Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

Bjorn: Thanks for the tip. I tried to do a conda build python-irodsclient BUILD START: python-irodsclient-0.5.0rc1-py27_0 updating index in: //anaconda/conda-bld/osx-64 updating index in: //anaconda/conda-bld/noarch Can't build /Users/crisl-adm/Tools/python-irodsclient due to unsatisfiable

Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

Hi Chris, I guess the easiest and recommended way is to use conda. We can help you to create a conda package for irodclient if you like. To get you started see here: https://bioconda.github.io/guidelines.html#python Cheers, Bjoern Am 24.01.2017 um 17:02 schrieb Lawrence, Cris W: > I am a

Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

Hi Cris, submit what ever you have to bioconda and we will review and merge it. It will end up in anaconda.org magically. If you don't want to use bioconda. You need an anaconda account and then use `anaconda login`. But be aware that you need to configure Galaxy to use your package ... bioconda

[galaxy-dev] Which "upstream" Ansible Playbook to use for local galaxy instance?

Dear Galatic Advisors, We're building a new set of machines to replace our current local galaxy instance (prod, dev and db VMs running CentOS against a local SLURM cluster with local storage, want to start using wsgi), and are planning to start using Ansible, instead of doing everything by

[galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

I am a Galaxy noob trying to write a Galaxy tool that needs to employ the python-irodsclient module. I can install it on my laptop via pip. But I am trying to make it available to Galaxy via planemo. Apparently, this module is not available in the conda channels. How else can I satisfy my

Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

Bjoern: OK….I am following the recipe submission process, but building in travis-ci is taking longer than I would have expected. I am over 10 minutes now. Can you give me some idea of how long a travis-ci build should take? - Cris On Jan 24, 2017, at 1:05 PM, Björn Grüning

Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

Bjoern Sorry to be a pest. One other question before I attempt any PR. The python-irodsclient is not itself a bioinformatics tool - it’s a wrapper for communicating with iRODS - a data management system and its dependency, pretty tables, I would surmise, is just a utility. After reading the

Re: [galaxy-dev] Resource temporarily unavailable

Thank you Nicola, it worked when I put retry_job_output_collection = 10, but only for some tools. For some of them is still the same. Especially if I run it on a data collections. And if I run the tool locally , not over the Slurm, it worked well. I am not sure if the problem is with Slurm

Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

This depends on how many others are submitting a package. Sorry it takes a while. On Jan 24, 2017 8:40 PM, "Lawrence, Cris W" wrote: > Bjoern: > > OK….I am following the recipe submission process, but building in > travis-ci is taking longer than I would have expected. I am

Re: [galaxy-dev] Problem with 'galaxy_packages' dependency resolver in versionless mode

Hello Bjoern Yes it looks like making the 'default' directory into a symlink makes this work. Thanks for your help and sorry not to get back to you sooner! Best wishes Peter On 20/01/17 16:56, Björn Grüning wrote: Hi Peter, can you try to make

Re: [galaxy-dev] How to satisfy a Galaxy tool dependency on python-irodsclient

Hi Cris, yes there is a better channel - it is conda-forge. But it will take you even more time to submit there and a more strict review. I would encourage you to submit to conda-forge, but for a starter and to not discourage you for the first time experience I recommended bioconda -- here I can

Re: [galaxy-dev] display at UCSC does not work

Dear All I just wanna close this thread and shortly tell you how - with the help of Dannon - we solved the problem in the end: The problem was at our side. Our Galaxy server is not visible from the out side. Only requests from the UCSC servers are allowed. Despite the claim by our IT