[galaxy-dev] Upload fails, webapp and job runner running on different machines

2011-03-23 Thread Louise-Amélie Schmitt
Hi everyone, I'm currently trying a new galaxy install with the webapp and the job runner running on different machines, sharing a nfs volume where the galaxy files are, and another one where the data is supposed to be stored, as specified in the file_path and new_file_path values in the

[galaxy-dev] new_file_path vs $TMP

2011-03-29 Thread Louise-Amélie Schmitt
Hello We managed to install Galaxy according to the unified method, with the runner and the web application running on separate machines sharing by NFS the same storage space where the Galaxy files are. The thing is, the data must be saved in another NFS storage space so we had to define the

[galaxy-dev] PostgreSQL issue: reserved keyword used as identifier

2011-04-08 Thread Louise-Amélie Schmitt
Hello everyone I just met a huge problem concerning the database. I'm currently trying to transfer my data from MySQL to PostgreSQL by writing a Perl script that would do the job. Here is the issue: In the form_definition table, one of the field identifiers is desc, which is a reserved SQL

Re: [galaxy-dev] PostgreSQL issue: reserved keyword used as identifier

2011-04-08 Thread Louise-Amélie Schmitt
Le vendredi 08 avril 2011 à 11:12 -0400, Sean Davis a écrit : 2011/4/8 Louise-Amélie Schmitt louise-amelie.schm...@embl.de: Hello everyone I just met a huge problem concerning the database. I'm currently trying to transfer my data from MySQL to PostgreSQL by writing a Perl script

Re: [galaxy-dev] PostgreSQL issue: reserved keyword used as identifier

2011-04-09 Thread Louise-Amélie Schmitt
On Fri, 8 Apr 2011 16:33:58 -0400, Kanwei Li kan...@gmail.com wrote: Hi Louise, Have you considered doing a SQL dump and import? Sounds easier to me than writing a perl script ;) -K Oh yes I did... Yeah, that solution sounded so sweet that is was the first thing I tried. But don't be

Re: [galaxy-dev] PostgreSQL issue: reserved keyword used as identifier

2011-04-09 Thread Louise-Amélie Schmitt
On Fri, 8 Apr 2011 19:02:23 -0400, Brad Chapman chapm...@50mail.com wrote: Louise-Amélie; I just met a huge problem concerning the database. I'm currently trying to transfer my data from MySQL to PostgreSQL by writing a Perl script that would do the job. I've used this ruby

[galaxy-dev] MySQL to PostgreSQL migration scripts available here

2011-04-11 Thread Louise-Amélie Schmitt
Hello everyone I finally managed to finish my two scripts. It's kind of dirty coded (I'm not a Perl fan + I was in a hurry), but at least they worked for me. I could successfully transfer the data from an old MySQL Galaxy to my new PSQL Galaxy. Before running the scripts, you should already have

Re: [galaxy-dev] Error when adding datasets

2011-04-14 Thread Louise-Amélie Schmitt
Von Kuster Cheers, L-A On Apr 14, 2011, at 5:38 AM, Louise-Amélie Schmitt wrote: Hello everyone I have an issue when trying to import new datasets or when putting a dataset into a history. I saw Edward Kirton had the same problem but he got no answer: http://lists.bx.psu.edu

Re: [galaxy-dev] Error when adding datasets

2011-04-14 Thread Louise-Amélie Schmitt
12:06:55 -0400, Greg Von Kuster g...@bx.psu.edu wrote: On Apr 14, 2011, at 11:49 AM, Louise-Amélie Schmitt wrote: Here is the result I got from the debug statements: galaxy.web.controllers.library_common DEBUG 2011-04-14 17:46:02,286 ### history: None This is the problem - when you

Re: [galaxy-dev] Error when adding datasets

2011-04-15 Thread Louise-Amélie Schmitt
the same error message with supposedly nonexistent histories. Thanks again L-A Le vendredi 15 avril 2011 à 13:47 +0200, Hans-Rudolf Hotz a écrit : On 04/15/2011 10:56 AM, Louise-Amélie Schmitt wrote: Hi Hans, thanks for your reply. - is your PostgreSQL database in sync with the database

