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

2014-11-28 Thread Björn Grüning
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

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

2014-12-16 Thread Björn Grüning
. Cheers, Yu di29her w...@lrz.demailto:w...@lrz.de On 16 Dec 2014, at 04:07, Björn Grüning bjo...@gruenings.eumailto:bjo...@gruenings.eu wrote: 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

Re: [galaxy-dev] samtools installation problems

2014-12-31 Thread Björn Grüning
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

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

2015-01-02 Thread Björn Grüning
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] galaxyp build for docker

2015-01-19 Thread Björn Grüning
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] Manually adding new tools from toolshed

2015-01-16 Thread Björn Grüning
Hi Ryan, what about a local bootstrapped ToolShed which is in sync with the public one (at least for the users you are interested on). Than you can install from this ToolShed. I guess this is less annoying than maintaining everything on your own. Cheers, Bjoern Am 16.01.2015 um 08:22 schrieb

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

2015-01-18 Thread Björn Grüning
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] restricting new accounts

2015-02-13 Thread Björn Grüning
Hi Michael, Have a look in your config/galaxy.ini file and set the allow_user_creation to False # Allow unregistered users to create new accounts (otherwise, they will have to # be created by an admin). #allow_user_creation = True Cheers, Bjoern Am 13.02.2015 um 10:24 schrieb Michael Thon:

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

2015-01-05 Thread Björn Grüning
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

2015-01-05 Thread Björn Grüning
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] R lib dependencies in the toolshed

2015-02-12 Thread Björn Grüning
Hi Nikos, can you provide us your tool_dependencies.xml file please? Thanks, Bjoern Am 11.02.2015 um 17:27 schrieb Nikos Sidiropoulos: Hi all, I have a package repository that installs an R package and another repository with a set of tools that use that package repository. Tools that

Re: [galaxy-dev] fastq format recognition

2015-02-13 Thread Björn Grüning
Hi Michael, have a look at this biostar question. https://biostar.usegalaxy.org/p/8070/ Hope this helps, Bjoern Am 13.02.2015 um 13:08 schrieb Michael Thon: I have a new galaxy installation on my server. I uploaded two fastq files and now I'm trying to run trimmomatic and fastqc. In both

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

2015-01-08 Thread Björn Grüning
Hi Ross, this is great! Have you seen this notebook? http://nbviewer.ipython.org/github/bgruening/notebooks/blob/master/R/extract_all_dependencies_from_an_r_package.ipynb It tries to do the same thing. Maybe it's also worth to mention? Maybe we can enhance it? Thanks, Bjoern Am 08.01.2015 um

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

2015-01-05 Thread Björn Grüning
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

[galaxy-dev] Announcement: Galaxy Docker Image 15.03

2015-03-25 Thread Björn Grüning
Hi all! We are proud to present you the next release of Galaxy Docker. https://github.com/bgruening/docker-galaxy-stable https://registry.hub.docker.com/u/bgruening/galaxy-stable/ A few highlights: * based on Galaxy 15.03, with all it's new awesome features * Docker image is now based on

[galaxy-dev] RFC: new param attribute for Galaxy tool XML

2015-02-28 Thread Björn Grüning
Hi all, we are planning to work on a project to implement a Galaxy fuse based shell. Probably starting with the work from Clare [1]. Next to our Galaxy IPython integration it should attract more bioinformaticians and should offer a new way to interact with Galaxy. This includes moving, deleting

Re: [galaxy-dev] Interested in GSOC idea Docker Swarm and Compose ask for advices.

2015-03-02 Thread Björn Grüning
Hi Afe, it's usually a good idea to search for issues that needs to be solved or some features that are missing. A good start for example is the Galaxy Trello board: https://trello.com/b/75c1kASa/galaxy-development The issue tracker of tools-iuc or tools-devteam:

Re: [galaxy-dev] RFC: new param attribute for Galaxy tool XML

2015-03-04 Thread Björn Grüning
AM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi Björn, Command line arguments are often case sensitive (e.g. samtools switches), but are Galaxy parameter names? Peter On Sat, Feb 28, 2015 at 9:11 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi all, we are planning to work

Re: [galaxy-dev] tophat error

2015-02-24 Thread Björn Grüning
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

