[galaxy-dev] Copying galaxy folder from linux to windows
Hi there, Since manually deleting the files from the galaxy database is not advised, I thought of just copying the galaxy-dist folder from the linux server to my windows. I copied everything except the 000 folder, where the datasets are located. I also have Cygwin installed in windows. I was wondering if galaxy would still run even if I just copied the folder. About my dataset cleanup problem: I tried running the cleanup scripts, but since the disk is full I cannot make any changes to universe_wsgi.ini (I get this KeyError problem). Any suggestions on how I could free some space/delete datasets? Is manually deleting tmp files also not advised? I am not allowed to remove/alter any other file aside from those within galaxy-dist. Any help would be greatly appreciated. Cheers, DM ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem with cleaning up galaxy datasets
Dear all, I have done what was suggested in this thread (remove the # sign), but somehow I still got the same error. Any suggestions on how to get past this? Cheers, Diana On Mon, Apr 16, 2012 at 12:51 AM, Jennifer Jackson j...@bx.psu.edu wrote: repost bounced msg, see why below - Date: Sat, 14 Apr 2012 22:33:22 +0200 From: Klaus Metzeler m...@klaus-metzeler.de To: Michael Moore michaelglennmo...@gmail.com Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Problem with cleaning up galaxy datasets Message-ID: 4F89DF12.6010606@klaus-**metzeler.de4f89df12.6010...@klaus-metzeler.de Content-Type: text/plain; charset=ISO-8859-1; format=flowed OK, this pointed me to the right direction. The universe_wsgi.ini file has a key that reads: database_connection = sqlite:///./database/universe.**sqlite?isolation_level=**IMMEDIATE This entry was commented out in my version of the file (ie, had a # in front of it). While Galaxy itself uses this database connection by default, but the cleanup script looks for this config file entry to locate the database. So, if anyone encounters the same problem, just un-comment this entry and all runs fine. Thanks for your help, Michael. -- Why did this bounce? Digest content not stripped (#2). If you reply to a thread in a digest, please 1. Change the subject of your response from Galaxy-dev Digest Vol ... to the original subject for the thread. 2. Strip out everything else in the digest that is not part of the thread you are responding to. Thanks Klaus for sending in the solution! - Galaxy team -- Jennifer Jackson http://galaxyproject.org __**_ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Deleting datasets from server
This would work for both .dat and tmp files? I was thinking about deleting them manually but the idea of them being connected to a database was bothering me. Other than minor errors, will there be no other serious repercussions? Thanks for the reply! DM On Thu, Apr 19, 2012 at 1:34 PM, JIE CHEN jiechenable1...@gmail.com wrote: Of course. I deleted lots of times. But be careful if some of the files are important. Once you deleted them, all the files will disappear from the user's history(or when you open them, you will run into errors). You should know the files you are deleting. On Wed, Apr 18, 2012 at 8:40 PM, diana michelle magbanua dmdrmagba...@gmail.com wrote: Hi there, I would just like to ask if I could just directly delete the .dat files from the database folder of Galaxy (or even just the tmp files). I am not allowed to delete any other file from the computer other than the ones in galaxy-dist. I have tried running the cleanup scripts, but since the disk is already full, I am experiencing some problems with the cleanup. I'm just new to using this application, so any help would greatly be appreciated. Cheers, Michelle ___ 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/ -- Diana Michelle DR Magbanua Professional Service C4 Rice Center International Rice Research Institute ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Getting the input name of the dataset
Hi there, I am new to Galaxy and I've just recently learned how to integrate a Perl script to it. Now, my code uses the input file's name as a header for a column in the output. When I ran it in Galaxy, I did get the filename, but it's the one ending in .dat (actually, I got the entire path of the file). I was wondering if it's possible to retain the original name of the file (or retrieve the name of the input dataset) and use it in the output file. I can't think of a Perl script for this yet, for my scripting's a bit rusty (I just started learning Perl last month). I've already checked the FAQs page, the wiki and the mailing list, but I did not get any useful hints. I hope my writing made sense. Thank you for your time! - Diana ___ 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/