Re: [galaxy-dev] Error when adding datasets

2011-04-18 Thread Louise-Amélie Schmitt
, Louise-Amélie Schmitt a écrit : Ooops, this is very right, I totally forgot about that. It woud have become problematic at some point I guess. Thank you for pointing this out! I changed it so the new database is associated with brand new appropriate directories. (and dropped and re-created

Re: [galaxy-dev] user and dataset management with LDAP: some questions

2011-04-26 Thread Louise-Amélie Schmitt
in advance for your help Regards, L-A Le mardi 12 avril 2011 à 16:41 +0200, Louise-Amélie Schmitt a écrit : Hello everyone I have a couple of questions regarding user and dataset management. 1) We use LDAP for user registration and logging, would it be possible to retrieve automatically

Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA

2011-05-19 Thread Louise-Amélie Schmitt
Hi, In a previous message, I explained how I did to multithreads certain jobs, perhaps you can modify the corresponding files for drmaa in a similar way: On 04/26/2011 11:26 AM, Louise-Amélie Schmitt wrote: Just one little fix on line 261: 261 if ( len(l) 1 and l[0

Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA

2011-05-19 Thread Louise-Amélie Schmitt
the same thing so jobs don't crash when resources requested are more than available? regards, Leandro 2011/5/19 Louise-Amélie Schmitt louise-amelie.schm...@embl.de mailto:louise-amelie.schm...@embl.de Hi, In a previous message, I explained how I did to multithreads certain jobs

Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA

2011-05-19 Thread Louise-Amélie Schmitt
Louise-Amélie Schmitt louise-amelie.schm...@embl.de mailto:louise-amelie.schm...@embl.de Hi again Leandro Well I might not have been really clear, perhaps I should have re-read the mail before posting it :) The thing is, it was not an issue of Torque starting jobs when

[galaxy-dev] Tools: dynamic check of file type?

2011-05-20 Thread Louise-Amélie Schmitt
Hello Is there a way to check the file type with a conditional tag set within a tool? For example, if the tool can accept several file types but I have to make cheetah shut off some stuff for a couple of them? Regards, L-A ___ Please

Re: [galaxy-dev] Tools: dynamic check of file type?

2011-05-20 Thread Louise-Amélie Schmitt
It's exactly what I needed!!! Thanks a lot! L-A Le 20/05/2011 12:29, Peter Cock a écrit : 2011/5/20 Louise-Amélie Schmittlouise-amelie.schm...@embl.de: Hello Is there a way to check the file type with a conditional tag set within a tool? For example, if the tool can accept several file

Re: [galaxy-dev] Tools: dynamic check of file type?

2011-05-20 Thread Louise-Amélie Schmitt
Well I'm still missing something... Is there a way to use the conditional tag sets in the tool's xml with it? To suppress the unnecessary options for a given file type? or more than one? regards, L-A Le 20/05/2011 13:15, Louise-Amélie Schmitt a écrit : It's exactly what I needed

Re: [galaxy-dev] Tools: dynamic check of file type?

2011-05-20 Thread Louise-Amélie Schmitt
That's exactly what I meant. I've been searching for a way to achieve this otherwise but I didn't find any idea. Does anyone have one? L-A Le 20/05/2011 15:49, Peter Cock a écrit : 2011/5/20 Louise-Amélie Schmittlouise-amelie.schm...@embl.de: Well I'm still missing something... Is there

Re: [galaxy-dev] Uploading Binary Files into Galaxy

2011-05-24 Thread Louise-Amélie Schmitt
Hi, Have you tried grep'ing the error message in the lib files to see where Galaxy goes to during the upload of these files? like: grep /The uploaded binary file contains inappropriate content/ `find *` I had a similar problem when I modified Galaxy to manage .gz files without uncompressing

Re: [galaxy-dev] Checkboxes/booleans in tools, again

2011-05-24 Thread Louise-Amélie Schmitt
on the list, please create a brand new email to galaxy-dev rather than replying to an existing message. Replying includes headers that reference the message you replied to, which means it threads with the original thread in mail readers and the list archive. Thanks, --nate Louise-Amélie Schmitt wrote

