Hi David,
numpy and scipy are not included as modules with the galaxy
distribution, but you can use the repositories from the toolshed and
depend on them.
http://toolshed.g2.bx.psu.edu/view/iuc/package_numpy_1_7
http://toolshed.g2.bx.psu.edu/view/iuc/package_scipy_0_12
An example usage is
Hi Han,
you can filter the output of every tool and react on it with the stdio
tag in Galaxy. for more information please have a look at the wiki page:
https://wiki.galaxyproject.org/Admin/Tools/ToolConfigSyntax#A.3Cstdio.3E.2C_.3Cregex.3E.2C_and_.3Cexit_code.3E_tag_sets
Cheers,
Bjoern
Hello,
Hi Eric,
please see the following ticket for it and vote it up :)
https://trello.com/c/dWvkfBKC
Sorry that there is no fix for it yet,
Bjoern
e the actual image is located at
___
Please keep all replies on the list by using reply all
Hi,
since a few days there are frequent error messages popping up in my
Galaxy log files.
galaxy.jobs.runners ERROR 2014-01-17 13:11:17,094 Unhandled exception
checking active jobs
Traceback (most recent call last):
File
/usr/local/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py,
line
Hi,
we want to put some more hard drives into your Galaxy Server. And we
plan to use the hierarchical ObjectStore for that purpose.
The new discs will be type=distributed id=primary and the old disc
will become type=disk id=secondary. If I understood correctly the
old disc is them in some
Hi,
if we want to include JAVA programs into Galaxy we are usually forced to
hardcode -Xmx4g -Xms3g or similar into the wrapper. Would it make sense
to have something like GALAXY_MEMORY, similar to GALAXY_SLOTS, to obtain
the maximum of allowed memory from the scheduler. With some cheetah
magic
Hi Stephanie,
I'm facing a problem in installing a tool from the tool-shed
repository for a while now and I still don't know how to make it.
I'm trying to install deepTools
(https://github.com/fidelram/deepTools) into our Galaxy instance but I
never got the tools neither properly installed
this.)
Best,
Geert
On 11/19/2013 12:26 PM, Bjoern Gruening wrote:
Hi,
I found that the GATK tools do not have the same requirement tag. For
example indel-realigner has version 1.4, realigner_target_creator has
version 1.3. Is that correct? What is the recent
Hi,
I found that the GATK tools do not have the same requirement tag. For
example indel-realigner has version 1.4, realigner_target_creator has
version 1.3. Is that correct? What is the recent version that is
required for GATK?
Also realigner_target_creator uses the gatk_picard_indexes location
Hi,
to chime into this discussion.
I found some inconsistency during my rsync endeavor and I'm curious if
there is any way to contribute to that service.
--
xenTro3 xenTro3 Frog (Xenopus tropicalis):
xenTro3 /galaxy/data/xenTro3/seq/xenTro3.fa
but only
/xenTro3.fa.gz exists.
---
ce6
Hi Peter,
thanks for raising this important topic.
I think the following trello card has a similar idea and a patch
attached.
https://trello.com/c/JnhOEqow
It would be great if we can simplify the naming of datasets, especially
if you run a workflow with several input, you would like to keep
Hi Greg,
I'm right now in implementing a setup_perl_environment and stumbled
about a tricky problem (that is not only related to perl but also for
ruby, python and R).
The Problem:
Lets assume a perl package (A) requires a xml parser written in C/C++
(Z).
(Z) is a dependency that I can import
, it is the inner environment_variable elements that do.
This should probably be resolved before the next release.
-John
On Wed, Oct 30, 2013 at 10:10 AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi Greg,
sorry for the confusion. You answered to Saskia
/2013, at 8:14 PM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Ahhh ... Thanks .. I can't believe I missed that. Thanks for spotting it.
No problem!
I'm not sure I understand enough about how this works to answer your
ruby_home question. Ill play with this more tomorrow
Hi Pieter,
I tried to reproduce it and looked over your files. I also tried to
reproduce it and can't. For me its showing up nicely:
http://testtoolshed.g2.bx.psu.edu/view/bgruening/upload_testing
So please try to reset metadata of that repository. And hopefully your
issues are gone magically
permission on the repo to user test1, then user test1 can
immediately reset all metadata on the repo.
Can you let me know what steps you are taking and the behavior you are seeing
that differs from this?
