Re: [galaxy-dev] The state of the MOTHUR merge?

Me finishing my re review and pressing the merge button. I tend to merge as it is at the moment and do some small adjustments afterwards ... This weekend Peter, this weekend! :) Am 03.06.2016 um 13:37 schrieb Peter van Heusden: > PR #429 on tools-iuc contains the updated MOTHUR toolsuite for

Re: [galaxy-dev] Refresh of screens in Galaxy Docker environment

> > Can you look into that? > > Thanks! > > George Weingart PhD > Huttenhower Lab > Harvard School of Public Health > > > *Before F5 pressed* > > Inline image 1 > > *After F5 pressed.* > > Inline image 2 > > On Wed, Apr 13, 2016 at 11:

Re: [galaxy-dev] Update on Qiime in Galaxy?

Hi Oksana, afaik a few more tests would be nice: https://github.com/galaxyproject/tools-iuc/pull/431 But it looks more a less good. If you want to do the final cleanup, this PR is probably ready to merge. Thanks! Bjoern P.S. CC Bérénice as she was working on it as well Am 19.05.2016 um 17:02

Re: [galaxy-dev] Any tool that uses Composite Datatypes

Hi, a very good example is the makeblastdb wrapper. You can find it here: https://github.com/peterjc/galaxy_blast/blob/master/tools/ncbi_blast_plus/ncbi_makeblastdb.xml#L91 Hope this helps, Bjoern > Hi All > > I am creating a database (neo4j) composite datatype in galaxy. The > database has

Re: [galaxy-dev] PSU Meet and Greet this Saturday

I wish I would be there! :) Am 22.04.2016 um 22:40 schrieb Suderman Keith: > I’ve heard back from one person. Would it help if I said that the Lappsgrid > project is buying lunch? :) > >> On Apr 21, 2016, at 11:41 PM, Suderman Keith wrote: >> >> Sorry for spamming the

Re: [galaxy-dev] Refresh of screens in Galaxy Docker environment

Hi George, are you using this Docker container? https://github.com/bgruening/docker-galaxy-stable If so which version? I haven't seen this behaviour so far. Ciao, Bjoern Am 14.04.2016 um 08:04 schrieb George Weingart: > Hello, > > We are installing Galaxy in a Docker environment and we are

Re: [galaxy-dev] Galaxy Bare/Core and custom upload tool

Hi Keith, with this PR merged https://github.com/bgruening/docker-galaxy-stable/pull/164 You can use the Galaxy Docker Image and pass in the -e BARE=True option. This will give you an production ready Galaxy Instance without tools, but with FTP Server, scheduler and activated TS. You could even

Re: [galaxy-dev] Troubleshooting BAM file upload issues

Hi Amelia, can you pleae check if you have samtools installed in your PATH? Ciao, Bjoern Am 22.03.2016 um 19:28 schrieb Amelia Ireland: > I'm setting up a Galaxy instance on a new server and am having some > issues with BAM file uploads. I'm using the BAM files supplied with > JBrowse for

Re: [galaxy-dev] planemo update failing on testtoolshed

Hi Peter, can you try to delete files with the web interface? I saw the tool name, do you know this small tool? https://github.com/bgruening/galaxytools/blob/master/tools/splitfasta/splitFasta.xml Cheers, Bjoern Am 18.03.2016 um 20:03 schrieb Peter van Heusden: > Hi there > > I'm trying to

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

om > <mailto:leo.bisca...@gmail.com>> wrote: > > Ok, thanks! > > Best regards, > > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning > <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>> > wrote: > >

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

ail.com>> wrote: > > Ok, thanks! > > Best regards, > > On Mon, Dec 28, 2015 at 5:36 PM Björn Grüning > <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>> wrote: > > > > Am 28.12.2015 um 20:33 schrieb Léo Biscassi:

Re: [galaxy-dev] playbook download error

Hi, try git clone --recursive https://github.com/galaxyproject/ansible-galaxy-tools.git Cheers, Bjoern Am 03.03.2016 um 19:54 schrieb William Ge: > Hi, all, > > > > I tried to download the playbook for automatic installation of Galaxy > tools, but encountered the following error: > > >