[galaxy-dev] Workflows and unknown number of output datasets

2011-05-27 Thread Louise-Amélie Schmitt
Hi everyone First let me thank all the Team Galaxy, the conference was really great. Kanwei asked me to send the tool I told him about. It's one of these tools for which you can't know the exact number of output datasets before tool run. Here are the files. It's really simple actually, but it

Re: [galaxy-dev] Error when adding datasets

2011-06-02 Thread Louise-Amélie Schmitt
can help as well. It is likely that LDAP is playing a role in this behavior. On Apr 14, 2011, at 1:00 PM, Louise-Amélie Schmitt wrote: The thing is, we use LDAP logging so we can't even access the website without logging in. Moreover, when I logged in, I arrived on the data analysis

Re: [galaxy-dev] Error when adding datasets

2011-06-03 Thread Louise-Amélie Schmitt
Le 02/06/2011 21:23, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: On Thu, 2 Jun 2011 11:48:55 -0400, Nate Coraorn...@bx.psu.edu wrote: Greg Von Kuster wrote: Hello Louise, I've CC'd Nate on this as he may be able to help - although no guarantees. I'm not expert enough in this area

[galaxy-dev] checkboxes bug fix

2011-06-06 Thread Louise-Amélie Schmitt
Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I deselected them, the value sent in the query remained as if they were still selected. Even when I re-ran the job, all the checkboxes were

[galaxy-dev] LDAP and API issue?

2011-06-17 Thread Louise-Amélie Schmitt
Hi everyone I'm currently trying to use the API, but I think that our LDAP logging doesn't really help. When I call the script specifying the port in the url, here's what I get: urlopen error [Errno 111] Connection refused Then when I don't specify it Here's what I get: HTTP Error 401:

Re: [galaxy-dev] LDAP and API issue?

2011-06-17 Thread Louise-Amélie Schmitt
) AuthType Basic AuthBasicProvider ldap AuthLDAPURL ldap://ocs.embl.org/cn=Users,dc=embl,dc=org?uid; AuthzLDAPAuthoritative off Satisfy any Allow from all /Location L-A Le 17/06/2011 14:14, Louise-Amélie Schmitt a écrit : Hi everyone I'm currently

Re: [galaxy-dev] LDAP and API issue?

2011-06-17 Thread Louise-Amélie Schmitt
Le 17/06/2011 16:50, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Ok, again sorry for being an idiot. I just had to modify the Apache .conf file related to Galaxy. For the time being I allowed everyone on the API (since it's not accessible via the Internet it's allright) so the all

[galaxy-dev] [API] Error message forwarding

2011-06-20 Thread Louise-Amélie Schmitt
Hi, I ran into a little something that is a bit annoying for debug when trying to upload files through the API with library_upload_from_import_dir.py. When the specified folder is wrong, python tries to process the error tuple like a dict, so the original error is hard to find. I modified

Re: [galaxy-dev] postgresql connection error: could not connect to server: No such file or directory...

2011-06-28 Thread Louise-Amélie Schmitt
Hi, Could you please show us the contents of your pg_hba.conf file? This is where you configure which machines can access the database through the network. Best, L-A Le 27/06/2011 20:33, Marco Moretto a écrit : Hi Gus, it seems that your postgres is not configured to accept connection

[galaxy-dev] [API] managing histories

2011-07-28 Thread Louise-Amélie Schmitt
Hello everyone, I'm currently trying to automate data loading and pre-processing through Galaxy's API, and I will need to delete and share histories at some point. I know the API is still very new but is there a way to do that by any chance? Thanks, L-A

[galaxy-dev] [API] Apache error?

2011-07-29 Thread Louise-Amélie Schmitt
Hello everyone, I'm working on a script that uploads files and launchs workflows on them, but I keep getting errors that appear more or less randomly when the display() and submit() functions are called. In a nutshell, there is a 1/3 chance the calls fail this way. Nevertheless, the actions

Re: [galaxy-dev] [API] Apache error?

