Re: [galaxy-dev] Picard installation dependency issues

Hi Scott, Martin, there was still a small problem in cairo. I made a PR to fix this ( https://github.com/galaxyproject/tools-devteam/pull/300) I should have paid a bit more attention ... Cheers, Marius On 1 December 2015 at 22:46, Scott Szakonyi wrote: > Hi Martin,

[galaxy-dev] bx-python issue with intersect and subtract tools

Hi all, I just used the subtract tool (installed under Operate on Genomic Intervals) on my own Galaxy server for the first time in a very long time and got this error message from the tool: Traceback (most recent call last): File

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

Hi, > Thanks Martin and Bjoern for your advice. > > Bjoern, does this modification to the galaxy.ini need to be made on all > Galaxy instances that want to install and run this tool once its > available in the shed? I assume it has nothing to do with the ability to > publish it in the first

Re: [galaxy-dev] Picard installation dependency issues

This is now updated in MTS. Thanks guys. M. On Tue, Dec 1, 2015 at 4:55 PM Marius van den Beek wrote: > Hi Scott, Martin, > > there was still a small problem in cairo. > I made a PR to fix this ( > https://github.com/galaxyproject/tools-devteam/pull/300) > I should have

Re: [galaxy-dev] Picard installation dependency issues

Hi Martin, I've been able to resolve all of the issues with Picard dependencies except for Cairo. It's still failing with this error: Tool shed repository:package_cairo_1_12_14 Tool shed repository changeset revision:f5ab0fdf3716 Tool dependency status:Error Tool dependency installation

Re: [galaxy-dev] Picard installation dependency issues

Excellent! Install completed! Thanks very much. On Tue, Dec 1, 2015 at 3:57 PM, Martin Čech wrote: > This is now updated in MTS. Thanks guys. > > M. > > On Tue, Dec 1, 2015 at 4:55 PM Marius van den Beek > wrote: > >> Hi Scott, Martin, >> >> there was

[galaxy-dev] Aberrant data allocation and SNP mapping problem

Dear Galaxy dev, I have two problems, which might be related to each other. 1) For a long time already, I continuously have ‘left over’ data allocation after deleting and purging histories. Someone from your team has repeatedly resolved that problem, but it root of the problem still persists.

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

Thanks Martin and Bjoern for your advice. Bjoern, does this modification to the galaxy.ini need to be made on all Galaxy instances that want to install and run this tool once its available in the shed? I assume it has nothing to do with the ability to publish it in the first place. Thanks Ulf

Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

You're currently seeing 91% usage? I just checked again and your disk calculation should have been up to date (the recalc procedure did not change anything), and I'm seeing 50% usage on your account. On Tue, Dec 1, 2015 at 3:45 AM, Felix Mayr wrote: > The login emailaddress I

Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

Hi Felix, I have recalculated disk for you again. Our team is aware of this problem and is working on a more permanent solution. We will take a look at your workflow/histories to rule out a tool or workflow function problem. If this does turn out to be a method issue instead, then contacting the

Re: [galaxy-dev] Aberrant data allocation and SNP mapping problem

The login emailaddress I use is felix.m...@gmail.com . ˜ Felix Mayr, MSc. Max Planck Institute for Biology of Ageing Research Group of Dr. Martin Denzel Metabolic and Genetic Regulation of Ageing

[galaxy-dev] December 2015 Galactic News

Hello all, The *December Galactic News * is hot off the presses. - 81 new publications, including 4 highlighted pubs - Event News

Re: [galaxy-dev] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

Hans Rudolph, thanks to Marius van den Beek this issue should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299 These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC repository (

[galaxy-dev] Publish tool with Python dependencies to the toolshed

Dear all I have a Python script that I would like to publish to the tool shed. It has a couple dependencies, all Python modules (argparse, PyVCF, PyYAML). It also needs a Python version 2.7<=X<3, which is not available per default everywhere. Firstly, how do I specify these dependencies in

Re: [galaxy-dev] Picard installation dependency issues

Hello Scott, thanks to Marius van den Beek the first two issues should be fixed with this PR: https://github.com/galaxyproject/tools-devteam/pull/299 These changes were already propagated to the Main Tool Shed. Note for tool developers: for future endeavours please use packages from the IUC

[galaxy-dev] Multiple web servers and handlers Galaxy failed

Hello everyone, I am trying to setup a Galaxy instance for a multi-user production environment and I tried to follow the instructions here: https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer

Re: [galaxy-dev] Picard installation dependency issues

Hi Martin, Thanks very much for your reply, and also to Marius. After some investigation, it appears that there is a firewall issue on my Galaxy server which is preventing the download of the file via FTP. I'm looking into options for that now. Best, Scott On Tue, Dec 1, 2015 at 9:56 AM,

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

Hi Ulf, you most probably want your tool to depend on package_python_2_7_10 from the iuc (it will ensure your tool has access to 2.7.10 no matter what python the Galaxy executing your tool is using) The package is being developed here