Re: [galaxy-dev] [Bosc] BOSC 2017: Call for Abstracts

2017-04-10 Thread Peter Cock
Hello all, This is a reminder that the main ISMB/ECCB 2017 abstract submission deadline is this Thursday 13 April - this is one of the biggest and broadest commutational biology conferences and there will I'm sure be a strong Galaxy presence. https://www.iscb.org/ismbeccb2017-keydates This

[galaxy-dev] galaxy startup errors and warnings

2017-04-10 Thread Matthias Bernt
Dear list, I get two messages where I do not know how to continue: The first seems to be severe: tool_shed.util.common_util WARNING 2017-04-10 07:37:39,800 The URL https://toolshed.g2.bx.psu.edu/repository/get_repository_dependencies?owner=devteam_revision=08a01b2ce4cd=column_maker raised the

[galaxy-dev] git clone 16.10 bwa 0.7.15 data manager

2017-04-10 Thread Bryan Hepworth
Hi All I've been trying to get a local galaxy running with an assortment of tools for a local researcher. I'm a linux administrator rather than a bioinformatics researcher and am familiar with how repo's work for RedHat, R and the like. I've built tools for other groups at work and from my

Re: [galaxy-dev] git clone 16.10 bwa 0.7.15 data manager

2017-04-10 Thread Peter Cock
Hi Bryan, I suspect the missing dependency BWA may reflect the switch away from Galaxy's home-grown packaging system to using Conda - enabled by default since v17.01, https://docs.galaxyproject.org/en/master/admin/conda_faq.html Newer dependencies will likely next get an old fashioned package

[galaxy-dev] cluster access

2017-04-10 Thread Matthias Bernt
Dear list, I'm just starting to get jobs submitted to our cluster as real system user. I read in the documentation that the name of the system user is determined by "the Galaxy user's email address (with the @domain stripped off)". But this does not work on our system, rather the username

Re: [galaxy-dev] cluster access

2017-04-10 Thread Peter Cock
This may depend on the cluster setup, and how Galaxy accesses it. What are you using? We use SGE (actually Univa Grid Engine) via DRMAA, and had to setup usern...@example.org email aliases just for this. Peter On Mon, Apr 10, 2017 at 3:36 PM, Matthias Bernt wrote: > Dear list,

Re: [galaxy-dev] cluster access

2017-04-10 Thread Matthias Bernt
Hi, sorry, I forgot this central piece of information: We also use Univa Grid Engine. What would be easier adapting galaxy's mapping to users or setting up email aliases? I would need to ask our cluster admins if they could realize this. Best, Matthias On 10.04.2017 16:39, Peter Cock

Re: [galaxy-dev] cluster access

2017-04-10 Thread Peter Cock
That's interesting. I didn't set this up on our system, but if the LDAP can tell Galaxy the real username, maybe we can avoid having to setup usern...@example.org aliases and insisting our users do that for logging into Galaxy. Hopefully some other SGE users can comment on how they got the