2011-08-02 Thread Louise-Amélie Schmitt
, Louise-Amélie Schmitt a écrit : Hello everyone, I'm working on a script that uploads files and launchs workflows on them, but I keep getting errors that appear more or less randomly when the display() and submit() functions are called. In a nutshell, there is a 1/3 chance the calls fail this way

[galaxy-dev] [API] About workflow parameters :)

2011-08-05 Thread Louise-Amélie Schmitt
Hello, Just a quick message to ask if you had the time to work on passing parameters to workflows through the API. Just to know, since I'm using workflows with the API. Best, L-A ___ Please keep all replies on the list by using reply

Re: [galaxy-dev] [API] About workflow parameters :)

2011-08-09 Thread Louise-Amélie Schmitt
since you could put in all the details, or just write back and I can create a simple ticket. Thanks! Jen Galaxy team On 8/5/11 6:59 AM, Louise-Amélie Schmitt wrote: Hello, Just a quick message to ask if you had the time to work on passing parameters to workflows through the API. Just to know

Re: [galaxy-dev] checkboxes bug fix

2011-08-15 Thread Louise-Amélie Schmitt
# for your local install, that would also be helpful for us to know. Best, Jen Galaxy team On 6/6/11 2:15 AM, Louise-Amélie Schmitt wrote: Hi, Since I haven't updated Galaxy for a while now I don't know if it was actually fixed but I had issues with my default-selected checkboxes: When I

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-24 Thread Louise-Amélie Schmitt
Thanks a lot! I found another way to do it but it is awfully more complicated so I'll change as soon as I have some time. Best, L-A Le 23/08/2011 19:49, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hi, I would need to make a tool that can get the API dataset id out of the input

Re: [galaxy-dev] checkboxes bug fix

2011-08-25 Thread Louise-Amélie Schmitt
again (change true to false) since it didn't work anymore. Best, L-A Le 15/06/2011 09:56, Louise-Amélie Schmitt a écrit : Hi, and sorry for the late reply Here is the last pull: 5355:50e249442c5a I'll try to be as concise as I can but I can send you

[galaxy-dev] API keys and id encryption (silly questions)

2011-08-29 Thread Louise-Amélie Schmitt
Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind an URL? Or did I miss the point? Also, why encrypt the

Re: [galaxy-dev] API keys and id encryption (silly questions)

2011-08-29 Thread Louise-Amélie Schmitt
Le 29/08/2011 15:52, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead of user names? Is it to to prevent anyone from figuring out who is behind

Re: [galaxy-dev] API keys and id encryption (silly questions)

2011-08-30 Thread Louise-Amélie Schmitt
Le 29/08/2011 18:54, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Le 29/08/2011 15:52, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Hello everyone, These questions are a bit silly but I'm really ignorant when it comes to security. Sorry about that. Why use API keys instead

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-30 Thread Louise-Amélie Schmitt
I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? Le 24/08/2011 15:00, Louise-Amélie Schmitt a écrit : Thanks a lot! I found another way to do it but it is awfully more

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-30 Thread Louise-Amélie Schmitt
Le 30/08/2011 16:51, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What was the 'file.' originally for? On the API side, a library or history's contents

Re: [galaxy-dev] [API] Get the hashed dataset id within Galaxy

2011-08-30 Thread Louise-Amélie Schmitt
Le 30/08/2011 18:00, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: Le 30/08/2011 16:51, Nate Coraor a écrit : Louise-Amélie Schmitt wrote: I just changed it and ran into an error, so I modified the line and it now works fine: $__app__.security.encode_id( '%s' % $input1.id ) What

Re: [galaxy-dev] Local installation of the tool shed

2011-11-24 Thread Louise-Amélie Schmitt
Hello Greg We tried to run the toolshed like you explained (thanks a lot for the quick answer btw), it starts fine, but when we try to access it on the web, we get this error in the browser: Server Error An error occurred. See the error logs for more information. (Turn debug on to display

