Re: [galaxy-dev] can not login to workflows after postgresql setup

2012-07-06 Thread J.W.F.van_der_Heijden
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

Re: [galaxy-dev] can not login to workflows after postgresql setup

2012-07-06 Thread J.W.F.van_der_Heijden
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

Re: [galaxy-dev] can not login to workflows after postgresql setup

2012-07-04 Thread J.W.F.van_der_Heijden
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

[galaxy-dev] error running workflow

2012-07-02 Thread J.W.F.van_der_Heijden
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.

[galaxy-dev] samtools view region

2012-06-20 Thread J.W.F.van_der_Heijden
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

Re: [galaxy-dev] samtools view region

2012-06-20 Thread J.W.F.van_der_Heijden
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: