Re: [galaxy-user] Do I need to have tool or dependencies installed in the server to run Galaxy tools?
Hi Sachit, the bismark wrapper is not finished, that's the reason its only in the test-toolshed. When its finished you do not neet bismark to be installed, but bowtie. Cheers, Bjoern I integrated Bismark in Galaxy in my server. I downloaded Bismark from Galaxy Tool shed. I just copied the Bismark into /tools directory and added some codes in tool_conf.xml to make it visible. Do I need to install the real Bismark application in the server too? I am really confused here. 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.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] Error installing MACS on local Galaxy
Hi Jennifer, I am now trying to run MACS 1.3.7.1. in Galaxy. I also ran python setup.py install and set variables $PATH and $PYTHONPATH for the commandline run. Nevertheless, MACS gives error: /ImportError: No module named MACS.OptValidator/ I checked - library OptValidator.py exists in the file system, and path to the folder is both in $PATH and $PYTHONPATH Any ideas? best regards, Jerzy On 10/17/2012 04:18 PM, Jennifer Jackson wrote: Hello Jerzy, The MACS wrapper in Galaxy currently supports version 1.3, which explains the problems with 1.4. Tool dependencies are noted on this wiki: http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies For the other errors, are you trying to run MACS on the command line or within Galaxy? For command line, some environment variables need to be set up, the MACS documentation has the details: http://liulab.dfci.harvard.edu/MACS/INSTALL.html Hopefully this helps, Jen Galaxy team On 10/17/12 2:09 AM, Jerzy Dyczkowski wrote: Hello, I cannot run MACS on the local Galaxy. When I install MACS version 1.4., it gives error something like cannot find macs. When I install version 1.3.7.1 it gives error /line 34, in module from MACS.OptValidator import opt_validate ImportError: No module named MACS.OptValidator/ I sourced PATH to the directory with this module. Any ideas? best regards, Jerzy -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email:jerzy.dyczkow...@eni-g.de Phone: +49 (0)551 39-12352 ___ 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/ -- Dr Jerzy Dyczkowski Bioinformatician Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE) Grisebachstr. 5 D-37077 Göttingen Email: jerzy.dyczkow...@eni-g.de Phone: +49 (0)551 39-12352 ___ 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
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 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/
Re: [galaxy-user] Export to file
Hi Jeremy, Thanks for your offer of help. By the time I got your email I had already added many new jobs to the history that are either running now or waiting to run. Since I read somewhere that if the history is running then there are problems exporting I shared a clone of the history with you. The clone should be identical to the history that I was having problems with yesterday. I can share with you the original history once the jobs have finished running (but it might take a while). Thanks, Dave On Wed, Oct 17, 2012 at 10:35 PM, Jeremy Goecks jeremy.goe...@emory.eduwrote: Dave, There's likely something problematic about your history that causing problems. Can you share with me the history that's generating the error? To do so, from the history options menu -- Share/Publish -- Share with a User -- my email address Thanks, J. On Oct 17, 2012, at 6:58 PM, Jennifer Jackson wrote: Hi Dave, Yes, if your Galaxy instance is on the internet, for entire history transfer, you can skip the curl download and just enter the URL from the public Main Galaxy server into your Galaxy directly. To load large data over 2G that is local (datasets, not history archives), you can use the data library option. The idea is to load into a library, then move datasets from libraries into histories as needed. Help is in our wiki here: http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files Take care, Jen Galaxy team On 10/17/12 3:21 PM, Dave Corney wrote: Hi Jen, Thanks for your response and suggestion. Just so that it is clear, for your second method, where I export to file and then use curl, I will download to my computer as an intermediate stage? Is there a simple way to take the history and datasets from PSU galaxy to our Princeton galaxy directly (without downloading to my computer first)? Unfortunately, we don't have FTP on our own galaxy, which is why I was looking for alternatives (each file is 2GB, so uploading through the browser won't work either). It seems that to import from file, the file needs to have a URL and I'm not sure how to go about that if the file is store locally on my computer. Thanks, Dave On Wed, Oct 17, 2012 at 6:12 PM, Jennifer Jackson j...@bx.psu.edu mailto:j...@bx.psu.edu wrote: Hi Dave, To export larger files, you can use a different method. Open up a terminal window on your computer and type in at the prompt ($): $ curl -0 'file_link' name_the_output Where file_link can be obtained by right-clicking on the disc icon for the dataset and selecting Copy link location. If you are going to import into a local Galaxy, exporting entire histories, or a history comprised of datasets that you have copied/grouped together, may be a quick alternative. From the history panel, use Options (gear icon) - Export to File to generate a link, then use curl again to perform the download. The Import from File function (in the same menu) can be used in your local Galaxy to incorporate the history and the datasets it contains. Hopefully this helps, but please let us know if you have more questions, Jen Galaxy team On 10/17/12 2:37 PM, Dave Corney wrote: Hi list, Is there a currently a known problem with the export to file function? I'm trying to migrate some data from the public galaxy to a private one; the export function worked well with a small (~100mb) dataset, but it has not been working with larger datasets (2GB) and I get the error: Server Error. An error occurred. See the error logs for more information. (Turn debug on to display exception reports here). Is there a limit on the file size of the export? If so, what is it? Thanks in advance, Dave _ 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 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 Galaxy User list should be used for the discussion of
Re: [galaxy-user] galaxy MAIN data problem
Hello Kshama, We would like to help. I looked for an account under your email address kasw...@masonlive.gmu.edu on the public Main Galaxy instance at http://main.g2.bx.psu.edu (http://usegalaxy.org), and did not find one, so I will tell you how to check for the data yourself, then you can share your account email address if you are still stuck. 1 - For unexplained data counting towards your quota: Check for datasets in histories that are deleted, but not permanently deleted. Inside a history, select Options (gear icon) - View Deleted Datasets to bring up those that were deleted. Each will note if permanently deleted or not and give the option to purge. Also check for complete histories that may be deleted, but also not permanently deleted (or purged). Select Options (gear icon) - Saved Histories, then view all to see active and deleted. The table will note if the data is deleted, but not purged. The option to purge/permanently delete will also be given. 2 - To locate the output of workflow that seems to be missing: Check for hidden datasets. From within a history (the history that launched the job, if no other history was created), select Options (gear icon) - View Hidden Datasets to bring up those that were hidden by the workflow. (Hiding intermediate datasets is a workflow option). Perhaps there was an error early on in the workflow, before the stage where a result would be written to a new history. I would also recommended that you experiment with a test run where the output is not written to a new history (if you have not already done so), just to rule out any problems central to the workflow (or the inputs), independent of the new history issue. Help is also in this wiki: http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets See Hidden Delete_vs_Delete_Permanently Hopefully this helps, but please let us know if you need more assistance, Jen Galaxy team On 10/17/12 7:20 PM, kaswath wrote: Hello Galaxy, I have a dataset about *20.8GB *to work with using the NGS analysis. I FTPd the dataset and created a workflow for the analysis and ran the job on the entire 20.8GB on Galaxy main around september 27th. I waited on about two to four days .no output of any sort ! I had requested the results be saved in a different history. I checked , but no new history with results was created ! I reran the job again after a week or so and still no results ! I had tried running this on small dataset and it had worked earlier ! Anyhow, getting back to this proble,m I have NOT receive any error message however , my USAGE bar on the top right is at 90% !! So I went back and deleted the old copies of my history I had , even so the usage bar is still at 90%! Before I ran my workflow I had the usage bar being way less ! Please can u let me know what is happening? Why I have not received any results on my analysis yet? I really need to get this done ASAP ! Thanks so much for all your help ! Regards Kshama. ___ 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/