2015-02-24 Thread Björn Grüning
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] Galaxy for Natural Language Processing

2015-04-13 Thread Björn Grüning
Hi Keith, Am 13.04.2015 um 20:12 schrieb Keith Suderman: Hello, Our group is investigating using Galaxy as a workflow engine for NLP (Natural Language Processing) tasks. Good choice! :) I have installed a local Galaxy instance and created wrappers for the services we use and so far

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

2015-04-22 Thread Björn Grüning
Hi Keith, Am 21.04.2015 um 21:21 schrieb Keith Suderman: On Apr 15, 2015, at 5:35 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Nice! Can I convince you to put these tools into the TS if everything is working? Maybe with a German beer? ;) Do you have a beer preference? Outing: I'm

Re: [galaxy-dev] follow up question regarding the 'toolform-upgrade'

2015-04-29 Thread Björn Grüning
Hi, I have a related question, does the text-area sanitization differentiate between the different newline formats? Hans-Rudolf can this be your problem? Ciao, Bjoern Am 29.04.2015 um 13:55 schrieb Hans-Rudolf Hotz: Hi all We just need some confirmation before we fix our tools: We

Re: [galaxy-dev] Bismark doesn't end and blocks the server

2015-06-08 Thread Björn Grüning
Hi, I think this is a general problem you encountered here with unsorted BAM files. We can reproduce it locally. Will let you know if I find a workaround. Cheers, Bjoer Am 05.06.2015 um 14:23 schrieb C. Ch.: Hi all, I have a clean local install of galaxy from git (commit:

Re: [galaxy-dev] install packagess without toolshed

2015-06-09 Thread Björn Grüning
installation. The only way I can see is by uploading it to ToolShed. But I would like to avoid that while I'm still learning to create these things ;) Best, Alexander 2015-06-09 17:16 GMT-05:00 Björn Grüning bjoern.gruen...@gmail.com: Hi Alex, here are some informations: https

Re: [galaxy-dev] BAM datatype - bam bai

2015-06-19 Thread Björn Grüning
Hi Alexander, Am 19.06.2015 um 01:44 schrieb Alexander Vowinkel: Hi, when I 'produce' a bam file in my output, I can download the bam file and a corresponding bai file. I am now wondering where does the bai file come from? From Galaxy! :) Galaxy has a concept of datatypes and metadata.

Re: [galaxy-dev] planemo shed_update - error

2015-06-27 Thread Björn Grüning
Hi Alexander, I have opend an issue: https://github.com/galaxyproject/planemo/issues/240 Thanks for reporting, Bjoern Am 27.06.2015 um 07:11 schrieb Alexander Vowinkel: Hi, I'm running: planemo shed_update --check_diff --shed_target toolshed and get a python error message (see

Re: [galaxy-dev] Bismark doesn't end and blocks the server

2015-06-10 Thread Björn Grüning
Hi Chris, as a workaround, can you try to set: retry_metadata_internally = False Cheers, Bjoern Am 09.06.2015 um 20:41 schrieb C. Ch.: Hi Bjoern, We could default to using sorted BAM files from Bismark as that is Ok with methylkit which we use for our downstream analysis. On the other hand

Re: [galaxy-dev] delete many galaxy tools

2015-06-12 Thread Björn Grüning
Hi Alexander, How can I delete multiple tools from my galaxy installation? So far I just know how to uninstall single ones through Manage installed tool shed repositories - But this is quite nasty if I want to uninstall many of them. in general you can do all these tasks with

Re: [galaxy-dev] docker-galaxy-stable tools fail

2015-06-13 Thread Björn Grüning
| Research and User Services (RUS) Supercomputing Institute for Advanced Computational Research | msi.umn.edu University of Minnesota | umn.edu boll0...@umn.edu | 612-624-1447 | Walter Lib Rm 556 On Sat, Jun 13, 2015 at 4:13 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Evan, can you

Re: [galaxy-dev] docker-galaxy-stable tools fail

2015-06-13 Thread Björn Grüning
Hi Evan, can you install other tools, or is this happening to all tools? Which version are you running? Thanks for reporting! Bjoern Am 13.06.2015 um 10:59 schrieb Evan Bollig PhD: Not sure why, but these tools fail to install inside the docker-galaxy-stable Dockerfile build:

