Re: [galaxy-dev] Problems with upload.py and changes to json.py

2014-11-03 Thread Robert Davidson
Darnit, I should have tried downloading again before sending the email - that solved the issue. Newest version of upload.py doesn't make use of from_json_string Cheers, Rob From: Robert Davidson bobbledavid...@yahoo.co.uk To: galaxy-dev@lists.bx.psu.edu

[galaxy-dev] Login issue with a nginx proxy

2014-11-03 Thread Alexandre Loywick
Hello galaxians, I'm currently trying to set up a production galaxy and make it available to the public but I face a weird issue, probably because of my nginx proxy configuration. Galaxy is on a kvm virtual machine running on a host using nginx as proxy. to make it a bit clearer: 172.30.24.35

[galaxy-dev] Nothing being tested on Test and main Tool Shed?

2014-11-03 Thread Peter Cock
Hello all, I am currently hoping to review the automated test results for some repositories which I have recently updated, in one case for dependency handling, the other functional changes: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer

[galaxy-dev] Repeats shown upside down on galaxy-central

2014-11-03 Thread Peter Cock
Hi all, I'm running galaxy-central as my development server, and noticed what to me is a regression with repeat parameters, e.g. https://github.com/peterjc/pico_galaxy/blob/master/tools/clc_assembly_cell/clc_mapper.xml Read group: [+ insert read group] * 1: Read Group * 2: Read Group which on

Re: [galaxy-dev] job_working / tmp folders

2014-11-03 Thread Shrum, Donald C
Thanks for the reply John, It turns out my problem was with the drama conf file (forgot about that one) and I'm just posting this reply on the off change google leads someone else to the solution :) -bash-4.1$ more /opt/pbs-drmaa/etc/pbs_drmaa.conf user_state_dir:

[galaxy-dev] (no subject)

2014-11-03 Thread Dave Clements
Hello all, A lot is happening in in the Galaxy in November, and a lot of good stuff happened in October too. Take a look at the November 2014 Galaxy Newsletter https://wiki.galaxyproject.org/GalaxyUpdates/2014_11 for the complete story, but here are some highlights: - *IRC Channel is Now

[galaxy-dev] Galaxy's dependency on old samtools vs tools wrapping later versions?

2014-11-03 Thread Peter Cock
Hello all, Galaxy currently requires samtools on the $PATH in order to sort and index BAM files automatically, and samtools 0.1.19 works fine. Unfortunately later versions of samtools index have a regression: https://github.com/samtools/samtools/issues/199 This has caught several people out

Re: [galaxy-dev] Galaxy's dependency on old samtools vs tools wrapping later versions?

2014-11-03 Thread Dave Bouvier
Peter, For the automated indexing of bam files, Galaxy uses the samtools version linked to as default under tool-dependencies/samtools/ This should normally be 0.1.19 or older, due to the not-yet-implemented handling of bam_index_build and other potential regressions that could be uncovered