff. It has happened with about 5 different histories. Is anyone else having this problem? And found a solution? Elwood Linney ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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
Re: [galaxy-user] Pb with ftp connexion (FileZilla)
Hi Fabrice, Are you connecting to `usegalaxy.org`? This changed when we moved main.g2.bx.psu.edu to usegalaxy.org. Thanks, --nate On Nov 8, 2013, at 6:32 AM, Fabrice Besnard wrote: Hi, I am trying to connect to the Galaxy server via Filezilla in order to upload datasets. The connexion fails, with this message: ECONNREFUSED - Connection refused by server. I have checked my password which works well to login to my account on the main server. Is it just temporal? Should I try to reset my password and give a new try? Thanks for assistance, best, -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +33-1-44-32-39-31 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] SNP finding
Hi Mark, This error is not tool related. Could you click the “bug” icon to send us an error report? —nate On Nov 11, 2013, at 8:33 AM, Mark Lindsay m.a.lind...@bath.ac.uk wrote: Dear Galaxy Users I wondered if anybody is having the same problem. I am trying to run CuffDiff using the latest version of GenCode18 and keep getting the following error message. Is there a problem with the network or is it me? Best wishes Mark Screen Shot 2013-11-11 at 13.32.12.png ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] jobs not running
Hi Ruth, The queue was very busy this morning as it would appear that someone is using the site for a workshop or class. I've cleared out these jobs since they were blocking regular use, and your jobs should begin running normally shortly. Sorry for the inconvenience. Thanks, --nate On Wed, Dec 4, 2013 at 8:20 AM, Ruth Eberhardt ru...@ebi.ac.uk wrote: Hi Apologies if this is the wrong mailing list. Is there a problem with jobs running on Galaxy today? I have jobs (MACS and FASTQC) which have been waiting to run for over 4 hours, bit not yet started to run. Many thanks Ruth ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Job of format conversion waiting for over 5 days
Hi Eduardo, I believe the job in question is not running because one of its inputs (#101) failed to have metadata set properly. This situation can be fixed by using the 'auto-detect' button on the failed dataset. --nate On Mon, Mar 31, 2014 at 5:20 PM, Eduardo Fox ofoxo...@gmail.com wrote: 2014-03-31 11:29 GMT+02:00 Eduardo Fox ofoxo...@gmail.com: Hello, Please I would like to know if it would be normal of a job to be queued for several days? It is a SAM to BAM conversion, and it has been waiting for over 5 days to run. I understand that the SAM file is pretty large but other similar conversions I made on the server recently were done within few minutes. Thanks! -- Eduardo G. P. Fox http://eduardofox.blogspot.com.br/ http://www.mendeley.com/profiles/eduardo-fox/ -- Eduardo G. P. Fox http://eduardofox.blogspot.com.br/ http://www.mendeley.com/profiles/eduardo-fox/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
