Re: [galaxy-dev] How to include local tools with Docker image of Galaxy ?

Hi, sure this is possible! :) We have some small documentation about this here: https://github.com/bgruening/docker-galaxy-stable/#integrating-non-tool-shed-tools-into-the-container--toc Cheers, Bjoern Am 01.02.2017 um 16:31 schrieb Md. Rezaul Karim: > Dear All, > > I'm a new user of Galaxy.

Re: [galaxy-dev] Request more details from Nikolaos Tur about pyBamTools & pyBamParser dependency packages message

Thank so much! This is exactly what I needed. What a gem :) Best, Jen On Tue, Jan 31, 2017 at 3:48 PM, Nikolaos Tur wrote: > Hi, > > sorry for long delay answer. Solution which Peter suggested is absolutely > right - owner of packages has to add changes. > Because I did

[galaxy-dev] How to include local tools with Docker image of Galaxy ?

Dear All, I'm a new user of Galaxy. I have been exploring the things and trying to use the Docker image of Galaxy. Eventually, I am planning to run the docker container on our local Cluster. I was wondering if there's any way to include local tools with the Dockerfile. For example using the

Re: [galaxy-dev] Peter Cock <p.j.a.c...@googlemail.com>

Thank you, Peter On Wed, Feb 1, 2017 at 3:11 PM, Eduardo de Paiva Alves wrote: > Hi Peter, > > I am wrapping https://rostlab.org/owiki/index.php/Tmseg which takes a > PSSM matrix as one of the inputs so I will add the psiblast locally > and test and let yo know how it

[galaxy-dev] Peter Cock <p.j.a.c...@googlemail.com>

Hi Peter, I am wrapping https://rostlab.org/owiki/index.php/Tmseg which takes a PSSM matrix as one of the inputs so I will add the psiblast locally and test and let yo know how it goes. Thank you Eduardo On 01/02/2017 10:10, "Peter Cock" wrote: Hi Eduardo,

Re: [galaxy-dev] Tools using Galaxy's Python library?

This went smoother today, and has served to refresh some of the details of how the Galaxy's venv etc all work. In my TravisCI setup for tool testing I currently "manually" install the tool dependencies, and thus am using pip with the same URL as the Tool Shed package: pip install

Re: [galaxy-dev] psiblast

Hi Eduardo, Certainly when Luobin Yang submitted the early work on the PSI BLAST wrapper we need the PSSM datatype to be defined, but as you note, that has been done: https://github.com/peterjc/galaxy_blast/commit/65252ee61fdd98e52454ff045fa069f04ec40c06 According to the minimal notes I made on