Hi Anna,
you need to install samtools into your system or via the toolshed. If
you install it via the toolshed you need to create a symlink.
Lets assume you have samtools installed in:
~/tool_deps/samtools/0.19/iuc/2828727744/
than you need to create a symlink from
~/tool_deps/samtools/0.19/iuc
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 put
Hi Adhemar,
can you please create a Trello card to keep track on this?
Cheers,
Bjoern
Am 03.12.2014 um 18:23 schrieb Adhemar:
> Hi,
> The workflow variables are awesome!
> https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/VariablesEdit
> It's really nice to have the output files properly nam
ere
> all these errors from LAPACK and ATLAS.
>
> Cheers,
> Yu
>
> di29her
> w...@lrz.de<mailto:w...@lrz.de>
>
> On 16 Dec 2014, at 04:07, Björn Grüning
> mailto:bjo...@gruenings.eu>> wrote:
>
> Hi Wang,
>
> can you point me to the exact ve
Hi David,
do you get the same error message as Wang?
Am 17.12.2014 um 23:10 schrieb Lapointe, David:
> I am having the same issue. The RHEL packages for atlas, blas, and lapack
> are installed, but numpy 1.7 won't install, while numpy 1.9 seems to
> install successfully.
>
_
Hi AK,
Am 22.12.2014 um 10:56 schrieb KRESS Arnaud (ESP):
> Hi gentlemen,
> I am currently struggling to create a custom package (to share via a
> toolshed) that would include a tool definition file and the associated
> binary. Once installed, I can launch a job but I get the following error
nstalled and a env.sh file is created.
> But I'm still getting the same error message, at what condition is this
> env.sh sourced at execution time ?
>
> AK
>
> Le Lundi 22 Décembre 2014 11:26 CET, Björn Grüning
> a écrit:
>
>> Hi AK,
>>
>>
Hi Ryan,
> I'm trying to install rpy for Galaxy, however it seems to not be available
> anymore. rpy2 is supposed to be the replacement. Does/will Galaxy migrate
> to rpy2? Some of the tools rely on rpy but since its not available
> anymore, the tools can't run.
Have a look at:
https://github.
Hi Ryan,
the Galaxy project uses Trello to keep track of such requests and bugs.
https://trello.com/b/75c1kASa/galaxy-development
Please create a card and track to progress :)
Cheers,
Bjoern
Am 23.12.2014 um 17:06 schrieb Ryan G:
> When browsing a data library, clicking on entries I want to sel
Here you go: https://trello.com/c/zOP0A6Ku
Merry Christmas,
Bjoern
Am 23.12.2014 um 17:06 schrieb Ryan G:
> When browsing a data library, clicking on entries I want to select is a bit
> cumbersome. It would be nice to use arrow keys, etc to select items, just
> like when selecting mail in Gmail.
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
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 anymor
Hi Michael,
which version of the FASTQC wrapper are you running? Can you point us to
the exact build and toolshed version?
Thanks,
Bjoern
Am 02.01.2015 um 21:22 schrieb Waldron, Michael H:
> Having a problem with directing FastQC output in Galaxy. User is running a
> job whose command line look
od/fastqc-0.11.2/FastQC
>
>
> Mike Waldron
> Systems Specialist
> ITS - Research Computing Center
> University of North Carolina at Chapel Hill
>
>
>
> From: Björn Grüning [bjoern.gruen...@gmail.com]
> Sent: Saturday, January 0
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
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 alterna
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:
https://github.com/bgruening/
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 0
itely need an automated 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
> wrote:
>
>> Hi Ross,
>>
>> this is great!
>>
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 Pet
llaborations
Thanks Ross for working on this!
Bjoern
> Comments and suggestions welcomed!
>
> On Sun, Jan 11, 2015 at 10:41 PM, Björn Grüning
> wrote:
>
>> Hi Ross,
>>
>> you are absolutely right.
>> My download_store repository is exactly for this purpos
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 stuc
Hi Edgar,
this is indeed possible. Please have a look at Galaxy data libraries:
https://wiki.galaxyproject.org/Admin/DataLibraries/Libraries
Cheers,
Bjoern
Am 30.01.2015 um 15:30 schrieb Fernandez Edgar:
> Good morning Gents,
>
> I hope everyone is well.
>
> I was wondering if it's possible t
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 t
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:
>
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
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 on a command line tool outside of galaxy
>> installation. I see in the admin interface that tophat has a
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
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 d
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:
https://github.com/galaxyproject
and document them.
Thanks, this kind of discussion I wanted to have :)
Cheers,
Bjoern
> -John
>
>
> On Tue, Mar 3, 2015 at 11:38 AM, Peter Cock wrote:
>> Hi Björn,
>>
>> Command line arguments are often case sensitive
>> (e.g. samtools switches), but are Gala
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 Ubuntu
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 f
Hi Keith,
> Hi Björn,
>
> Thanks for the quick reply.
>
> It might help to take a look at what I have so far. Our Galaxy server is
> running at http://grid.anc.org:8000
> The front page contains a very basic tutorial (and I use the term loosely)
> with instructions for creating a simple wor
Hi Michael,
Am 07.04.2015 um 21:46 schrieb Michael Crusoe:
> On Wednesday, March 25, 2015, Björn Grüning
> wrote:
>
>> Hi all!
