[galaxy-dev] Galaxy can't find valid files in user folder

2012-07-02 Thread Ciara Ledero
Hi all, My apologies for reposting this, but I thought I ought have asked this in a separate thread instead of appending it to a previous message. Anyway, I was able to set up a folder for a user (in my case, my own non-admin user account). universe_wsgi.ini's been configured to allow users to

Re: [galaxy-dev] ValueError: Maximum key size is 448 bits

2012-07-02 Thread Sajoscha Sauer
Ok, found it! The 'id_secret' parameter in the universe_wsgi.ini was just too long. But I think something changed there, because we didn't change the id_secret, and it was working before. Anyway, now it's working! Cheers, Sajoscha On Jun 27, 2012, at 4:09 PM, Sajoscha Sauer wrote: Hi,

[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.

Re: [galaxy-dev] error running workflow

2012-07-02 Thread Hans-Rudolf Hotz
Hi Jaap are you using 'SQLite', if so, I recommend to switch to 'PostgreSQL', see: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server/#Switching_to_a_database_server Regards, Hans On 07/02/2012 02:26 PM, j.w.f.van_der_heij...@lumc.nl wrote: Hi all, I have added

[galaxy-dev] Trackster : samtools not found error

2012-07-02 Thread Yec'han Laizet
Hello, I try to use the visualization tool of my local instance of galaxy under ubuntu. Everytime I try to create a feature track from a sam file, I get the following error: /bin/sh samtools not found I have installed samtools from ubuntu reposotories and it works well as I can call it from

[galaxy-dev] problems installing mothur via toolshed

2012-07-02 Thread Hollander, Mattias de
Hi, I am trying to install the mothur toolsuite via the toolshed but this returns in an HTTP 500 error: URL:

[galaxy-dev] GMOD Summer School application deadline

2012-07-02 Thread Scott Cain
Hello, The deadline to apply for the GMOD Summer School is in one week, July 9th. The application is available as a Google Form: https://docs.google.com/spreadsheet/embeddedform?formkey=dG5hNGFiQ3UwYTV2LUZxZW04Qm1yZXc6MQ In the GMOD Summer School (August 24-29, 2012) we will cover the

Re: [galaxy-dev] problems installing mothur via toolshed

2012-07-02 Thread Greg Von Kuster
Hello Matthias, I've just updated the tool shed to changeset revision 7332:e54f7684c919 and I've successfully installed the mothur toolsuite. This revision includes a fix that may be related to the issue you encountered. However, before you try reinstalling, can you reply with answers to

[galaxy-dev] sanitizer for carriage return

2012-07-02 Thread Jennifer Jackson
___ On 7/1/12 3:05 AM, Katrien Bernaerts wrote: Dear, I am making a Galaxy appliciation with a text area. In the text area, the user can copy/paste sequences. However, all carriage returns (e.g. after the comment line) are converted to

Re: [galaxy-dev] FastQC Tool Errors

2012-07-02 Thread Josh Nielsen
Sure enough, this fixed the problem. I just installed the latest Sun JRE and it is working now. Thanks for the suggestion! I would have never guessed. -Josh On Mon, Jun 25, 2012 at 11:34 AM, simon andrews simon.andr...@babraham.ac.uk wrote: Yes, that's the broken version of gcj. I don't

Re: [galaxy-dev] Trackster : samtools not found error

2012-07-02 Thread Jeremy Goecks
Hello, It's likely that samtools is not in Galaxy's path because Trackster uses the same path as Galaxy does. Also, many tools in Galaxy use the Galaxy PySam egg rather than the samtools binary, so it's possible that you can run a tool that uses samtools without the binary in Galaxy's path.