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 wrote:
> I'v run into this sam
, Ido Tamir wrote:
> 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:
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 program
Its better to post usage questions at https://biostar.usegalaxy.org/
best,
ido
On Apr 28, 2014, at 2:50 PM, Jess Gaunt wrote:
> I hope this is the correct place to submit this problem. I'm using Galaxy
> main and there appears to be an error in the calculation of the disk space
> I'm using.
make a good point about the
> environment file, I will modify the new 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
>
>
> O
+ R libraries and use only
> that specific version from your tool with tags.
>
> For an example please see various R tools from:
>
> https://github.com/bgruening/galaxytools
>
> Cheers,
> Bjoern
>
> Am 25.04.2014 14:25, schrieb Ido Tamir:
>> Hi,
>> h
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:
…
I don't want to hack around in the t
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:
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 wrote:
> I have many jobs stuck in the 'new' state on our local Galaxy instance. The
> jobs can't be stopped using the Ad
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, beca
Hi,
I have to move my galaxy instance to a different file system location.
Is there anything that I have to look out for besides the obvious like absolute
paths in some data configs?
thank you very much,
ido
___
Please keep all replies o
On Nov 5, 2013, at 6:28 PM, Nate Coraor 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_
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
Hi,
my users start to take comparability serious and start to downsample.
But it seems like the random_lines_two_pass.py tool is very slow with large
input files, like bed files with 40million reads to e.g. 33million reads
https://bitbucket.org/galaxy/galaxy-dist/src/2469c53051ea/tools/filters/ra
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 wrote:
> Hi Ido and Carlos,
>
> can you check if that tarball is working?
>
> http://downloads.sourceforge.net/project/math-atlas/Developer%20%28unstable%
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 wrote:
> Hi Carlos,
>
>>> Hi Peter and Carlos,
>>>
On Mon, Sep 16, 2013 at 8:57 PM, Carlos Borroto
wrot
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 insta
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.
bes
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 freque
Hi,
we would like to coordinate with another institution and their galaxy setup
regarding tools installed from multiple toolsheds (and their position/group in
the panel) should be similar.
Is there a way to achieve that with scripting?
Suppose I would start the galaxy install from scratch also
On Jul 31, 2013, at 8:52 AM, shenwiyn 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 regularjobs,longjobs
th job running.
>
> --
> James Taylor, Assistant Professor, Biology/CS, Emory University
>
>
> On Wed, Jul 24, 2013 at 11:02 AM, Ido Tamir wrote:
>> Hi,
>>
>> what is the relationship between workers defined in universe and
>> job_conf.xml? e.g.:
>>
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
a) do I have to specify the sum of the workers in job_conf.xml
Hi,
I work myself through the job_conf.xml and have a question:
a)
In your advanced example you have:
scripts/drmaa_external_runner.py
scripts/drmaa_external_killer.py
scripts/external_chown_script.py
Does this mean that remote_cluster jobs c
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
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
ust found 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 Tu
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 hashe
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 could
Dear galaxy maintainers,
we have the problem that killing jobs running on drmaa before they run leading
to a deleted_new state,
kills our handlers (sometimes?). The job gets sent to the handler, but the
handler never acknowledges the jobs (local and drmaa) and
all submitted jobs afterwards stay
ould like to be able to disable
> on a per 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 wrote:
>>
&g
Hi,
I am trying to create a sqlite datatype. But whenever I upload the database its
corrupted.
With the latest galaxy-dist checkout
changeset: 8153:5dcbbdfe1087
tag: tip
user:Daniel Blankenberg
date:Tue Nov 06 12:57:23 2012 -0500
summary: Allow rerun to access hidde
e = util.parse_xml( repository_xml_file )
root = tree.getroot()
tool_shed_url = root.get( 'url' )
for repository_elem in root:
repository_name = repository_elem.get( 'name' )
repository_description = repository_elem.get( 'description' )
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 group
> Hi all,
>
> How can I speed up the galaxy? Like how to use more cores and memeries.
http://wiki.galaxyproject.org/Admin/Config/Performance/Production%20Server
http://wiki.galaxyproject.org/Admin/Config/Performance/Web%20Application%20Scaling
HTH,
ido
__
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