Re: [galaxy-dev] Feature Request: Ability to specify a directory to read xml files for tool configuration

2015-06-11 Thread Björn Grüning
Hi Ryan, have you looked at this option? # Set to True to enable monitoring of tools and tool directories # listed in any tool config file specified in tool_config_file option. # If changes are found, tools are automatically reloaded. Watchdog ( # https://pypi.python.org/pypi/watchdog ) must be

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-03 Thread Björn Grüning
on a Galaxy flavour generator: http://wookoouk.github.io/galaxyFlavorGenerator/ Maybe we could exchange ideas here? Thanks for you mail, Bjoern Tiago On Sun, 02 Aug 2015 10:23:20 +0200 Björn Grüning bjoern.gruen...@gmail.com wrote: Hi, I will think about this, but this comes

Re: [galaxy-dev] 20 August GalaxyAdmins Meetup: Genomic Data Management; Tool Installation Automation

2015-08-20 Thread Björn Grüning
Hi Mark, please have a look at https://github.com/bgruening/galaxy-rna-workbench-extra Here we try to develop small scripts to load data into a library and setting up everything for a workshop. Indeed this container was used for a few workshops already but is still under development. The plan is

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-01 Thread Björn Grüning
Hi Oksana, both variables are used during container build to create users and home directories. This does not happen during container startup. They are buildtime variables. All Galaxy ENV vars are runtime variables and do have an impact during startup. Can you tell us more about what you want

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-02 Thread Björn Grüning
On Aug 1, 2015, at 1:10 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Oksana, both variables are used during container build to create users and home directories. This does not happen during container startup. They are buildtime variables. All Galaxy ENV vars are runtime

Re: [galaxy-dev] install_tool_shed_repositories.py returns HTTP Error 400: Bad Request

2015-08-04 Thread Björn Grüning
Hi Mic! please see my answer here: https://github.com/galaxyproject/usegalaxy-playbook/issues/8 If possible don't cross post :) Cheers, Bjoern Am 04.08.2015 um 07:26 schrieb Mic: Hello, I found this shed_tool_conf.xml (

Re: [galaxy-dev] passing the name attribute from the DB to a sniffer

2015-08-04 Thread Björn Grüning
Hi, Am 03.08.2015 um 08:26 schrieb Josh Woodring: Dear all, I am working on porting crop modelling tools Crop Science? Awesome! Made my day! into a custom version of galaxy; unfortunately though, the files are rigidly formatted in similar ways and not easily distinguished. As such, while

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-04 Thread Björn Grüning
Am 04.08.2015 um 00:00 schrieb Tiago Rodrigues Antao: On Mon, 03 Aug 2015 17:30:05 +0200 Björn Grüning bjoern.gruen...@gmail.com wrote: I would recommend you Galaxy Flavours. We have a few, for example RNA-Seq, ChIP-seq etc ... join us! :) That was my first port of call, but they lacked

Re: [galaxy-dev] Galaxy run.sh process crashing

2015-08-04 Thread Björn Grüning
Hi, are you running your jobs via a scheduler? Maybe your scheduler is killing your jobs after X minutes? Ciao, Bjoern Am 04.08.2015 um 01:12 schrieb Hans Vasquez-Gross: Hi, We have been running galaxy for the last year fine on our website to run short running scripts ( 10 seconds) and

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-05 Thread Björn Grüning
Hi Brian, thanks for you mail! Very appreciated, please see my comments inline. We only have one cluster, so we will have both test and production environments running on it. I understand that at a minimum we'd need different Galaxy home dir and UID/GID. For our local deployment of

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-05 Thread Björn Grüning
, Oksana On Wed, Aug 5, 2015 at 4:30 AM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Brian, thanks for you mail! Very appreciated, please see my comments inline. We only have one cluster, so we will have both test and production environments running on it. I understand

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-05 Thread Björn Grüning
Thanks! @Brian please add your ideas and use cases so we can figure out a way how to support this :) Thanks, Bjoern Am 05.08.2015 um 16:26 schrieb Oksana Korol: Created issue #74, with reference to this discussion. Cheers, Oksana On Wed, Aug 5, 2015 at 9:52 AM, Björn Grüning

