Hi,
I updated to the latest galaxy distribution (after one year). And now
every job fails with:
/home/imba/solexa/.profile.sh: line 118: ulimit: virtual memory: cannot modify
limit: Operation not permitted
The limit is ridiculously high:
ulimit -v 6000
Its just to prevent some badly
did you check if the metadata on the input was set correctly/at all?
This happens sometimes in our galaxy instance. Metadata is not set correctly,
and jobs run after metadata is set by hand.
No reupload necessary.
best,
ido
On 06 Nov 2014, at 17:13, Lance Parsons lpars...@princeton.edu wrote:
Hi,
has anything changed in galaxy in this regard?
Any way to modify an environment before a tools is run?
I now have a tool relying on R-devel and bioconductor devel, both of which I
can load in a module.
The tool comes from the toolshed with xml like:
command interpreter=Rscript
…
I don't
/galaxytools
Cheers,
Bjoern
Am 25.04.2014 14:25, schrieb Ido Tamir:
Hi,
has anything changed in galaxy in this regard?
Any way to modify an environment before a tools is run?
I now have a tool relying on R-devel and bioconductor devel, both of which I
can load in a module.
The tool comes
point about the
environment file, I will modify the new env tags to allow a file
attribute and just source that file. This will give you your per
destination environment files - hopefully this is satisfactory.
That sounds great!
best,
ido
On Fri, Apr 25, 2014 at 8:22 AM, Ido Tamir ta
Hi,
my tool needs both a file with chromosome lengths and the total mappable genome
size.
I would like to hardcode the mappable genome size per build somewhere.
However the user should have to use only one drop down to select both. How can
I achieve this?
e.g. currently:
param name=FAI
In my case it was uncompleted metadata in one of the input files.
(but maybe it was not new state but something else?)
HTH,
ido
On Mar 26, 2014, at 5:25 PM, David Hoover hoove...@helix.nih.gov wrote:
I have many jobs stuck in the 'new' state on our local Galaxy instance. The
jobs can't be
I have CEAS as a tool. I wrapped the standalone CEAS version. I tried adding a
binary datatype for the annotation db but even with the binary datatype upload
somehow did not work (IIRC galaxy tried to convert it to ascii).
I then put the database as a selectable parameter in a dropdown list,
This seems to happen often e.g.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix
a) are there general guidelines in the wiki on how to avoid these problems when
creating tools?
b) is there a way to check automatically if all input fields are correctly
escaped in
On Nov 5, 2013, at 6:28 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi Ido,
Thanks for the feedback. Replies below.
On Nov 5, 2013, at 9:54 AM, Ido Tamir wrote:
This seems to happen often e.g.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix
I'm
Yes this tar 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
tar xvfj atlas3.11.11.tar.bz2
shows no errors on OSX and creates one ATLAS folder.
best,
ido
On Sep 20, 2013, at 11:17 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi Ido and Carlos,
can you check if that tarball is working?
If I might chime in, I am a bit worried about all the automatic installation
going on in galaxy, and it seems that the trend is to enhance this.
A small R or python script calling into well known libraries that come from
well known repositories (bioconductor etc… ) I can check.
(Of course I
IIRC then you can change the order of tools manually by copying around the
individual tools in shed_tool_conf.xml
In my case it builds the integrated_tool_panel.xml in reverse order within the
section.
I still have labels between the section defined in the tool_conf.xml.
But no subsections.
Why the dislike for quick turnover? Could somebody present the arguments for
people not having been at the BOF?
People don't have to upgrade - unless its breaking changes that e.g. disable
the possibility to download from the public toolshed which forced me to upgrade.
The alternative to
On Jul 31, 2013, at 8:52 AM, shenwiyn shenw...@gmail.com wrote:
Hi Thon Deboer ,
I am a newer in Galaxy.I installed my Galaxy with Torque2.5.0 ,and Galaxy
uses the pbs_modoule to interface with TORQUE.But I have some question of the
job_conf.xml :
1.)In your job_conf.xml ,you use
Hi,
what is the relationship between workers defined in universe and job_conf.xml?
e.g.:
[server:handler0]
use = egg:Paste#http
port = 9092
host = 127.0.0.1
use_threadpool = true
threadpool_workers = 5
plugins workers=4
!-- workers is the number of threads for the runner's work queue.
to do with job running.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Jul 24, 2013 at 11:02 AM, Ido Tamir ta...@imp.ac.at wrote:
Hi,
what is the relationship between workers defined in universe and
job_conf.xml? e.g.:
[server:handler0]
use = egg:Paste
Hi,
I work myself through the job_conf.xml and have a question:
a)
In your advanced example you have:
destination id=remote_cluster runner=drmaa tags=longjobs/
destination id=real_user_cluster runner=drmaa
!-- TODO: The real user options should maybe not be considered
runner
Hi,
I grabbed some xml files from Hannons website for his fastx toolkit (improved
over galaxys default version).
Then I created a repository, uploaded the xml files,
but the toolshed complains that it could not find the tools for
creating metadata in the xml files.
Could somebody please tell me
you post, and I think we are having the similar issue as your.
(I posted it in the mailing yesterday, you can find it for the detail of my
problem).
I am wondering if you are able to fix your problem?
Cheers,
Derrick
On Tue, Dec 11, 2012 at 12:13 AM, Ido Tamir ta...@imp.ac.at wrote
Is it possible to backport this onto the latest distribution?
Yes, I'm lazy, but there are also others that are still updating
within the next weeks and will have problems without them being
aware of this fix.
best,
ido
On Jan 21, 2013, at 9:50 PM, Nate Coraor wrote:
Hi all,
The commit[1]
Its hashed (sha1) and you can not reverse the hash. Storing passwords in a
reversible manner is bad practice.
http://galaxy-central.readthedocs.org/en/latest/_modules/galaxy/util/hash_util.html
You could maybe authenticate your users from the other program with the same
method against the
If you did what the links posted previously suggested (inc. parallelization of
tools, mutliple server processes),
there is nothing more you can do.
Most of the tools galaxy just calls, so its the tool that you have to change.
Often genomic tools are also IO bound, so a faster storage system
file type basis. If this is the problem and the galaxy team
agrees to accept a patch for address the issue, I would be happy to
try to implement the fix.
-John
On Fri, Dec 7, 2012 at 8:39 AM, Ido Tamir ta...@imp.ac.at wrote:
from http://wiki.galaxyproject.org/Admin/Datatypes/Adding
Hi,
how do I get tools from one local toolshed (or the main galaxy toolshed)
into another tool-shed? Is it possible to clone the content of a complete
tool-shed - all repositories
at once into another tool-shed?
Can I then import all the tools at once into a local galaxy instance?
We have a
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