Re: [galaxy-dev] Local installation of the tool shed

2011-11-25 Thread Louise-Amélie Schmitt
, 2011, at 10:34 AM, Louise-Amélie Schmitt wrote: Hello Greg We tried to run the toolshed like you explained (thanks a lot for the quick answer btw), it starts fine, but when we try to access it on the web, we get this error in the browser: Server Error An error occurred. See the error logs

Re: [galaxy-dev] Local installation of the tool shed

2011-11-25 Thread Louise-Amélie Schmitt
,modencode_worm,modencode_fly,yeast_sgd # GeneTrack servers: tool-data/shared/genetrack/genetrack_sites.txt genetrack_display_sites = main,test On Nov 25, 2011, at 3:01 AM, Louise-Amélie Schmitt wrote: Hello Greg Please find attached the file you asked for. Just in case, I also sent you

[galaxy-dev] Web links not leading to appropriate location anymore.

2011-11-30 Thread Louise-Amélie Schmitt
Hello, We're experiencing a major issue in the web application and don't know where to look for a potential solution: Whichever link we click on it always brigs us back to the welcome page (galaxy/root). There are a few exceptions to that: - saved histories, saved datasets and api key in the

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

2011-11-30 Thread Louise-Amélie Schmitt
Thanks a lot Ross, it works fine now. Best, L-A Le 30/11/2011 11:34, Ross a écrit : Louise, I had the same problem. After hg revert -r 3ee9430186fb everything was back to normal for me. I hope this helps.. 2011/11/30 Louise-Amélie Schmitt louise-amelie.schm...@embl.de mailto:louise

Re: [galaxy-dev] Web links not leading to appropriate location anymore.

2011-11-30 Thread Louise-Amélie Schmitt
? require_login = True On Nov 30, 2011, at 5:34 AM, Ross wrote: Louise, I had the same problem. After hg revert -r 3ee9430186fb everything was back to normal for me. I hope this helps.. 2011/11/30 Louise-Amélie Schmitt louise-amelie.schm...@embl.de mailto:louise-amelie.schm...@embl.de Hello

[galaxy-dev] About database indexes

2011-12-06 Thread Louise-Amélie Schmitt
Hello, Since our local Galaxy is a little sluggish, we were wondering if it could be related to broken or missing database indexes (we're using PostgreSQL), so we would like to know how they are managed in Galaxy, and if there is a way to restore them automatically. Thanks, L-A

[galaxy-dev] Tool creation: how to restrict input dataset selector to appropriate file types?

2011-12-07 Thread Louise-Amélie Schmitt
Hello, I'm running in a strange issue which I cannot seem to find a solution for. In every tool I created from scratch, the input dataset selector does not only include the datasets corresponding to the file types I set in the format= attribute in the param tag in my XML tool file, but

Re: [galaxy-dev] Tool creation: how to restrict input dataset selector to appropriate file types?

2011-12-07 Thread Louise-Amélie Schmitt
: The only thing that sticks out to me is the 'export' format listed in inputs. What are the children datatypes of export, or how is that set up? The filter logic automatically includes all children datatypes of the specified formats. -Dannon On Dec 7, 2011, at 5:10 AM, Louise-Amélie Schmitt

[galaxy-dev] Switching TorquePBSpro: qsub error 111 (cannot connect to server)

2012-01-17 Thread Louise-Amélie Schmitt
Hello, We want to move Galaxy's jobs from our small TORQUE local install to a big cluster running PBS Pro. In the universe_wsgi.ini, I changed the cluster address as follows: default_cluster_job_runner = pbs:/// to: default_cluster_job_runner = pbs://sub-master/clng_new/ where sub-master is

[galaxy-dev] Error download composite dataset from history

2012-01-18 Thread Louise-Amélie Schmitt
Hello! I'm running into an error when trying to download a composite dataset from the history with the floppy disk icon. Here is the error message in the logs: galaxy.web.controllers.dataset ERROR 2012-01-18 16:32:10,324 Unable to remove temporary library download archive and directory