Re: [galaxy-dev] Galaxy instance with multiple partitions

2015-08-11 Thread Björn Grüning
Thanks! Ray On Tue, Aug 11, 2015 at 4:20 PM, Björn Grüning bjoern.gruen...@gmail.com wrote: Hi Raymond, Galaxy as a very sophisticated support for this called ObjectStore. Please have a look at the API and the Wiki (the wiki can be improved so much on this). https

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-06 Thread Björn Grüning
Hi, the first one is the one we are currently working on. It's an interface to create your own Galaxy Docker flavours. Drag Drop your tools data managers and so on ... click build and either get a Docker Image or a Docker file. But everything is in flux at the moment. So please jump in and

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-04 Thread Björn Grüning
des Science et de la technologie Agriculture et Agroalimentaire Canada / Gouvernement du Canada iyad.kandal...@agr.gc.ca / Tel: 613-759-1228 / TTY: 613-773-2600 -Original Message- From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of Björn Grüning Sent

Re: [galaxy-dev] Adding categories to Main

2015-08-07 Thread Björn Grüning
Hi Keith, the Galaxy team can add new categories to the Tool Shed very easily and such a mail is exactly the way to go. As soon as the Galaxy teams has added the category you can use tools like planemo to upload all your tools at once. https://github.com/galaxyproject/planemo Looking forward to

Re: [galaxy-dev] Problem with ChemicalToolBox dependencies

2015-08-13 Thread Björn Grüning
Hi, can you please check if you have all dependencies from this list as well? https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList Thanks, Bjoern Am 13.08.2015 um 22:56 schrieb Léo Biscassi: Hello everyone! I have a Problem when installing the tool ChemicalToolBox. The error

Re: [galaxy-dev] Externalizing Galaxy config in docker-galaxy-stable

2015-08-06 Thread Björn Grüning
Hi, Am 06.08.2015 um 15:19 schrieb Tiago Rodrigues Antao: On Thu, 06 Aug 2015 14:00:02 +0200 Björn Grüning bjoern.gruen...@gmail.com wrote: the first one is the one we are currently working on. It's an interface to create your own Galaxy Docker flavours. Drag Drop your tools data

Re: [galaxy-dev] Data upload as part of workflow?

2015-08-06 Thread Björn Grüning
Hi, this does not answer your question 100% but I have a tool that will simply enable you to paste a URL into a box and this will be fetched. It's in this package: https://toolshed.g2.bx.psu.edu/view/bgruening/chemical_data_sources and it called Online-Data. Ciao, Bjoern Am 06.08.2015 um 17:51

Re: [galaxy-dev] Workflow editor stuck on loading workflow

2015-07-14 Thread Björn Grüning
Hi Ryan, try to look at the JS console. I suspect some problem with one of the tools in your workflow. Cheers, Bjoern Am 14.07.2015 um 22:02 schrieb Ryan G: Hmmm this only happens on a specific workflow. How can I debug this? On Tue, Jul 14, 2015 at 3:37 PM, Ryan G

Re: [galaxy-dev] tabular file displayed without tabs

2015-10-27 Thread Björn Grüning
Hi Ryan, is it recognised as 'tabular'? Ciao, Bjoern Am 27.10.2015 um 04:42 schrieb Ryan G: > Hi - I have a tools that generates a tab-delimited text file as output. > when I click the eye icon to view the data, all the fields are compressed > as if there were no tabs. If I expand the history

Re: [galaxy-dev] Bismark installation dependencies error

2015-10-28 Thread Björn Grüning
Hi Jose, which version of Galaxy are you using? @Dave can this be one of the old un-compressing changes? Cheers, Bjoern Am 28.10.2015 um 15:31 schrieb Jose Juan Almagro Armenteros: > Hello, > > I have tried to install the last version of Bismark from the toolshed and I > got an error while

[galaxy-dev] Remote Contribution Fest - Metagenomics Tools and Workflows 30th December + 1st November

2015-11-10 Thread Björn Grüning
Hello all, We are planning a remote contribution fest for Galaxy tool developers to hack and data scientists to develop, document and create metagenomic Tools and Workflows. It will take place on 30th of November and 1st of December 2015! The remote nature of this should give people who don't

