Re: [galaxy-dev] tophat error

Am 24.02.2015 um 10:03 schrieb Peter Cock: On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon mike.t...@gmail.com wrote: The main problem for me was that I was not aware that the tophat tool had a dependency on a command line tool outside of galaxy installation. I see in the admin interface that

Re: [galaxy-dev] tophat error

Am 24.02.2015 um 13:01 schrieb Nicola Soranzo: Il 24.02.2015 10:19 Björn Grüning ha scritto: Am 24.02.2015 um 10:03 schrieb Peter Cock: On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote: The main problem for me was that I was not aware that the tophat tool had a dependency

Re: [galaxy-dev] galaxyp build for docker

Hi Evan, Am 19.01.2015 um 17:43 schrieb Evan Bollig PhD: Hey Bjoern, I'm playing with your docker recipes (https://github.com/bgruening/docker-recipes) today and I've been waiting for the galaxyp image build to complete for about 3 hours. For the majority of that time it has been stuck on

Re: [galaxy-dev] Partial automation for generating those twisty R dependency tool shed installation sequences

solution as this is a really infuriating aspect of trying to make code relying on R/BioC packages reproducible. On Thu, Jan 8, 2015 at 11:28 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Ross, this is great! Have you seen this notebook? http://nbviewer.ipython.org/github/bgruening

Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi Ryan, I have tried to collect a minimal set of dependencies you need to have installed: https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList And we have a Galaxy Docker container that is working and should define and test a fresh Galaxy installation:

Re: [galaxy-dev] Mercurial is out of date for Toolshed

Hi Ryan, unfortunately not (yet). But I'm really surprised you are getting this error. It working for me and in our docker containers and other deployments. Can we try to detect the root cause of this error? Do you have conflicting mercurial version. Cheers, Bjoern Thanks. Is there an

Re: [galaxy-dev] Problem using FastQC in Galaxy

Hi, why do you need biopython for FASTQC? You can install biopython from the ToolShed and can depend on it: https://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_64 Cheers, Bjoern Am 05.01.2015 um 19:01 schrieb Alfredo Guilherme Silva Souza: Has anyone used the Biopython in Galaxy

Re: [galaxy-dev] package_numpy_1_7 can't be installed

Hi Wang, can you point me to the exact version your try to install. There is an old numpy_1_7 package which should be deprecated. We had a lot of trouble installing ATLAS and LAPACK and decided to deprecate all packages which depends on LAPACK and ATLAS. Now we do not require both libraries

Re: [galaxy-dev] samtools installation problems

Hi Nathan, please try the following. ln -s /path/to/your/shed_tools/samtools/0.1.19/devteam/what/ever/ /path/to/your/shed_tools/samttools/default The important part is that it is samtools 1.0 and that the default link is a link to the folder in which you find the env.sh file. I hope this will

[galaxy-dev] Help testing Galaxy - new release is coming soon

Hi! As far as I know the Galaxy team is preparing a new release for next week with a ton of great new features, like Interactive Environments, multiple History view, Dataset collections and many more ... If you want to help testing, trying out the latest features or just give feedback we have

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