Thanks!
Greg Von Kuster
On Oct 29, 2013, at 1:03 PM, Bjoern Gruening bjoern.gruen
Ahhh ... Thanks .. I can't believe I missed that. Thanks for spotting it.
No problem!
I'm not sure I understand enough about how this works to answer your
ruby_home question. Ill play with this more tomorrow and see how things work
with my tools and maybe have more feedback then
Sure,
Hi Greg,
do you mean that patch?
https://bitbucket.org/galaxy/galaxy-central/commits/all?search=83bed9c7dbbc
I can reproduce that error and it is not fixed with latest
galaxy-central, or did you only applied it to next-stable?
You can test with my augustus repository if you like.
Hi,
This tools has been passing its nightly tests fine,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
However, there now appears to be a silent installation failure
(the install hasn't worked but there was no install error):
Automated tool test results
I think I can
Hi,
one of our users has created a large workflow with 300 steps. Yes he
really loves Galaxy :)
Unfortunately, its not possible to use the graphical user interface
anymore with so many steps. You can't connect boxes and scrolling is
also slow.
It there any hint how to solve, any workflow
Hi Saket,
On 21 October 2013 13:38, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi,
one of our users has created a large workflow with 300 steps. Yes he
really loves Galaxy :)
Unfortunately, its not possible to use the graphical user interface
anymore with so many steps. You
Am Samstag, den 12.10.2013, 19:42 +0100 schrieb Peter Cock:
On Thu, Aug 1, 2013 at 10:27 AM, Nicola Soranzo sora...@crs4.it wrote:
Il 2013-07-30 17:18 Peter Cock ha scritto:
Hello all,
Re:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010153.html
Hi Peter,
bjoern.gruen...@gmail.com wrote:
Hi Peter,
I saw your are working again on the job splitting features. I may have a
features request:
Well, not really working on it - just reporting a regression using it.
Ah ok :)
For some tools you have different file formats as input
Am Mittwoch, den 16.10.2013, 01:41 -0500 schrieb Eric Rasche:
Hi Bjoern,
On 10/16/2013 01:26 AM, Bjoern Gruening wrote:
Hi Eric,
Hello all,
I've been digging through the available galaxy tool config files and
have been unable to find a solution, so I bring my problem to you.
I
, Bjoern Gruening wrote:
Hi Joachim,
I had such problems if my XML file is invalid. Than I get immediately
the 'installed:' text and can click install again, without any change.
Also I would really recommend to reset your toolshed. These white
ghosts can have unpredictable effects
Hi,
it does not mean anything, but for me its working locally on a Fedora
(stable) machine.
If I can anything do to fix that, please let me know.
Bjoern
On Sun, Sep 29, 2013 at 1:17 PM, Björn Grüning wrote:
I updated R, numpy, scipy, scikit and removed the atlas dependency. It
seems to
Hi Joachim,
try to remove the last part '?r=ts=1380535239use_mirror=surfnet'
Cheers,
Bjoern
Hi all,
The download URL seems not to be accepted in tool_dependencies.xml. It
is an URL from sourceforge, the direct link to a package.
The error upon uploading the tool to my toolshed:
Am Montag, den 30.09.2013, 14:02 +0100 schrieb Peter Cock:
On Mon, Sep 30, 2013 at 1:58 PM, Dave Bouvier d...@bx.psu.edu wrote:
Peter,
It looks like there may be a version conflict between package_numpy and
either a system numpy or the Galaxy numpy egg. I'll investigate and keep you
Hi Joachim,
I had such problems if my XML file is invalid. Than I get immediately
the 'installed:' text and can click install again, without any change.
Also I would really recommend to reset your toolshed. These white
ghosts can have unpredictable effects.
If you can upload your tools to the
Hi Ramon,
Code:
tool id=predictionModelTool name=Modelo de Deteccao de Risco
...
command interpreter=bashr_wrapper.sh $script_file/command
inputs
...
/inputs
configfiles
configfile name=script_file
...
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
I did an extra test. Started with a clean 'galaxy-dist'. This time
both repositories fail with the same error. I guess before something
was cached for the repository
is broken at least on OSX.
Other people have the same issue:
http://code.google.com/p/libarchive/issues/detail?id=299
On Sep 20, 2013, at 10:41 AM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Hi Carlos,
Hi Peter and Carlos,
On Mon, Sep 16, 2013 at 8:57 PM, Carlos
Hi,
I tried to things to solve it.
