Re: [galaxy-dev] Travis CI for Galaxy repositories?

Hi Peter, this error on occurs on push, because only during push to master the TS upload is triggered. This error is directly from the TS and this is the reason you don't see it before. You need to include the tool_data_table_conf.xml.sample in your repository, referencing your all_fasta

Re: [galaxy-dev] cognoma

Hi Calvin, thanks for the pointer! I added my 5 cents to this discussion. Cheers, Bjoern On 18.07.2016 22:21, Calvin Morrison wrote: Hi guys, a recruiter hit me up recently and mentioned a local hackathon.. I took a look at their big biologist machine learning online service idea, but it

Re: [galaxy-dev] cleanup datasets error

Hi Philipp, have you followed this from the readme? Note that if you would like to run any of thecleanup scripts , you will need to add the following to|/export/galaxy-central/config/galaxy.ini|:

Re: [galaxy-dev] PLINK 1.90 wrapper

Hi Jochen, you can contact the owner using the TS interface. Under preferences you should have such an option. I have cc'ed Øyvind as you was also interested in working on this. Cheers, Bjoern On 30.05.2016 10:51, Jochen Bick wrote: Hi all, > > I just found the plink tool in two version

Re: [galaxy-dev] Tool shed tools, manual dep installation

Hi David, which sites are blocked? Can you access tools that take it's binaries from https://github.com/galaxyproject/cargo-port? If so Eric has ported all URLs over to cargo-port sometime ago. So we just need to update the packages for you. This only holds true for IUC packages and we

Re: [galaxy-dev] shed_tool_conf.xml

As Peter already mentioned a XML validator is a nice tool for this purpose. For example this one: http://www.xmlvalidation.com A stupid way to do that is to remove the half bottom of your xml and open it using Firefox for example. If OK Add the half top of the half bottom -> firefox

Re: [galaxy-dev] mirDeep2 install error

Hi Jochen, can you please try again I updated the recipes. Sorry for the inconvenience, Bjoern On 22.03.2016 10:24, Jochen Bick wrote: Hi, I tried to install suite_mirdeep_2_0. There is an error in the dependencies of package_squid_1_9g the download link has change to

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

. Let's move this discussion to github. Thanks again! Bjoern Cheers, On Tue, Mar 15, 2016 at 4:50 AM Bjoern Gruening <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>> wrote: Saw it! Will review it today, this looks really nice! On 15.03.2016 08:28, Léo Bi

Re: [galaxy-dev] Galaxy tools for docking protein-compounds.

Saw it! Will review it today, this looks really nice! On 15.03.2016 08:28, Léo Biscassi wrote: Hi Bjorn, I've created the pull request [1] in your repository. I will be grateful if you can assist me with the functional tests on the docking tool and the final validation of the tool

Re: [galaxy-dev] Developing package wrappers

Hi Tiago, for simple tool_dependencies you can use the new planemo depbash command from Peter: https://github.com/galaxyproject/planemo/pull/310 For more complicated once I recommend to use the TTS for the time being. You can create the initial repository install from it and change your

Re: [galaxy-dev] Installing Cairo into Gakaxy

ed test section but I would >> like to clean these up first. >> >> Once done I will post a link in this thread. >> >> Christian University of Manchester >> From: Björn Grüning >> [bjoern.gruen...

Re: [galaxy-dev] Question about using dynamic options and refresh_on_change for rendering 2 associated select lists

Awesome, thanks Greg! On 09.10.2015 15:50, Greg Von Kuster wrote: I’ve finally had a chance to update the wiki - I’ve updated the following section to include information about the “dynamic_options=…” option for populating the select list:

Re: [galaxy-dev] Tool with multiple outputs.

Hi Léo, maybe you can use a dataset collection instead. This is a new way to handle multiple datasets of the same type. For an example see this tool: https://github.com/bgruening/galaxytools/blob/master/tools/rna_tools/rna_shapes/RNAShapes.xml#L218 Cheers, Bjoern On 10.09.2015 23:01, Léo

Re: [galaxy-dev] FastQC galaxy issue

Hi, are you running fastqc on the compressed tarfile? Or is this file unpacked already when you are running fastqc on it? Thanks, Bjoern On 10.09.2015 09:39, Hakeem Almabrazi wrote: Hi, I have encountered the following issue when I try to use FastQC tool in Galaxy. The fastqc file is

Re: [galaxy-dev] custom tool - accessing user's data in bash script

Hi Piotr, I guess you need to work a lot with symlinks. link all your Galaxy inputs to a temp folder, provide the path to the temp folder to KNIME + a path to a second tempfolder with the results and tell Galaxy to collect all files int the result folder. Cheers, Bjoern On 11.09.2015