Re: [galaxy-dev] IPython and Rstudio are missing

2015-11-11 Thread Björn Grüning
Unfortunately, Rstudio and Ipython still did not show up. >> >> Thank you in advance. >> >> Best wishes, >> >> Mic >> >> On Sat, Nov 7, 2015 at 9:58 AM, Björn Grüning <bjoern.gruen...@gmail.com> >> wrote: >> >>> Hi Mic, >

Re: [galaxy-dev] ProFTPD with SQLite

2015-11-12 Thread Björn Grüning
Hi Mic, Am 12.11.2015 um 01:22 schrieb Mic: > Hello, > I installed all tools from the toolshed which I needed for Galaxy (15.10) > and noticed that I can not upload bigger files than 2 GB to Galaxy without > a FTP server. > > I installed on Ubuntu 14.04 ProFTPD in the following way: > >

Re: [galaxy-dev] Tmhmm and signal P

2015-11-12 Thread Björn Grüning
Hi Olivier, you need to have signalp in version 3. You have installed it already and it is now on your $PATH? > Signal P: with v3.0: it can’t localize it (signal not found) (I can’t even > launch it in command line) What is the error if you run it on command line? Ciao, Bjoern > >

Re: [galaxy-dev] rgFastQC.py error - cannot find executable /fastqc

2015-11-16 Thread Björn Grüning
Hi Mic, do you have Java installed? cheers, Bjoern Am 17.11.2015 um 02:05 schrieb Mic: > Hello, > I installed FastQC (~/shed_tools/toolshed.g2.bx.psu.edu/repos/*devteam* > /fastqc/*2d094334f61e*/ > > *FastQC ).* > However, I got the following error while running it: > > > *Fatal error: Exit

Re: [galaxy-dev] feature request

2015-11-09 Thread Björn Grüning
Hi Ryan, can you create a github issue with this suggestion :) Thanks, Bjoern Am 09.11.2015 um 22:37 schrieb Ryan G: > I'd put this into Trello, but Trello is blocked from my place of business... > > I have a data library with over 200 files in it. Half of them are > "clipped" and the other

Re: [galaxy-dev] netcdf 4.3 error

2015-11-02 Thread Björn Grüning
Hi Olivier, can you change it here with a PR: https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_netcdf_4_3/tool_dependencies.xml We will upload this package and fix it as soon as the patch gets merged. Cheers, Bjoern Am 02.11.2015 um 16:23 schrieb Olivier CLAUDE: > Hello,

Re: [galaxy-dev] tool-shed delete problem

2015-11-02 Thread Björn Grüning
Hi Alper, there is no option to delete a repository, but you can deprecate one. Is this what you are trying? Cheers, Bjoern Am 03.11.2015 um 03:30 schrieb Kucukural, Alper: > Hi, > Could you help me to delete crisprseek from https://toolshed.g2.bx.psu.edu/? > I am the owner but cannot delete. I

Re: [galaxy-dev] Developing package wrappers

2015-11-02 Thread Björn Grüning
Hi Tiago, in the following my few comments. If you like to submit this to IUC-tools a WIP would be nicer to comment on. * Booleans can be treated like this. Note the changed truevalue and falsevalue. This will reduce this: #if str ($selExtraOpts.search_complete_random_tree) == "true":

Re: [galaxy-dev] OpenMS caused Error downloading from URL

2015-11-05 Thread Björn Grüning
Hi Mic and Olivier, if there is broader interest in OpenMS please let me know. We have new wrappers and new installation instructions here: https://github.com/bgruening/galaxytools/tree/master/tools/openms + pre-compiled binaries as this takes ages to compile. Cheers, Bjoern Am 05.11.2015 um

Re: [galaxy-dev] recurring issues with revisions of packages from toolshed

2015-10-15 Thread Björn Grüning
Am 15.10.2015 um 11:43 schrieb Christian Brenninkmeijer: > Note these are personal views of another admin not official Galaxy views. > > The version issues is a hard one to solve, as automatically updating upstream > project is also dangerous as that leaves them in a state that has not be >

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

2015-10-15 Thread Björn Grüning
nto Galaxy for this. > So far, looking forward to joining forces :). !!! Greetings to Munich! Bjoern > Cheers, > Sebastian > > > Björn Grüning schrieb: >> Hi Sebastian, >> >> I think we try to work on this during our upcoming hackathon. >> >> https://gi

