Re: [galaxy-dev] Current history via the REST API (or blend4j)

2016-05-24 Thread Suderman Keith
> On May 23, 2016, at 3:34 PM, Carl Eberhard wrote: > > There's a way to get the current history data through a non-api url: > /history/current_history_json That works, but to get the current history for a user I need to set the galaxysession cookie. So it is not

Re: [galaxy-dev] It 's possible to purge deleted datasets with last galaxy code ?

2016-05-24 Thread Yvan Le Bras
Hi Sarah, Did you activate the "allow_user_dataset_purge" function on the galaxy.ini ? allow_user_dataset_purge = True Cheers, Yvan - Mail original - > De: "Sarah Maman" > À: galaxy-dev@lists.galaxyproject.org > Envoyé: Lundi 23 Mai 2016 18:57:22 >

Re: [galaxy-dev] tabular file displayed without tabs

2016-05-24 Thread Yvan Le Bras
Hi Ryan, I have seen the same strange behavior with some tabular files. My findings were to display these tabular datasets through the scratchbook Just a "bidouille" ;) Maybe this will work for you too Cheers, Yvan - Mail original - > De: "Ryan G"

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Peter Cock
On Tue, May 24, 2016 at 11:42 AM, Raymond Wan wrote: > Hi Peter, > > > On Tue, May 24, 2016 at 6:29 PM, Peter Cock wrote: >> In case you didn't know, Galaxy likes to keep all BAM files in >> coordinate sorted order with a BAI index (using

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Raymond Wan
Hi Peter, On Tue, May 24, 2016 at 6:29 PM, Peter Cock wrote: > In case you didn't know, Galaxy likes to keep all BAM files in > coordinate sorted order with a BAI index (using samtools). > Somehow this is failing on your system (perhaps a suitable > version of

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Peter Briggs
Hello Ray Just to clarify, for us it wasn't dependent on the tool - it was actually the version of samtools installed in the 'galaxy' user's environment i.e. on the 'galaxy' user's PATH. I set it explicitly by creating a file called "local_env.sh" in the 'config' directory of the Galaxy

[galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Raymond Wan
Dear all, We are experiencing a crash of our Galaxy instance (latest git log is early January 2016) and it seems unable to restart. The last entries in paster.log says the following: galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,593 Enabling 'histories' API controller, class:

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Peter Cock
Hi Raymond, In case you didn't know, Galaxy likes to keep all BAM files in coordinate sorted order with a BAI index (using samtools). Somehow this is failing on your system (perhaps a suitable version of samtools is not on the $PATH). I'm sure a Galaxy expert can and will comment, but it looks

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Raymond Wan
Hi Peter, On Tue, May 24, 2016 at 6:29 PM, Peter Briggs wrote: > One of my colleagues encountered a similar-sounding error on our local test > instance, where an unsorted BAM file seemed to crash the Galaxy handler > processes and prevented them from restarting. >

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Peter Briggs
Hello Ray One of my colleagues encountered a similar-sounding error on our local test instance, where an unsorted BAM file seemed to crash the Galaxy handler processes and prevented them from restarting. In our case the default samtools version in the Galaxy environment was 0.1.18; we found

Re: [galaxy-dev] Unsorted BAM file --> Galaxy crash?

2016-05-24 Thread Christian Brenninkmeijer
To follow up on what Peter says It is the code in https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/datatypes/binary.py from line 182 class Bam( Binary ): This code (set_meta) is called after the tool has finished running while it is copying the resulting data into the galaxy

[galaxy-dev] wheels.galaxyproject.org

2016-05-24 Thread Patrice Dehais
Hello Since yesterday I've the following warning at Galaxy () start-up : Retrying (Retry(total=4, connect=None, read=None, redirect=None)) after connection broken by 'ConnectTimeoutError(object at 0x3149390>, 'Connection to wheels.galaxyproject.org timed out. (connect timeout=15)')':

Re: [galaxy-dev] wheels.galaxyproject.org

2016-05-24 Thread Nicola Soranzo
It's a general problem: https://github.com/galaxyproject/galaxy/issues/2399 Cheers, Nicola On 24/05/16 16:10, Patrice Dehais wrote: Hello Since yesterday I've the following warning at Galaxy () start-up : Retrying (Retry(total=4, connect=None, read=None, redirect=None)) after connection

Re: [galaxy-dev] not sure what I can do about this...

2016-05-24 Thread Peter Cock
Hi Fernandez, We saw something very like that with mixed versions of Linux, specifically our Galaxy head node where pysam was installed had CentOS 7, but the node where Galaxy was trying to run the metadata detection was CentOS 6. Unfortunately I do not have a record of the exact traceback - but

Re: [galaxy-dev] not sure what I can do about this...

2016-05-24 Thread Fernandez Edgar
Hello guys, I’m still stuck on this error. I’ve installed a brand new galaxy v16.01 And when I start it, I get the big error mentioned below. Here’s the last message in the error: ImportError: /home/galaxy/galaxy-v16.01/.venv/lib/python2.7/site-packages/pysam/libchtslib.so: undefined symbol:

Re: [galaxy-dev] not sure what I can do about this...

2016-05-24 Thread Fernandez Edgar
Hello Peter, What would your suggestion be? Wait until a new version of galaxy is compatible with my Oracle Linux 6 ? Best regards, Edgar Fernandez System Administrator (Linux) Direction Générale des Technologies de l'Information et de la Communication Université de Montréal PAVILLON

Re: [galaxy-dev] Current history via the REST API (or blend4j)

2016-05-24 Thread Carl Eberhard
most_recently_used *was* broken - thanks for finding that. A pull request going back to the 16.01 release is here: https://github.com/galaxyproject/galaxy/pull/2407 A planning issue for a session API is here: https://github.com/galaxyproject/galaxy/issues/2404 On Tue, May 24, 2016 at 4:16 PM,

Re: [galaxy-dev] tabular file displayed without tabs

2016-05-24 Thread Carl Eberhard
Ok - if it's not zebra striped and it's word wrapping, then it's somehow not displaying as tabular - you're correct. If you click on the 'View details' button of that dataset (the 'i' with the circle around it shown when the dataset is expanded in the right hand side of the 'Analyze Data' page),

Re: [galaxy-dev] not sure what I can do about this...

2016-05-24 Thread Peter Cock
Hi Edgar, Are your Galaxy server AND your cluster are all running Oracle Linux 6? If yes, my guess about the cluster using an older version of Linux compared to the Galaxy server is unrelated. Peter On Tue, May 24, 2016 at 7:47 PM, Fernandez Edgar wrote: > Hello

Re: [galaxy-dev] Current history via the REST API (or blend4j)

2016-05-24 Thread Carl Eberhard
Yeah - I understand what you're trying to do now and you're right. In an effort to make the API stateless I think we've introduced a gap in functionality for a good, practical use case. I've been wanting to replace the history/current_history* endpoints for a while now with a session API (that