1: I uploaded a new version to:
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_atlas_3_10 this time
with target_filename=ATLAS.tar.bz2. That is a rather new feature, so
you will need a recent Galaxy version. The prosite is that we do not
need to call
On Fri, Sep 20, 2013 at 1:48 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi,
I tried to things to solve it.
Was this specifically to solve ATLAS under Mac OS X,
or more generally include the problem shown on the
Galaxy (Test) Tool Shed?
Yes. My hope was to use tarfile from
Hi Simon,
it's just a guess but can you try the attached patch if you have a
reproducible case. It is not tested, but at least it should point you in
the right direction. If its working, I will create a pull request.
Cheers,
Bjoern
My optimism was short lived. I think I've hit a galaxy bug in
Hi Simon,
thank you very much for your comments!
I can see man years of effort being spent on solving this problem within
Galaxy. I was going to title this email Danger, Will Robinson, but I
didn't want to be disrespectful.
I think the path being embarked upon, tool dependency
Hi James,
thanks for your thoughts on abstraction of common tasks.
For most of these things we have now patches in bitbucket.
Similar recipes could be:
autoconf: default to configure; make; make install, allow providing
configuration options
Hi,
I want to start a discussion about the storage of tarballs to guarantee
the availability to some degree. Currently, I store most of my tarballs
in my github account, if I do not trust the official ftp/http server.
Anyone has the same problems/concerns? Is there an official
Hi JJ,
I've had occasion to use some of the samtools misc utilities in galaxy
tools.
Should those also be copied to the $INSTALL_DIR/bin when
package_samtools is installed?
Sorry, I do not get the question :(
Are you asking to enhance the existing samtools definition?
Thanks,
JJ
granted jjohnson write permission to the IUC samtools account.
Thanks,
Bjoern
On 9/17/13 7:08 AM, Bjoern Gruening wrote:
Hi JJ,
I've had occasion to use some of the samtools misc utilities in galaxy
tools.
Should those also be copied to the $INSTALL_DIR/bin when
Hi John,
On Tue, Sep 17, 2013 at 3:03 AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi all,
that is now implemented in:
https://bitbucket.org/galaxy/galaxy-central/pull-request/219/implementation-of-the-a-r_environment-to/diff
Any comments are much appreciated.
Fantastic
Hi Pieter,
yes that is possible. Have a look at other repositories. You can only
choose between different tool versions, it there are more than one
'installable version' of a tool. It is not the case in your example.
Lets imagine I only fix some help text in the tool. I do not want to
have
to the previous revision after noticing that this update has an
unexpected bug
Regards,
Pieter.
-Original Message-
From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
Sent: donderdag 12 september 2013 13:15
To: Lukasse, Pieter
Cc: 'Greg Von
Am Mittwoch, den 11.09.2013, 10:21 +0100 schrieb Peter Cock:
On Wed, Sep 11, 2013 at 10:12 AM, Joachim Jacob | VIB |
joachim.ja...@vib.be wrote:
It is not necessarily bad. If we all test each others tools (dependencies,
interface, output,...) we might get to the best of all worlds :-) (I
Hi Richard,
you can navigate to the 'repository actions' - 'Browse repository tip
files' and have a look at all files in the latest revision of your tool.
Cheers,
Bjoern
Hello,
Is there a way to see the code for the tool wrappers in the tool shed
without downloading them? I seem to
needs for building the path, must go to the
tool dependencies.
Thanks for your help!
No problem!
Salve,
Bjoern
Lionel
On 5 Sep 2013, at 17:22 , Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Hi Lionel,
Bjoern and others,
I'm back at that. I published my tool
Hi Lionel,
I've been scratching a bit my head about how galaxy builds dependency,
fruitlessly so far... Here is my problem: I have a local tool (not
installed through a toolshed) that makes use of another tool (aragorn)
that I installed from the toolshed.
Aragorn requires the aragorn
will search in that file (with the
keys specified in your tool.xml) and create the path to your repository.
Try the attached xml file and delete your repository.xml file.