Re: [galaxy-dev] Galaxy Interactive Environment devs

2015-10-14 Thread Björn Grüning
Am 13.10.2015 um 13:41 schrieb Sebastian Schaaf: > Hey Eric, > > We are not yet on IEs, No, no, no. How can this happen? ;) > but we plan to upgrade our local production > instance soon (a recent version is already 'waiting' to take over), > apart from other goodies we intended to allow one

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

2015-10-14 Thread Björn Grüning
at least the > 'dead end' problem with the resulting tgz archives was solved. We are > currently assembling the codes into a toolshed entry, but I need to ask > Ashok tomorrow about the current progress. > > Is there still interest on it or is everything already on the move..? > >

Re: [galaxy-dev] recurring issues with revisions of packages from toolshed

2015-10-19 Thread Björn Grüning
Hi Sarah, can you create a reproducible example in a Docker container for me? Together with a friend I will have a look at this. But we need to short reproducible example :) Thanks, Bjoern > Dear all, > > I continuously have several issues with tool dependency packages from > the toolshed and

Re: [galaxy-dev] recurring issues with revisions of packages from toolshed

2015-10-17 Thread Björn Grüning
Hi Sarah, as far as I can tell this is exactly how it should work. Thanks for clarifying! Bjoern > Just to avoid confusion, I would like to explain how I understand the > meaning of "revisions" and "versions". > > Revisions are what shows up the in tool list as the orange triangle > with a

Re: [galaxy-dev] recurring issues with revisions of packages from toolshed

2015-10-17 Thread Björn Grüning
is loaded try to run an R script > which loads the packages as a test. > > Something like: > library(Cairo) > args<-commandArgs(TRUE) > writeLines(capture.output(sessionInfo()), args[1]) > sessionInfo() > > But even then the tool goes green with an R error, >

Re: [galaxy-dev] Installing Cairo into Gakaxy

2015-10-06 Thread Björn Grüning
NSTALL_DIR/lib/pkgconfig:$INSTALL_DIR/share/pkgconfig > Yes, I have fixed this here: https://github.com/galaxyproject/tools-iuc/pull/298 Thanks, Bjoern > > Christian > > > From: Björn Grüning > [bjoern.gruen...@gmail.com] Sent: Tuesda

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

2015-10-07 Thread Björn Grüning
Hi Lance, I will help if I can. I also think we should begin too write 2-3 nice tools in the beginning to test the handshake between them and lay the ground work. This will also help to get familiar with the tool. I still hope some one else from the community shows interest! :) Thanks, Bjoern

Re: [galaxy-dev] QIIME tools for Galaxy (WIP, call for collaborators)

2015-10-07 Thread Björn Grüning
nsider to join our hackathon: https://github.com/galaxyproject/tools-iuc/issues/299 We are always open for new ideas. Would be great to get a nice suite and a few workflows for metagenomic in the near future! :) Thanks, Bjoern > All the best, > > Yvan > > - Mail original --

Re: [galaxy-dev] Installing Cairo into Gakaxy

2015-08-26 Thread Björn Grüning
Hi Christian, looking at the R package and on the Docker build instructions, R seems to be installed with cairo support: https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_r_3_2_1/tool_dependencies.xml https://github.com/natefoo/docker-build/blob/master/R/build.sh Are you

Re: [galaxy-dev] Installing Cairo into Gakaxy

2015-08-28 Thread Björn Grüning
. Any farther help or suggestions greatly appreciated. Christian University of Manchester From: Björn Grüning [bjoern.gruen...@gmail.com] Sent: Wednesday, August 26, 2015 7:19 PM To: Christian Brenninkmeijer; galaxy-dev@lists.galaxyproject.org Subject

[galaxy-dev] IUC Tools & Collections Hackathon

2015-09-01 Thread Björn Grüning
We are planning a remote hackathon on September 17th and 18th for Galaxy tool developers to hack on dataset collections. Dataset collections enable MapReduce style workflows in Galaxy and have come a long way over the last year+. Several groups are using dataset collections and newer tools to

Re: [galaxy-dev] docker-galaxy image with custom tools as new container?

