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

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 uncovere

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

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 alre

[galaxy-dev] (no subject)

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 for the complete story, but here are some highlights: - *IRC Channel is Now

Re: [galaxy-dev] job_working / tmp folders

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: /panfs/storage.local/galaxy-da

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

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

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

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 https://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi

[galaxy-dev] Login issue with a nginx proxy

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 (

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

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 To: "galaxy-dev@lists.bx.psu.edu" Sent: Monday, 3 November 2