Hope that helps,
Cheers,
Bjoern
Cheers,
Lionel
On 09/05/2013 01:21 PM, Bjoern Gruening wrote:
Hi Lionel,
I've
Hi Simon,
you are right. Public usernames, or usernames associated with a
repository can't be changed. If you can that is a bug, please fill a
trello card with it. The reason is to guarantee reproducibility. If
anyone has installed your repository the triple
(username,revision,toolshed) is saved
Hi Nikos,
Hi all
I installed bismark from the toolshed (bgruening) with all
dependencies having been installed successfully and I generated the
genomes according to the instructions.
While trying to test the tool I got the following error.
galaxy.jobs.handler ERROR 2013-09-04
Hi Nicola!
Il giorno mer, 07/08/2013 alle 16.28 +0200, Bjoern Gruening ha scritto:
Also, we may wish to add a dependency on BOOST, e.g.
http://testtoolshed.g2.bx.psu.edu/view/iuc/package_boost_1_53
once this is on the main Tool Shed.
Ok, time to step up and migrate all the stuff
Hi Greg,
I tried to extend my old list [1] but I'm not allowed to edit it. Maybe
you can add the following items to it.
This time I collected a few items that are relevant for the Galaxy site
of the Tool Shed ( When the user is installing via webinterface )
- offer an upgrade option, I think
Hi,
if I try to install a repository via API I get the following error:
Traceback (most recent call last):
File
/home/gruening/projects/code/galaxy-central/lib/galaxy/web/framework/__init__.py,
line 189, in decorator
rval = func( self, trans, *args, **kwargs)
File
Hi Thomas,
I think you are running a to new version of gplot
http://blog.rstudio.org/2012/09/07/ggplot2-0-9-2/
opts is now deprecated and likely causes that error. Can you downgrade
the gplot version?
We are working on a R dependencies mechanism but we are not done yet,
sorry.
Hope that helps,
.
Thanks!
On Aug 12, 2013, at 11:31 AM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
On Mon, 2013-08-12 at 16:26 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 4:19 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi Peter,
Hi Bjoern ( Greg),
RE: http
describe using 3 similar repositories
in my local tool shed. Please let me know if you still encounter this issue.
Thanks,
Greg Von Kuster
On Aug 13, 2013, at 12:49 PM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Hi Dave,
for us I think everything is fixed. But we had
Please let me know if I've misunderstood the steps you used to produce
the behavior you saw.
Thanks very much,
Greg Von Kuster
On Aug 12, 2013, at 7:44 AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 12:41 +0100, Peter Cock wrote
very much for reporting this!
Greg Von Kuster
On Aug 15, 2013, at 9:01 AM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Hi Dave,
the bug is unfortunately still present in the latest Galaxy version.
If you try to install
http://toolshed.g2.bx.psu.edu/view/iuc
Hi Shane,
please find a new bismark version with an updated dependency on samtools
0.1.19 here:
http://toolshed.g2.bx.psu.edu/view/bgruening/bismark
Thanks for reporting that issue,
Bjoern
I've had a bit of a time trying to get Bismark working on our Galaxy
instance. The install doesn't
Hi Greg,
seems to work fine!
Hello Bjoern,
On Aug 21, 2013, at 2:51 AM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Hi Greg,
a first test seems to work as expected for me, will test again with the
whole CTB.
Great - thanks!
If I understood your commit you
We should create a Tool Shed Hackathon, I'm an expert in producing
'white ghosts' :)
Thanks Peter,
As soon as I can get the steps to produce white ghost, I'll get a fix
committed - I've not been able to produce one yet.
Greg Von Kuster
On Aug 21, 2013, at 5:41 AM, Peter Cock
Hi Sridhar,
we are developing a DESeq2 tool at the moment, if you want to join get
in touch with me. Its developed here:
https://github.com/bgruening/galaxytools/tree/master/deseq2
I will upload our latest progress during the day.
Cheers,
Bjoern
Dear users,
Could anybody suggest the
Hi,
back for testing and migrating to the tool shed. Sorry in advance!
During installation via the API I'm usually watching the status with
'Manage installed tool shed repositories'.
Installation is still running but I now get these error:
URL:
11:36:00.000, Bjoern Gruening wrote:
On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
Maybe I should retitle this thread...
On Mon, Aug 12, 2013
Hi Jun,
I have managed to use something like
outputs
data format=fasta name=output label=#echo os.path.splitext
(str ($input.name))[0]#-ORF.fasta/
/outputs to display the wanted label for the dataset in the
history.