2015-09-05 Thread Björn Grüning
Hi Piotr, Am 04.09.2015 um 17:58 schrieb Piotr Grabowski: > Dear Galaxy-Devs, > > I am currently developing a tool/workflow based on KNIME platform for data > analysis. The plan is for my group to publish this tool at some point and > we decided that Galaxy might be a very good platform to base

Re: [galaxy-dev] Adding categories to Main

2015-09-12 Thread Björn Grüning
s and see what we need later. >>>> >>>> Cheers, >>>> Keith >>>> >>>> On Aug 7, 2015, at 12:25 PM, Martin Čech <mar...@bx.psu.edu> wrote: >>>> >>>> Dear Keith, >>>> >>>> I have created 'NL

Re: [galaxy-dev] FastQC galaxy issue

2015-09-12 Thread Björn Grüning
Hi, I'm not sure FASTQC can deal with gz files natively. In the documentation I found they use zcat: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/INSTALL.txt So maybe this is your problem? Bjoern > Hi Bjoern, > > Thank you for your response. To answer your question, yes I am

Re: [galaxy-dev] Galaxy Tools and Collections Remote Hackathon (Thursday and Friday)

2015-09-17 Thread Björn Grüning
Hello everyone! Today and tomorrow we will try to improve Galaxy tools to consume and create collections. You are welcome to join and contribute in any way. For example code contributions, not matter how small, but also in improving documentations and our [best-practice

Re: [galaxy-dev] not sure what I can do about this...

2015-09-29 Thread Björn Grüning
Hi Edgar, please download the latest version of tbl2asn from here: ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/by_program/tbl2asn/ and replace it with your version, this will probably fix your error. Cheers, Bjoern Am 29.09.2015 um 14:05 schrieb Fernandez Edgar: > Hello Gents, > >

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

2015-10-02 Thread Björn Grüning
Thanks Greg for this nice example, I guess this is useful for others as well! I will try to put it into the Wiki soon. Am 30.09.2015 um 20:05 schrieb Greg Von Kuster: > Here’s the answer to my question: > > The ability to use associated dynamic select lists on Galaxy tool forms where >

Re: [galaxy-dev] Installing Cairo into Gakaxy

2015-09-27 Thread Björn Grüning
ages installed before the using package. >> Including Cairo before package_3_2_1 >> >> On an Ubuntu 14.04.LTS (updated today) >> Memory 15.6 GiB >> Processor Intel Xeon(R) CPU E5-1660 v3 @ 3.00Ghz x 16 >> OS type 64-bit >> >> I also tried it on my la

Re: [galaxy-dev] Installing Cairo into Gakaxy

2015-10-06 Thread Björn Grüning
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...@gmail.com] > Sent: Sunday, September 27, 2015 10:4

Re: [galaxy-dev] Bx-python and numpy eggs

2015-11-27 Thread Björn Grüning
Hi Jose, can you please try to set: enable_beta_tool_command_isolation = True in your galaxy.ini file? Thanks, Bjoern Am 27.11.2015 um 16:01 schrieb Jose Juan Almagro Armenteros: > I bit more of information. I have this problem running tools from the last > version of deepTools (1.5.11.0) ,

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

2015-12-01 Thread Björn Grüning
n. Cheers, Bjoern > Thanks > Ulf > > On 01/12/15 16:41, Björn Grüning wrote: >> Hi Ulf, >> >> just adding to Martins great explanation that you should set >> >> enable_beta_tool_command_isolation = True >> >> in your galaxy.ini file if you are usin

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

2015-12-02 Thread Björn Grüning
Hi Hans, as non-Apple user I now a little bit lost here. Can you please read this one: http://stackoverflow.com/questions/10357804/configure-error-c-compiler-cannot-create-executables It seems to be a fruit problem :) The error message is not so meaningful than I had hoped. Cheers, Bjoern Am

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

2015-12-04 Thread Björn Grüning
Hi Makis, as a small pointer, please have a look at the ansible playrole we provide: https://github.com/galaxyproject/ansible-galaxy-extras or the Galaxy Docker Image: https://github.com/bgruening/docker-galaxy-stable all steps are described here and can be reused. Cheers, Bjoern Am

