Re: [galaxy-dev] can not login to workflows after postgresql setup
Hi all, I tried to reconnect with the SQLite database but this time when I try to log in to use workflows it says that my password is invalid. When I try to reset it with the forgotten password option I get this message again: Mail is not configured for this Galaxy instance. Please contact an administrator. What can I do? Jaap From: Jeremy Goecks [jeremy.goe...@emory.edu] Sent: Wednesday, July 04, 2012 11:38 PM To: Heijden, J.W.F. van der (HG) Cc: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] can not login to workflows after postgresql setup I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Moving to a new database will make all your previous data inaccessible as it's no longer in the database that Galaxy is using, so this behavior is expected. You could: (a) reconnect Galaxy to your SQLite database and export (download) your workflow and then (b) change Galaxy to use your PostGres database and import (upload) your workflow. Also it seems that I am no longer able to upload files. It's only a 300kb test file but it seems to be uploading forever. The database used should not affect uploading. Are you still having problems? Best, J. ___ 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] can not login to workflows after postgresql setup
Hi, Any ideas yet on how to configure my mail in galaxy? Kind regards Jaap From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of j.w.f.van_der_heij...@lumc.nl [j.w.f.van_der_heij...@lumc.nl] Sent: Friday, July 06, 2012 11:13 AM To: jeremy.goe...@emory.edu Cc: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] can not login to workflows after postgresql setup Hi all, I tried to reconnect with the SQLite database but this time when I try to log in to use workflows it says that my password is invalid. When I try to reset it with the forgotten password option I get this message again: Mail is not configured for this Galaxy instance. Please contact an administrator. What can I do? Jaap From: Jeremy Goecks [jeremy.goe...@emory.edu] Sent: Wednesday, July 04, 2012 11:38 PM To: Heijden, J.W.F. van der (HG) Cc: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] can not login to workflows after postgresql setup I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Moving to a new database will make all your previous data inaccessible as it's no longer in the database that Galaxy is using, so this behavior is expected. You could: (a) reconnect Galaxy to your SQLite database and export (download) your workflow and then (b) change Galaxy to use your PostGres database and import (upload) your workflow. Also it seems that I am no longer able to upload files. It's only a 300kb test file but it seems to be uploading forever. The database used should not affect uploading. Are you still having problems? Best, J. ___ 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] can not login to workflows after postgresql setup
Hi all, I did manage to log in now after the postgres installation by re-registering. However my workflow is gone. Is there a file stored in galaxy by default which I can reupload to retrieve my workflow?. Also it seems that I am no longer able to upload files. It's only a 300kb test file but it seems to be uploading forever. I'm guessing that some settings need to be adjusted. But I have no clue which ones. Help is very much appreciated! Jaap From: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] on behalf of j.w.f.van_der_heij...@lumc.nl [j.w.f.van_der_heij...@lumc.nl] Sent: Wednesday, July 04, 2012 2:29 PM To: bernd.ja...@pasteur.fr; galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] can not login to workflows after postgresql setup Hi all, I have set up postgresql to work with galaxy because the standard mysqlite didn't work with my workflow. Now that postgresql seems to be working I can not login to galaxy. When I try to login it says that it can't find my username. And also when I click forgot password it says: Mail is not configured for this Galaxy instance. Please contact an administrator. Any ideas? Kind Regards Jaap ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] error running workflow
Hi all, I have added some tools to my local install of Galaxy. To get to my final results I have to do a lot of steps. When I try to run every step separately it turns out to work out fine. But when I try to run all steps at once with a workflow I get the following error message. OperationalError: (OperationalError) database is locked u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2012-07-02 11:34:48.135419', 'queued', 529] I have noticed that the processes eat a lot of my computer resources. Other than that I have no clue what the problem could be. Any tips are appreciated. Kind regards, Jaap van der Heijden ___ 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] samtools view region
Hi all, I was working on the integration of the samtools view to work with Galaxy. The idea is to filter an indexed bam file on a chromosome with samtools view -bh in.bam.bai chr1. After some research I noted that samtools will only execute this command when it can find the corresponding sorted bam file, so the in.bam. The problem is that Galaxy renames all the files. So in.bam will be for instance dataset_1.dat. When I index the bam file I will get an indexed bam file named dataset_2.dat. Samtools can't detect then that dataset_1.dat is the sorted bam file and dataset_2.dat is the bai file. Now I was wondering if it is possible to rename files in the ~/galaxy-dist/database/files/000 with a command line. So that dataset_2.dat will be moved to dataset_1.dat.bai. Does anyone know how to do that? Kind Regards, Jaap ___ 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] samtools view region
Hi Peter, Thanks for you quick answer! But I am very new to Galaxy. Could you explain something about those symlinks? Regards, Jaap From: Peter Cock [p.j.a.c...@googlemail.com] Sent: Wednesday, June 20, 2012 4:01 PM To: Heijden, J.W.F. van der (HG) Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] samtools view region On Wed, Jun 20, 2012 at 2:59 PM, j.w.f.van_der_heij...@lumc.nl wrote: Hi all, I was working on the integration of the samtools view to work with Galaxy. The idea is to filter an indexed bam file on a chromosome with samtools view -bh in.bam.bai chr1. After some research I noted that samtools will only execute this command when it can find the corresponding sorted bam file, so the in.bam. The problem is that Galaxy renames all the files. So in.bam will be for instance dataset_1.dat. When I index the bam file I will get an indexed bam file named dataset_2.dat. Samtools can't detect then that dataset_1.dat is the sorted bam file and dataset_2.dat is the bai file. Now I was wondering if it is possible to rename files in the ~/galaxy-dist/database/files/000 with a command line. So that dataset_2.dat will be moved to dataset_1.dat.bai. Does anyone know how to do that? Kind Regards, Jaap The simple answer is a wrapper script which makes symlinks for the BAM file and its BAI file using the normal naming conventions. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
