Re: [galaxy-dev] Bam upload fails: samtools not found
Peter, After restart of galaxy, the problems was resolved. I've had a similar issue before, where environment settings were not detected after a prolonged uptime of Galaxy. That issue was also resolved after restart. Anyway, problem is fixed for now. thanks for the answers. Geert On 05/05/2014 07:28 PM, Peter Cock wrote: Sorry - that has gone off list, can we continue this on the mailing list please? On Mon, May 5, 2014 at 6:27 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Mon, May 5, 2014 at 6:22 PM, Geert Vandeweyer geert.vandewey...@uantwerpen.be wrote: yes, it's on the galaxy users path. I log in using BASH as the shell. path is loaded using .profile in case that matters. geert Does the upload job run on the main Galaxy server, or your cluster? If on the cluster, you will need to check the path settings for jobs - which may not include those .profile settings. Peter -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandewe...@ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Get the user credentials from the tool.
Hello John,
If it is at all possible to send the data to the web service instead ...
Unfortunately, I cannot push the data to the web service, because this
is the BES one and the interface is defined in the spec.
As far as I understand reading the mailing list there is no way to pull
data through FTP (only upload).
The API key looks interesting even I do not completely understand it.
Is it possible to manipulate the key(s) programmatically?
It would be great to generate a temporal key, execute the service and
remove the key after that.
In general I would discourage this because it is difficult to do in a generic
way ...
I understand that the problem is when Galaxy is behind a proxy. In my
case I control the URL for the galaxy.
${ __app__.model.User.get( $__user_id__ ).api_keys[0].key }
I absolutely lost here...
should I know $__user_id__ or this is a variable already known to the tool?
Thank you very much for the help,
Dmitry
On 5/6/2014 4:39 AM, John Chilton wrote:
Hello Dmitry,
This use case isn't really addressed by Galaxy currently.
There is not a generic way of doing grabbing the users credentials
like this or producing URLs from inside the tool. This depends on a
lot of different things - how Galaxy's proxy is configured, etc... so
in many (all?) cases Galaxy would not be able to fetch the users raw
credentials. Your best bet is going to be to use the Galaxy's API -
tools can fetch a user's API key and you can use Galaxy's API to build
a URL that includes this key.
Your users will all need API keys set to use the tool. There have been
some other galaxy-dev discussions about using the API from tools -
http://osdir.com/ml/galaxy-development-source-control/2013-12/msg00105.html.
In general I would discourage this because it is difficult to do in a
generic way - for instance there is no way for the tool to accurately
determine what the URL of Galaxy should be - but it should be possible
to tailor something to your setup if absolutely needed.
If you are really keen to use the Galaxy API to do this and you
understand the limitations - we can try to work through the exact
details.
If it is at all possible to send the data to the web service instead
of sending a reference - the genomespace exporter
(https://bitbucket.org/galaxy/galaxy-central/src/74b6e23ed7882f3c091d2b66ce85025241372017/tools/genomespace/genomespace_exporter.xml?at=default)
might be a good example of how to do this in a more generic fashion.
-John
On Tue, Apr 29, 2014 at 11:16 AM, Dmitry redmi...@list.ru wrote:
Hello,
Is there any way to provide a protected resource link to the external
application?
My tool is supposed to call a Web service via SSL which should access to the
Galaxy resources.
In ideal it would be something like
ftp://user:passw...@mygalaxy.net/fasta.gz
The Web service then downloads the resource and do the computation.
Since user is already provided the login to galaxy, I do not want to ask the
password again on a tool page.
Sincerely,
Dmitry
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[galaxy-dev] drmaa
Hi all, I've configured galaxy with the drama python module. This is really more of a drama question... We have no default queue set in moab and I can't seem to find a way to specify a queue in the docs I've been looking at here - http://drmaa-python.readthedocs.org/en/latest/tutorials.html I'd like to be able to specify a queue based on various pieces of logic in my destinations.py script. Any suggestions would be appreciated. Donny FSU Research Computing Center ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] drmaa
Hi Donny, You should be able to specify the queue using the nativeSpecification field of drmaa requests, e.g. in your job_conf.xml: destination id=batch runner=pbs_drmaa param id=nativeSpecification-q batch/param /destination Documentation on job_conf.xml's syntax by runner can be found here: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster --nate On Tue, May 6, 2014 at 5:53 PM, Shrum, Donald C dcsh...@admin.fsu.eduwrote: Hi all, I've configured galaxy with the drama python module. This is really more of a drama question... We have no default queue set in moab and I can't seem to find a way to specify a queue in the docs I've been looking at here - http://drmaa-python.readthedocs.org/en/latest/tutorials.html I'd like to be able to specify a queue based on various pieces of logic in my destinations.py script. Any suggestions would be appreciated. Donny FSU Research Computing Center ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