Re: [galaxy-dev] Error download composite dataset from history

2012-01-19 Thread Louise-Amélie Schmitt
Hi Ross Thanks a million, I hg-pull'ed it solved the problem!! Please push it to galaxy-dist? ;) I ran in another little bug though, but nothing serious, you might even have already spotted it by now: In lib/galaxy/web/framework/__init__.py the line 873 made the whole thing crash due to a

Re: [galaxy-dev] Error download composite dataset from history

2012-01-19 Thread Louise-Amélie Schmitt
Hi Ross, Yeah, it was probably a merging issue. I confess I didn't double-check in Bitbucket. *slaps hand* Actually hg behaved strangely this time, and didn't report all failed merges so I had to look for the conflicting files manually. Hopefully there will be no remaining error. Sorry

Re: [galaxy-dev] Switching TorquePBSpro: qsub error 111 (cannot connect to server)

2012-01-30 Thread Louise-Amélie Schmitt
: drmaa://[native_options]/ I'm a bit confused, I would have expected something like: drmaa://[machine]/[native_options]/ like for TORQUE. Did I miss something? Best, L-A Le 19/01/2012 19:43, Nate Coraor a écrit : On Jan 16, 2012, at 5:22 AM, Louise-Amélie Schmitt wrote: Hello, We want to move

Re: [galaxy-dev] Switching TorquePBSpro: qsub error 111 (cannot connect to server)

2012-01-30 Thread Louise-Amélie Schmitt
-A Le 30/01/2012 17:18, Nate Coraor a écrit : On Jan 30, 2012, at 7:37 AM, Louise-Amélie Schmitt wrote: Hi Nate, Thanks for the info! I'm trying to understand how the URL for DRMAA works but I don't understand how we can set it so it uses a different machine. Our Galaxy runner runs on machine

Re: [galaxy-dev] Switching TorquePBSpro: qsub error 111 (cannot connect to server)

2012-02-01 Thread Louise-Amélie Schmitt
: On Jan 30, 2012, at 12:07 PM, Louise-Amélie Schmitt wrote: Hi Nate, Thanks for the leads! But setting DRMAA_LIBRARY_PATH means I'm in trouble since the libraries are on machine B which is maintained by our IT dept. I cannot access them from machine A. Is it a desperate situation? Will it work if I

Re: [galaxy-dev] Syntax issue for adding new tool

2012-02-07 Thread Louise-Amélie Schmitt
Hello, I'm not sure this will fix the issue but you might have to use -p $param_file.params instead of -p $params in your command line. Best, L-A Le 06/02/2012 22:15, Jeffrey Long a écrit : Hi all, I am having trouble with what looked to me at first to be a simple syntactical issue with

Re: [galaxy-dev] Looking for recommendations: How to run galaxy workflows in batch

2012-02-07 Thread Louise-Amélie Schmitt
Hello Dannon Could it be possible to have the input dataset's display name appended to the new history's name instead of plain numbers when the Send results in a new history option is checked? This new feature is indeed very useful (thanks a million for it) but the numbered suffixes

Re: [galaxy-dev] Switching TorquePBSpro: qsub error 111 (cannot connect to server)

2012-02-17 Thread Louise-Amélie Schmitt
, but pbs_python links against libtorque, which is part of the torque client, which must be installed somewhere on the local system. Ok, thanks a lot! Best, L-A Best, L-A Le 30/01/2012 18:20, Nate Coraor a écrit : On Jan 30, 2012, at 12:07 PM, Louise-Amélie Schmitt wrote: Hi Nate, Thanks

Re: [galaxy-dev] Galaxy and Cluster options

2012-02-17 Thread Louise-Amélie Schmitt
Hi Tanguy, You can set that at the very bottom of your universe_wsgi.ini file. I did it myself with Torque to set a different behavior for a couple of tools, it works fine. The related Wiki page is here: http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster :) Best, L-A Le 17/02/2012

Re: [galaxy-dev] Switching TorquePBSpro: qsub error 111 (cannot connect to server)

2012-02-17 Thread Louise-Amélie Schmitt
are normally separate. For instance: http://pkgs.org/download/torque-drmaa If going from source, you can enable DRMAA compilation with --enable-drmaa; I don't recall if that is on by default (I don't think it is). chris On Feb 17, 2012, at 3:49 AM, Louise-Amélie Schmitt wrote: You don't