>>
>> We are proud to present you the next release of Galaxy Docker.
>>
>> https://github.com/bgruening/docker-galaxy-stab
Hi Keith,
Am 21.04.2015 um 21:21 schrieb Keith Suderman:
> On Apr 15, 2015, at 5:35 AM, Björn Grüning 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?
Out
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:
>
> W
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:
> 40b69cb948eed2cece8
Hi Alex,
here are some informations:
https://wiki.galaxyproject.org/ToolDependencyRecipes
https://wiki.galaxyproject.org/ToolDependenciesTagSets
https://wiki.galaxyproject.org/PackageRecipes
https://wiki.galaxyproject.org/SimpleRepositoryDependencies
But the best way probably is to learn from exa
> The problem is: I don't know how to load it into my local
>> galaxy 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,
&g
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 han
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
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
http://
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:
>
> indel_real
Evan F. Bollig, PhD
> Scientific Computing Consultant, Application Developer | 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
>
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 metada
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 (se
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 wrote:
>
>> It looks
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 to
way to do this that I don't see, please let
> me know.
>
> Cheers, Oksana
>
>
>
>> On Aug 1, 2015, at 1:10 PM, Björn Grüning
>> wrote:
>>
>> Hi Oksana,
>>
>> both variables are used during container build to create users and
>> home
uild/run.
Uh nice!
Martin Page and Jeroen Galle are currently working 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 wrot
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 (
> https://raw.githubusercontent.com/galaxyproject/usegalaxy-playbook/c55
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
Am 04.08.2015 um 00:00 schrieb Tiago Rodrigues Antao:
> On Mon, 03 Aug 2015 17:30:05 +0200
> Björn Grüning 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,
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,
>
> -Original Message- From: galaxy-dev
> [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf Of
> Björn Grüning Sent: August-04-15 4:42 AM To: Tiago Rodrigues Antao;
> Björn Grüning Cc: galaxy-...@lists.bx.psu.edu; Martin Page (TSL);
> Oksana; Jeroen Galle Subject:
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
for those who need it. That said, I
> would welcome any standardized solution, be it run time or build time.
>
> Cheers,
> Oksana
>
> On Wed, Aug 5, 2015 at 4:30 AM, Björn Grüning
> wrote:
>
>> Hi Brian,
>>
>> thanks for you mail! Very appreciated, p
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
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
cont
Hi,
Am 06.08.2015 um 15:19 schrieb Tiago Rodrigues Antao:
> On Thu, 06 Aug 2015 14:00:02 +0200
> Björn Grüning 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
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
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
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://wiki.galaxyproject.org/ObjectStore
http://galaxy.readthedocs.org/en/stable/lib/galaxy.objectstore.html
I can also send yo
e offer to send me your configuration! Let me play
> around with it a bit and see how hard it is, first...
Ciao,
Bjoern
> Thanks!
>
> Ray
>
>
>
> On Tue, Aug 11, 2015 at 4:20 PM, Björn Grüning
> wrote:
>> Hi Raymond,
>>
>> Galaxy as a very
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 occ
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
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 us
manually in the order that required
>> packages 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
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 expr
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 i
Keith
>>>>
>>>> On Aug 7, 2015, at 12:25 PM, Martin Čech wrote:
>>>>
>>>> Dear Keith,
>>>>
>>>> I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for
>>>> you to test out the Tool Shed envir
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 runn
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
guide](https://github.com/g
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
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,
>
> So
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
> selecting
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
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
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
A
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 -
>
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 pr
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..?
Hi Simon,
the Galaxy Docker Image is using Slurm you can look at it here:
https://github.com/bgruening/docker-galaxy-stable
Hope this helps,
Bjoern
Am 15.10.2015 um 06:38 schrieb Simon Gladman:
> Hi there all,
>
> Has anyone had success setting up job_conf.xml for slurm based clusters? I
> am
>>> We are not yet on IEs,
>> No, no, no. How can this happen? ;)
> I interpret ";)" as "Indeed I remember all the issues you poor guys are
> faced with" ;)
>>
>>> but we plan to upgrade our local production
>>> instance soon (a recent version is already 'waiting' to take over),
>>> apart from oth
pes into 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
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
> ve
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 "!".
all the R 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 err
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
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 v
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 inst
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,
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":
--sea
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
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 15
Hi Mic,
please check any other file than a VCF file. Try a txt file for example.
Thanks,
Bjoern
Am 07.11.2015 um 00:54 schrieb Mic:
> Hi Eric,
> I added your line to ipython.xml and rstudio.xml and restarted Galaxy, but
> still Rstudio and Ipython do not appear on my test.vcf file by clicking th
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 ha
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
d Ipython still did not show up.
>>
>> Thank you in advance.
>>
>> Best wishes,
>>
>> Mic
>>
>> On Sat, Nov 7, 2015 at 9:58 AM, Björn Grüning
>> wrote:
>>
>>> Hi Mic,
>>>
>>> please check any other file than a
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