Re: [galaxy-dev] Docker tools

Hi Abdulrahman, this does not belong to a tool, this is more a configuration for an admin. The tools does not care where it runs. So what you need to do is to set up a job destination and configure your tools to use this destination. Here is a small documentation about it:

Re: [galaxy-dev] Missing modules after upgrade to 16.01

Hi, please have a look at this script and run it: ./scripts/common_startup.sh Also make sure you have samtools installed. Ciao, Bjoern Am 01.03.2016 um 13:39 schrieb C. Ch.: > Hi, > > I've upgraded to 16.01 and have error messages indicating missing > modules. This produces problems while

Re: [galaxy-dev] packaging R scripts

I will update this post with more informations as needed: https://biostar.usegalaxy.org/p/16259/ Thanks, Bjoern Am 26.02.2016 um 09:37 schrieb Gildas Le Corguillé: > Hi, > > For me, three solutions : > - You can find existing packages which will install your library >

Re: [galaxy-dev] packaging R scripts

Hi Xianrong and Gildas, this method works, but is a little bit outdated. Please use the setup_r_environment like used here: https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_deseq2_1_8_2/tool_dependencies.xml You can use this script with small modifications to create you

[galaxy-dev] Galaxy Docker 16.01 released!

Hi all! We have released a new version of our Galaxy Docker Image. https://github.com/bgruening/docker-galaxy-stable https://registry.hub.docker.com/u/bgruening/galaxy-stable/ https://quay.io/repository/bgruening/galaxy A few highlights: * based on Galaxy 16.01, with all it's new awesome

Re: [galaxy-dev] Custom tool with multiple inputs for different datasets. How to preferrentially select

Am 24.02.2016 um 17:44 schrieb Ryan G: > Next question - My custom tool take as input mulitple datasets from > different tools and collates all the information. For instance, 1 input > as tabular input, sampleManifest, another input is also tabular, > expressionData. > > When the tool is

Re: [galaxy-dev] correctly installing to toolshed

Hi, is the script rm_consecutive_sameScore.pl part of your TS repo and next to your tool XML file or where is it stored? Thanks, Bjoern Am 23.02.2016 um 17:46 schrieb Xianrong Wong: > Hi, I'm new to publishing tools/repository on the toolshed. I have used > planemo and lint and tests as well

Re: [galaxy-dev] Docker and alpine linux

Hi Tiago, thanks for the heads-up. I also tried alpine some time ago but Galaxy needs some external dependencies which Nate is building also with a ppa for Debian based systems. So this is not so easy to migrate. What we could do is to orchestrate the containers and its deps:

Re: [galaxy-dev] Gemini installation error

Hi Sebastian, can you check your python version and update it if possible. It seems to be an anaconda problem as far as I can see and not related to Galaxy as we do not install this python version... Also try to use the system-python version. Hope this helps, Bjoern Am 13.02.2016 um 17:10

Re: [galaxy-dev] NGS.plot script freeze

Hi Phillipp, what means the script freezes? Galaxy, or only the tool turns red? Cheers, Bjoern Am 09.02.2016 um 12:58 schrieb Philipp Rathert: > Dear All, > > we are trying to use NGS-plot on our local docker-galaxy-stable instance. > > The script freezes whenever we click on the tool. > >

Re: [galaxy-dev] Jupyter

Am 10.02.2016 um 15:25 schrieb Jasper Koehorst: > I am currently experimenting with jupyter and it finally works as I am > able to use the environment on a local machine. > However beside python2.7 how do I load a galaxy history file into for > example R, Bash, etc? I could not really find any

Re: [galaxy-dev] Importing workflows via command-line/Docker script

ain, > Cam > > On 27/01/2016 7:17 pm, "Björn Grüning" <bjoern.gruen...@gmail.com> wrote: > >> Hi Cam, >> >> as Marius already pointed out this is easily possible with bioblend. >> I would create a small script that takes the path to the GA fi