Re: [galaxy-dev] universe_wsgi.ini

2012-02-24 Thread Louise-Amélie Schmitt
Hello Daniel, I had similar issues when setting up our own. The POST size limit is not set by Galaxy. If I remember correctly it's in your Apache config, though I don't remember exactly where it was. For the .loc files, here is an example: dm3-btdm3D.melanogaster 3

Re: [galaxy-dev] universe_wsgi.ini

2012-02-27 Thread Louise-Amélie Schmitt
to save space and time? I really do appreciate the help -- thanks! Daniel *From:*galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Louise-Amélie Schmitt *Sent:* Friday, February 24, 2012 12:23 AM *To:* galaxy-dev@lists.bx.psu.edu *Subject:* Re: [galaxy

[galaxy-dev] NFS, Cluster and working directories questions

2012-02-28 Thread Louise-Amélie Schmitt
Hello, We're currently trying to switch to a big cluster but we have a lot of doubts and questions, especially since the I/O is a serious issue for our NFS. - We saw the outputs_to_working_directory option in the .ini file, but it only concerns output files, is there a way to make a local

[galaxy-dev] [API] allow_user_impersonation

2012-02-28 Thread Louise-Amélie Schmitt
Hello everyone! I just wanted to know if the user impersonation will be available through the API someday :) It could be veeery useful for triggering automatic QA on the data without having to share the resulting histories afterwards. Best regards, L-A

Re: [galaxy-dev] NFS, Cluster and working directories questions

2012-03-12 Thread Louise-Amélie Schmitt
Hi Nate, and thanks for the reply - We saw the outputs_to_working_directory option in the .ini file, but it only concerns output files, is there a way to make a local copy of all the input files in the job working directory? (including indices) Hi L-A, Unfortunately no. This option was only

[galaxy-dev] drmaa module does not load

2012-03-26 Thread Louise-Amélie Schmitt
Hello everyone, I wanted to start the drmaa job runner and followed the instructions in the wiki, but I have this error message when I start Galaxy: galaxy.jobs ERROR 2012-03-23 15:28:49,845 Job runner is not loadable: galaxy.jobs.runners. drmaa Traceback (most recent call last): File

Re: [galaxy-dev] drmaa module does not load

2012-03-27 Thread Louise-Amélie Schmitt
Le 26/03/2012 16:13, Nate Coraor a écrit : On Mar 26, 2012, at 5:11 AM, Louise-Amélie Schmitt wrote: Hello everyone, I wanted to start the drmaa job runner and followed the instructions in the wiki, but I have this error message when I start Galaxy: galaxy.jobs ERROR 2012-03-23 15:28:49,845

Re: [galaxy-dev] drmaa module does not load

2012-03-27 Thread Louise-Amélie Schmitt
Le 27/03/2012 11:03, Louise-Amélie Schmitt a écrit : Le 26/03/2012 16:13, Nate Coraor a écrit : On Mar 26, 2012, at 5:11 AM, Louise-Amélie Schmitt wrote: Hello everyone, I wanted to start the drmaa job runner and followed the instructions in the wiki, but I have this error message when I

[galaxy-dev] [request] drmaa way too chatty

2012-03-27 Thread Louise-Amélie Schmitt
Hi everyone, The drmaa runner literally floods the Galaxy output with its own output (dozens of lines every second) which makes the Galaxy log impossible to read. Would there be a way to separate the two of them? I tried to look into the code but I'm not fully sure about what exactly produces

Re: [galaxy-dev] add a tool to galaxy

2012-03-28 Thread Louise-Amélie Schmitt
Hi, Try: --no_overlap $singleOrPair.no_overlap Best, L-A Le 28/03/2012 18:59, cai cai a écrit : Hi All, I am trying to add a tool to Galaxy, here is my xml configuration: ## Set params based on whether reads are single-end or paired. #if $singleOrPair.readType ==

Re: [galaxy-dev] Error on local galaxy using SAM-to-BAM tool on a cluster

2012-04-12 Thread Louise-Amélie Schmitt
Hi, I'm having the same issue, has it been fixed since then? Thanks, L-A Le 07/11/2011 21:43, Nate Coraor a écrit : On Nov 4, 2011, at 1:11 PM, Carlos Borroto wrote: Hi, Reading a little more about this problem, I see Galaxy uses python tempfile library

[galaxy-dev] Just wanted to say...

