Re: [galaxy-user] Include a data folder into Galaxy
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. 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/
Re: [galaxy-user] Bowtie and BWA queue..other jobs dont
Hi Antony, Jobs are sent to different clusters by type, so it is not unusual to see some jobs complete quickly while others take longer. Jobs on the NGS cluster (where Bowtie and BWA would be run) are processing as normal, but Galaxy was very busy over the weekend and continues to be busy this morning. Right now I see that you have only one NGS job in the queue - so perhaps at least some of your work has completed since this question was originally sent in on Saturday. If your work is urgent, a cloud instance is the recommended alternative for large NGS jobs: http://getgalaxy.org/cloud Best, Jen Galaxy team On 6/23/12 5:47 PM, Antony Jose wrote: Hi, Bowtie and BWA jobs seem to be forever on queue, but other jobs run normally. Is there a problem or is this expected? Thank you. Antony -- Antony M Jose, Dept. of Cell Biology Molecular Genetics, University of Maryland, Rm 2116, Bioscience Research Building, College Park, MD - 20742. ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ -- Jennifer Jackson http://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/
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] Include a data folder into Galaxy
Hi, What I did was to create a directory with sub-directories for each user or data set. Then you can change the universe_wsgi_ini in line 375 and put your directory path there library_import_dir=your path Then as admin you can upload the files from the directory, actually you create a link to them and also change the accession permission to those files. Best, Luciano On Mon, Jun 25, 2012 at 1:49 AM, Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de 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. 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/ -- *Luciano Cosme* - PhD Candidate Texas AM Entomology Vector Biology Research Group www.lcosme.com 979 845 1885 co...@tamu.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] Problem with Depth of Coverage on BAM files (GATK tools)
Hello Lilach, Currently, the human reference genome indexed for the GATK-beta tools is 'hg_g1k_v37'. The GATK-beta tools are under active revision by our team, so we expect there to be little to no change to the beta version on the main public instance until this is completed. Attempting to convert data between different builds is not recommended. These tools are very sensitive to exact inputs, which extends to naming conventions, etc. The best practice path is to start and continue an analysis project with the same exact genome build throughout. If you want to use the hg19 indexes provided by the GATK project, a cloud instance is the current option (using a hg19 genome as a 'custom genome' will exceed the processing limits available on the public Galaxy instance). Following the links on the GATK tools can provide more information about sources, including links on the GATK web site which will note the exact contents of the both of these genome versions, downloads, and other resources. Hopefully this helps to clear up any confusion, Best, Jen Galaxy team On 6/21/12 7:50 AM, Lilach Friedman wrote: Hi Jennifer, Thank you for this reply. I made a new BWA file, this time using the hg19(full) genome. However, when I am trying to use DepthOfCoverage, the reference genomr is stucked on the hg_g1k_v37 (this is the only option to select), and I cannot change it to hg19(full). Most probably, because I selected hg_g1k_v37 in the previous time I tried to use DepthOfCoverage. It seems as a bug? How can I change it? Thanks, Lilach 2012/6/18 Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu Hi Lilach, The problem with this analysis probably has to do with a mismatch between the genomes: the intervals obtained from UCSC (hg19) and the BAM from your BWA (hg_g1k_v37) run. UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'. Even though these are technically the same human release, on a practical level, they have a different arrangement for some of the chromosomes. You can compare NBCI GRCh37 http://www.ncbi.nlm.nih.gov/genome/assembly/2758/ with UCSC hg19 http://genome.ucsc.edu for an explanation. Reference genomes must be /exact/ in order to be used with tools - base for base. When they are exact, the identifier will be exact between Galaxy and the source (UCSC, Ensembl) or the full Build name will provide enough information to make a connection to NCBI or other. Sometimes genomes are similar enough that a dataset sourced from one can be used with another, if the database attribute is changed and the data from the regions that differ is removed. This may be possible in your case, only trying will let you know how difficult it actually is with your analysis. The GATK pipeline is very sensitive to exact inputs. You will need to be careful with genome database assignments, etc. Following the links on the tool forms to the GATK help pages can provide some more detail about expected inputs, if this is something that you are going to try. Good luck with the re-run! Jen Galaxy team On 6/18/12 4:42 AM, Lilach Friedman wrote: Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals. I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Matching pattern: XT:A:U, and then SAM-to-BAM) and the intervals file (in advanced GATK options). The consensus genome is hg_g1k_v37. I got the following error message: An error occurred running this job: /Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main # ERROR -- # ERROR A USER ERROR has occurred (version 1.4-18-g80a4ce0): # ERROR The invalid argume /Is it a bug, or did I do anything wrong? I will be grateful for any help. Thanks! Lilach/ / ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server atusegalaxy.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/ -- Jennifer Jackson http://galaxyproject.org -- Jennifer Jackson http://galaxyproject.org ___ The