However when I applied the same code to other tool
Hi Galaxy Tool developers!
I have started to integrate the HOMER suite into Galaxy. My initial
attempt can be found here:
https://github.com/bgruening/galaxytools/tree/master/homer
Currently, we make use of:
- Tool Shed definitions of all required 3rd Party Software
- datatype definitions
-
repository and branch. Regarding matplotlib and numpy, I
currently only see matplotlib depending on the 74c21f9bdc39 revision of
numpy. Is this still an issue, or has it been resolved?
--Dave B.
On 8/12/13 11:36:00.000, Bjoern Gruening wrote:
On Mon, 2013-08-12 at 16:32 +0100, Peter
Hi,
Hi Bjoern Greg,
The Biopython package looks OK on the test tool shed,
http://testtoolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
This includes the lines:
package name=numpy version=1.7.1
repository changeset_revision=ad6ebe2c75ef
name=package_numpy_1_7
Hi Peter,
On Wed, Apr 24, 2013 at 5:05 PM, Iry Witham iry.wit...@jax.org wrote:
Hi Team,
I am trying to get GATK tools added to my cloud instance and keep getting
the following error: [Errno 2] No such file or directory:
On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote:
Hi all,
I'm currently trying out installation of tools from the Tool Shed
on a secondary Galaxy server (not our production server nor
my development setup). This is running galaxy-dist, current
latest stable I believe:
$ sudo -u galaxy
On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 12:50 +0100, Peter Cock wrote:
Hi all,
I'm currently trying out installation of tools from the Tool Shed
on a secondary Galaxy
On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 2:04 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 13:59 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 12:54 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08
On Mon, 2013-08-12 at 14:30 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 2:18 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 14:13 +0100, Peter Cock wrote:
I expect that in the meantime this bug will hit other people
as well (and until the Tool Shed
Ok reverted it!
Its now to a normal bash definition and I removed the atlas and lapack
definitions. So it should build but it has performance regressions.
If the new galaxy stable is out, I will upload the new version.
Hope it builds now for you.
Bjoern
bjoern.gruen...@gmail.com wrote:
Hi Peter,
Hi Bjoern ( Greg),
RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I'm wondering why in the Biopython package dependencies
matplotlib is currently marked as prior installation required? i.e.
package name=numpy version=1.7.1
repository
On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
Maybe I should retitle this thread...
On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Aug 12, 2013 at 3:10 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Ok reverted it!
Its now to a normal
On Mon, 2013-08-12 at 16:26 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 4:19 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Hi Peter,
Hi Bjoern ( Greg),
RE: http://toolshed.g2.bx.psu.edu/view/biopython/package_biopython_1_61
I'm wondering why in the Biopython package
On Mon, 2013-08-12 at 16:32 +0100, Peter Cock wrote:
On Mon, Aug 12, 2013 at 4:25 PM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
On Mon, 2013-08-12 at 15:55 +0100, Peter Cock wrote:
Maybe I should retitle this thread...
On Mon, Aug 12, 2013 at 3:43 PM, Peter Cock p.j.a.c
Hi Can,
something went wrong with your join utility part of your Ubuntu
installation.
Can you translate that for us?
'join (GNU coreutils) 8.20\nCopyright (C) 2012 Free Software Foundation,
Inc.\nLisans GPLv3+: GNU GPL s\xc3\xbcr\xc3\xbcm 3 ve sonras\xc4\xb1
Hi Geert,
Hi,
Is there a default notation to specify perl modules (threading modules)
in a tool configuration or in a submission to the toolshed?
I've got some tools to share that make extensive use of these modules,
and they are not default in a perl distribution. Hence, I'd like to
AM, Bjoern Gruening
bjoern.gruen...@gmail.com wrote:
Ok, time to step up and migrate all the stuff to main.
Cheers,
Bjoern
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
Hi Peter,
On Wed, Aug 7, 2013 at 3:54 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Wed, Aug 7, 2013 at 3:36 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
On Aug 7, 2013, at 10:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Greg et al,
For the NCBI BLAST+
Hi Saskia,
you need to fix that wrapper. Its a merge conflict you need to resolve
by your own (indicated by ==).
Cheers,
Bjoern
I am working on putting a tool into the toolshed. I have a bash script
wrapper. I uploaded the first version fine, but when I wanted to
upload a revision, some
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