2012-04-16 Thread Louise-Amélie Schmitt
I love the improvements you recently made to the web interface layout in galaxy-central, it's really neat! Collapsing the margins and making everything smoother makes the interface really easier to read. Thanks for the hard work, as always, L-A

[galaxy-dev] Tool syntax: How to get history name?

2012-04-18 Thread Louise-Amélie Schmitt
Hi everyone, I as wondering if there was a way to get the history name of an input dataset within a tool (i.e. in the cheetah between the command tags), is there? Thanks, L-A ___ Please keep all replies on the list by using reply all in

Re: [galaxy-dev] Tool syntax: How to get history name?

2012-04-18 Thread Louise-Amélie Schmitt
Ok, after a lot of testing and searching in the libs, I found the solution: $inputdataset.dataset.history.name Le 18/04/2012 10:22, Louise-Amélie Schmitt a écrit : Hi everyone, I as wondering if there was a way to get the history name of an input dataset within a tool (i.e. in the cheetah

[galaxy-dev] run job as real user error: environment variables issue?

2012-04-19 Thread Louise-Amélie Schmitt
Hi everyone, I'm currently trying to set up our local Galaxy so it can run jobs as the real user. I followed the documentation and set the galaxy user as a sudoer. However, I get an error message whenever I'm trying to run a job: galaxy.jobs.runners.drmaa ERROR 2012-04-19 14:57:48,376

Re: [galaxy-dev] run job as real user error: environment variables issue?

2012-04-20 Thread Louise-Amélie Schmitt
Mmm... for some reason LD_LIBRARY_PATH was ignored but it looks like it's working fine when I set the lib path in a .conf file in /etc/ld.so.conf.d/ Hopefully it'll not break again :) Best, L-A Le 19/04/2012 17:19, Louise-Amélie Schmitt a écrit : Hi everyone, I'm currently trying to set up

[galaxy-dev] Error: Job output not returned from cluster

2012-04-23 Thread Louise-Amélie Schmitt
Hello everyone, I'm still trying to set up the job submission as the real user, and I get a mysterious error. The job obviously runs somewhere and when it ends it is in error state and displays the following message: Job output not returned from cluster In the Galaxy log I have the

Re: [galaxy-dev] Error: Job output not returned from cluster

2012-04-24 Thread Louise-Amélie Schmitt
At first we thought it could be an ssh issue but submitting jobs and getting the output back isn't a problem when I do it from my personal user manually, so it's really related to Galaxy. We're using PBS Pro btw. And I'm still at loss... :( L-A Le 23/04/2012 15:42, zhengqiu cai a écrit : I

Re: [galaxy-dev] Error: Job output not returned from cluster

2012-04-25 Thread Louise-Amélie Schmitt
Hi, Thanks a lot it actually helped. It is not exactly as straightforward in drmaa.py but somehow I could manage. However, it was not the problem. For some reason, the user needs to write files from the node to job_working_directory/00X// and the latter is not world-writable. I had to

[galaxy-dev] Error running job as real user: looking et the wrong dir?

2012-04-25 Thread Louise-Amélie Schmitt
Hi everyone, I'm (still) having issues with running jobs as the real user on our PBS Pro cluster. When I try running a job, it ends up in error state and displays the following error message: touch: cannot touch `/home/galaxy/.drmaa/9167860.pbs-master2.embl.de.started': Permission denied

[galaxy-dev] Running jobs as real user and extra_file_path

2012-04-25 Thread Louise-Amélie Schmitt
Hi everyone, I just wanted to ask how the extra_file_path is handled in case of job running as the real user since the file_path is only writable by the galaxy user. Any clue? Thanks, L-A ___ Please keep all replies on the list by using