Re: [galaxy-dev] Importing workflows via command-line/Docker script

Hi Cam, as Marius already pointed out this is easily possible with bioblend. I would create a small script that takes the path to the GA file as input, preferably also a URL, and populates this in Galaxy. I would be interested to include such a script in the Main Docker container, so everyone

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

> Oksana > > Message: 1 > Date: Sat, 23 Jan 2016 19:55:47 +0100 > From: Björn Grüning <bjoern.gruen...@gmail.com > <mailto:bjoern.gruen...@gmail.com>> > To: Oksana Korol <oko...@gmail.com <mailto:oko...@gmail.com>>, >

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

con > in production. > > Cheers, > Oksana > > On Mon, Jan 25, 2016 at 9:52 AM, Björn Grüning > <bjoern.gruen...@gmail.com <mailto:bjoern.gruen...@gmail.com>> wrote: > > Hi, > > can you please check this setting? > > > https://github.c

Re: [galaxy-dev] Setting up visualization on Galaxy on CentOS

Hi Oksana, this work for me in 16.01 (upcoming). Please make sure you are logged into your Galaxy as some user, not anonymous and than the Phyloviz Visualisation will be available from the small chart-symbol next to the (i) symbol. Hope this helps, Bjoern Am 22.01.2016 um 23:53 schrieb Oksana

Re: [galaxy-dev] Bowtie2

Awesome! Glad you got it to work. Am 13.01.2016 um 21:19 schrieb Laforest, Martin: > Seems to work after server reboot... > > Thanks > > Martin > > De : Laforest, Martin > Envoyé : 13 janvier 2016 10:00 > À : 'galaxy-dev@lists.galaxyproject.org' > Objet : RE: Bowtie2 > > Oups I made a

Re: [galaxy-dev] RFC: new

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> >>

[galaxy-dev] RFC: new

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

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. >>>> >>&

[galaxy-dev] Happy new year!

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

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

Hi Léo, idneed we have a small community that is bringing Cheminformatics into the Galaxy. It's called ChemicalToolBox and is located here: https://github.com/bgruening/galaxytools/tree/master/chemicaltoolbox We have all the basic stuff for manipulating checmical structure files, fingerprint

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

s unfortunately no option afaik. > best, > > On Mon, Dec 28, 2015 at 4:33 PM Björn Grüning <bjoern.gruen...@gmail.com> > wrote: > >> Hi, >> >> yes we had some idea, but nothing materialised so far. We started with >> the visualisation, because this wa

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

ith Tool development or git. This is exciting! Cheers, Bjoern > Best regards, > > On Mon, Dec 28, 2015 at 5:12 PM Björn Grüning <bjoern.gruen...@gmail.com> > wrote: > >> >> >> Am 28.12.2015 um 20:06 schrieb Léo Biscassi: >>> Hi, >>> >>>

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

nks for reply. > Would be great idea join forces in this project. How do you plan extend > ChemicalToolBoX with docking? I would like to know more details. > > Att. > > On Mon, Dec 28, 2015 at 4:09 PM Björn Grüning <bjoern.gruen...@gmail.com> > wrote: > >> Hi Léo,

Re: [galaxy-dev] IE setup problem

>>> 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 >>>>>

Re: [galaxy-dev] IE setup problem

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: >

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

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] How does one create a viewer for a new datatype to display a webpage if eyeball is clicked?

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

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] Multiple web servers and handlers Galaxy failed

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

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] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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] gcc error during pixman-0.32.4 installation on Mac OS X 10.11

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] Publish tool with Python dependencies to the toolshed

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] Question about contributing a Visualization plugin to Galaxy

ould like to have the ToolShed providing visualisations. For the time being the best thing we can do is to join github repositories to have as less as possible. So the few repos out there get more attraction. Cheers, Bjoern > Thanks! > > Greg Von Kuster > > >> On Nov 30

Re: [galaxy-dev] Question about contributing a Visualization plugin to Galaxy

Hi Greg, please have a look at: https://github.com/bgruening/galaxytools/tree/master/visualisations All these visualisations are self-contained. You can simply drag and drop them into the plugin folder and it will work. So no need for a PR. I also have a hack for you to integrate this into a