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

2015-12-05 Thread Björn Grüning
Sounds great Hans, gfortran is only needed on OS-X for Linux we can ship precompiled binaries. Moreover if you setup your production instance keep this list in mind. https://wiki.galaxyproject.org/Admin/Config/ToolDependenciesList Cheers, Bjoern > Hi Marius, > > I bow to your efforts in

Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

2015-12-04 Thread Björn Grüning
Hi Bob, you could write a special visualisation for your specific datatype. This does not work with the eyeball, but with the visualisation button associated to every dataset. For a few visualisation examples please see the following links: *

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

2015-12-02 Thread Björn Grüning
Hi, which operating system are you using? We ship precompiled binaries for x64-linux systems. So I wonder why your Galaxy is trying to compile R. Can you provide us with the INSTALLATION.log from the R package? Thanks, Bjoern Am 03.12.2015 um 00:49 schrieb Hans Rudolph: > Hi Björn, > > thanks

Re: [galaxy-dev] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

2015-12-07 Thread Björn Grüning
Hi Bob, > Good morning Bjorn, > > > The way I understand Galaxy is worksteps involve a tool using History > inputs and creates History output files. I view the results from > the tool one click's on the eyeball to see the output file content. > > In following this same flow, I was trying to

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

2015-12-02 Thread Björn Grüning
Hi, we just did not updated the packages. Sorry. I have now pushed everything to the TS's. Hopefully it is working now for you. Cheers, Bjoern > Thanks to Marius and Martin for fixing pixman-0.32.4! > > This new pixman-0.32.4 version (owned by devteam) is also used by the > new devteam

Re: [galaxy-dev] How does one run Javascript or HTML as a tool?

2015-12-12 Thread Björn Grüning
Hi Bob, > Thank you Eric, > > But I want to be clear after spending 3 days with help from others trying to > get this to work. > > 1. Config/plugin/visualization is where code goes to have a Galaxy internal > module display a user defined data type -- mine is binary Yes. > 2.

Re: [galaxy-dev] IE setup problem

2015-12-17 Thread Björn Grüning
Hi, you need to have node installed. And then simply run: ./lib/galaxy/web/proxy/js/main.js --ip 0.0.0.0 \ --port 8800 --sessions $GALAXY_ROOT/database/session_map.sqlite \ --cookie galaxysession --verbose from your Galaxy root dir. Cheers, Bjoern Am 18.12.2015 um 06:58 schrieb Mic: >

[galaxy-dev] Happy new year!

2015-12-31 Thread Björn Grüning
Hi Galaxy Developers, last year was a blast for Galaxy and it seems that the Galaxy core team is preparing a new release soon with some big big features :) I really enjoy working with the Galaxy community and wish you all a happy new year. Let's keep rocking the Galaxy and make Bioinformatics

[galaxy-dev] RFC: new

2016-01-01 Thread Björn Grüning
Hi Galaxy developers, this is a RFC to get the implementation details right for a new action type in `tool_dependencies.xml`. Since years we try to save a very crucial sustainability problem: **Non-sustainable links**! A little bit of history At first we tried to

Re: [galaxy-dev] IPython and Rstudio are missing

2016-01-01 Thread Björn Grüning
or your email, I found on the bottom of this >>>> site https://wiki.galaxyproject.org/Admin/Config/nginxProxy a >>>> configuration for IE, but I am not quite sure whether it is enough. To >>>> update the documentation would be really awesome. >>>> >>&

Re: [galaxy-dev] RFC: new

2016-01-05 Thread Björn Grüning
gt; Remy > > 2016-01-04 17:50 GMT+01:00 Eric Rasche <e...@tamu.edu>: > >> Hi Peter, >> >> >> On 01/02/2016 11:54 PM, Peter Cock wrote: >> >> >> >> On Friday, 1 January 2016, Björn Grüning < <bjoern.gruen...@gmail.com> >>

Re: [galaxy-dev] IE setup problem

2015-12-22 Thread Björn Grüning
>>> The following Apache modules I have enabled (*sudo a2enmod rewrite >>>>> deflate expires proxy proxy_html xsendfile xml2enc proxy_wstunnel*) >>>>> >>>>> What did I do wrong so I can not start Rstudio and IPython inside >>>>>

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