Re: [galaxy-dev] Installing Cairo into Gakaxy

where did you get the cairo R package from? Christian From: Bjoern Gruening [bjoern.gruen...@gmail.com] Sent: Thursday, September 03, 2015 1:31 PM To: Christian Brenninkmeijer; Björn Grüning; galaxy-dev@lists.galaxyproject.org; Dave Bouvier Subject: Re: [g

Re: [galaxy-dev] Installing Cairo into Gakaxy

ll install log. Note the CAIRO_CFLAGS line was hard coded into recipe_manager.py for this test. Thanks Christian From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Friday, August 28, 2015 6:05 PM To: Christian Brenninkmeijer; Bjoern Gruening; galaxy-dev@lists.gal

Re: [galaxy-dev] Installing Cairo into Gakaxy

Hi, I have CCed Dave here. He took over the maintenance of R many moons ago. Dave can it be that we need to include some cairo headers, shared objects into the tarball from docker-build? Thanks, Bjoern On 28.08.2015 16:16, Christian Brenninkmeijer wrote: Thank you Björn for the link to the

Re: [galaxy-dev] Automated training environments - was Re: 20 August GalaxyAdmins Meetup: Genomic Data

Hi Mark, Thanks Bjorn, Have already pulled a few of your Docker containers (And have been learning an awful lot from your Github code the BioBlend source) Glad to see this is useful for the community. Will try and get further with this later (My Docker machine is being restored from

Re: [galaxy-dev] Change genome build for multiple files

Hi Frederik, at least with the API this is possible! Sorry for not being helpful at all! Bjoern Hi is there a convenient way to change the genome build for a lot of files at once (e.g. a whole data library)? I want to ‘update’ to a newer genome build and the only way I found is to go

Re: [galaxy-dev] galaxy.ini

Hi Bryan, if you are running a old Galaxy instance this file was called universe_wsgi.ini and was located in your Galaxy root folder. Cheers, Bjoern On 14.07.2015 12:35, Bryan Hepworth wrote: Hi For the woefully inept, where in the heck is galaxy.ini stored? I saw the documentation that

Re: [galaxy-dev] bowtie dataset pair input

Hi Ryan, latest wrappers are here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 And a PR would be great! But as far as I can see this is already implemented and you can choose as option `Paired-end Dataset Collection`, isn't it? Ciao, Bjoern On 24.06.2015

Re: [galaxy-dev] samtools dependency changes ?

Hi Wolfgang, I only can tell you that we also have problems with handling BAM files properly in Galaxy. Our issue is more due to unsorted BAM files, but as far as I understood this is because the metadata creation changed from using samtools to using pysam. Maybe this helps you in finding a

Re: [galaxy-dev] Adding packages for bedtools and ucsc-utils for Trackster?

Peter, I'm in a hurry ... have a look at https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse Developed by IUC member Eric Rasche. Cheers, Bjoern On 18.06.2015 10:00, Peter van Heusden wrote: I've tried that - I've added the Environment Modules for the relevant tools to the

Re: [galaxy-dev] Bug in galaxy-dist/latest_15.05 for Share history with user function

Hi Peter, it seems that bugfixes are not backported to bitbucket. We had the same trouble here and I migrated to git real quick. It is pretty easy. Check out 15.05 in bitbucket and clone one github repo with the same branch. Now you can swap the .hg and .git folders. Make a backup of

Re: [galaxy-dev] Error bootstrapping a toolshed

Hi Marius, do you mind to create a PR against the dev brach of Galaxy? https://github.com/galaxyproject/galaxy Thanks, Bjoern Hello everyone, I had some trouble bootstrapping a new toolshed with the 15_05 release (worked fine in the past), and I thought the solution might be interesting.

Re: [galaxy-dev] connecting composite data elements to a display application

Hi Brian, sorry to be so late to this adventure ... Can you give me a few more details about your web-application? Have you considered to use the VIS framework from Galaxy or the interactive environment framework? This will give you more control over your datasets, because it's build-in into

Re: [galaxy-dev] Galaxy for Natural Language Processing

On 24.04.2015 03:18, Keith Suderman wrote: Hi Björn, On Apr 22, 2015, at 8:00 AM, Björn Grüning bjoern.gruen...@gmail.com mailto:bjoern.gruen...@gmail.com wrote: Do you have a beer preference? Outing: I'm one of the rare Germans that do not drink alcohol ;) That must be awkward ;) :)