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

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] Bx-python and numpy eggs

e problem. > > Thank you! > > Regards, > > Jose > > > > 2015-11-27 17:59 GMT+01:00 Björn Grüning <bjoern.gruen...@gmail.com>: > >> Hi Jose, >> >> can you please try to set: >> >> enable_beta_tool_command_isolation = True >> >

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

; > Regards, > > Jose > > 2015-11-27 22:01 GMT+01:00 Björn Grüning <bjoern.gruen...@gmail.com>: > >> Awesome! >> >> Sorry for the inconvenience ...! >> Is matplotlib installing for you? Can you confirm this error? >> >> https://github

Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

Am 24.11.2015 um 20:36 schrieb Tiago Antao: > On Tue, 24 Nov 2015 10:38:05 +0100 > mabernard wrote: > >> So I'm in to but not at the date you propose sorry. >> Is the possible the week before (between 7th and 11th) or 2 weeks >> later (between 29th to 1st)? >

Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

ct haplotypes.. or not ;) >> Furthermore, we begin using other pipelines as Ddocent and it will be cool >> to put it on Galaxy >> >> So ready to go further with a remote hackathon. Maybe on March or April 2016 >> ? >> >> Wishing you the best.

Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

Hi Tiago, I like this idea very much and I will try to help as much as I can. I hope someone else will join otherwise I will be in for a tandem hack :) Cheers, Bjoern Am 16.11.2015 um 17:05 schrieb Tiago Antao: > Dear all, > > This is an email to inquire about the potential community interest

Re: [galaxy-dev] Potential Hackathon proposal: RADSeq

Am 23.11.2015 um 20:56 schrieb Tiago Antao: > On Mon, 23 Nov 2015 12:08:17 -0600 > Eric Rasche wrote: > >> Maybe you all would consider doing something akin to Marten's mention >> of the Jenkins hackathons where they have short (10-30 minute) >> seminars on background

Re: [galaxy-dev] Dataset tags lost when copying or sharing history

Hi Brian, thanks for the bug report. If you don't mind please add this to: https://github.com/galaxyproject/galaxy/issues Thanks, Bjoern Am 18.11.2015 um 23:15 schrieb Brian Claywell: > One of our users is using dataset tags to manage the datasets in an RNA-seq > experiment, and has reported

Re: [galaxy-dev] ProFTPD with SQLite

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

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] IPython and Rstudio are missing

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, >

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

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] netcdf 4.3 error

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

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] Bismark installation dependencies error

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

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

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] recurring issues with revisions of packages from toolshed

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

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

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] recurring issues with revisions of packages from toolshed

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)

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] QIIME tools for Galaxy (WIP, call for collaborators)

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] QIIME tools for Galaxy (WIP, call for collaborators)

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)

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

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] Question about using dynamic options and refresh_on_change for rendering 2 associated select lists

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] not sure what I can do about this...

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] Installing Cairo into Gakaxy

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] Galaxy Tools and Collections Remote Hackathon (Thursday and Friday)

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] Adding categories to Main

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] docker-galaxy image with custom tools as new container?

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] Installing Cairo into Gakaxy

. 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

Re: [galaxy-dev] Installing Cairo into Gakaxy

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] 20 August GalaxyAdmins Meetup: Genomic Data Management; Tool Installation Automation

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] Problem with ChemicalToolBox dependencies

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] Galaxy instance with multiple partitions

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

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] Data upload as part of workflow?

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] Externalizing Galaxy config in docker-galaxy-stable

, 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

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] passing the name attribute from the DB to a sniffer

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

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] Externalizing Galaxy config in docker-galaxy-stable

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] Externalizing Galaxy config in docker-galaxy-stable

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] planemo shed_update - error

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] docker-galaxy-stable tools fail

| 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] Bismark doesn't end and blocks the server

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] follow up question regarding the 'toolform-upgrade'

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] Galaxy for Natural Language Processing

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] Interested in GSOC idea Docker Swarm and Compose ask for advices.

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:

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

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

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