[galaxy-dev] Backup strategy

2011-08-31 Thread Oleksandr Moskalenko
Hello, Considering the fact that a galaxy instance can grow to be quite large I wonder what Galaxy backup strategies and implementations other people actually have in use and are happy with. Thanks, Alex ___ Please keep all replies on

Re: [galaxy-dev] passing environment to pbs runner

2011-09-14 Thread Oleksandr Moskalenko
Providing the correct environment using the .bashrc for the user that the pbs jobs are submitted under works for me. Many thanks to Glen Beane! Cheers, Alex On Sep 14, 2011, at 9:03 AM, Nate Coraor wrote: Glen Beane wrote: On Sep 13, 2011, at 6:01 PM, Oleksandr Moskalenko o

Re: [galaxy-dev] Rpy-1.0.3 and R-2.13.1

2011-09-22 Thread Oleksandr Moskalenko
On Sep 22, 2011, at 1:56 PM, Assaf Gordon wrote: Hello, It seems this issue (rpy) pops up every now and then: Has anyone managed to get rpy-1.0.3 working properly with R-13.1 (including loading packages) ? I already replied to Assaf, so this is a list copy. Yes, this combination works.

Re: [galaxy-dev] Rpy-1.0.3 and R-2.13.1

2011-09-22 Thread Oleksandr Moskalenko
'), 'src', '/usr/share/R/include', '/apps/R/2.13.1/include' ] * Build rpy with python setup.py install On Sep 22, 2011, at 3:38 PM, Oleksandr Moskalenko wrote: On Sep 22, 2011, at 1:56 PM, Assaf Gordon wrote: Hello, It seems this issue (rpy) pops up every

[galaxy-dev] bug report submission bug

2011-10-03 Thread Oleksandr Moskalenko
Someone shared a history with me for the purpose of debugging their Galaxy problem in our local Galaxy instance. I set the error_email_to to our bug reporting email address, but I can't submit a bug report using the bug icon in the history for datasets in an error state. The traceback is below.

Re: [galaxy-dev] bug report submission bug

2011-10-06 Thread Oleksandr Moskalenko
Got another problem with the bug reporting tool: POST /dataset/report_error HTTP/1.1 500 - http://galaxy.hpc.ufl.edu/dataset/errors?id=775; Mozilla/5.0 (compatible; MSIE 9.0; Windows NT 6.1; Trident/5.0)Error - type 'exceptions.UnboundLocalError': local variable 'dataset_id' referenced before

[galaxy-dev] Garli and Tandem Repeats Finder wrappers

2011-10-27 Thread Oleksandr Moskalenko
I would like to avoid reinventing the wheel if possible, so I wonder if anyone has wrappers for Garli (https://www.nescent.org/wg_garli/Main_Page) and Tandem Repeats Finder (http://tandem.bu.edu/trf/trf.html) they could share. Thanks,

[galaxy-dev] Wrong smtplib exception

2011-11-09 Thread Oleksandr Moskalenko
I have a diff for a bug that's been present in at least the last two releases of galaxy-dist when python 2.6(.5) is used, which doesn't have SMTPError in smtplib: --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -607,7 +607,7 @@ def send_mail( frm, to, subject, body,

Re: [galaxy-dev] rgenetics galaxy

2011-11-25 Thread Oleksandr Moskalenko
On Nov 25, 2011, at 6:52 AM, Ivan Merelli wrote: Hi, I'm trying to use rgenetics in galaxy, but I have some problem in installting rpy-1.0.3 with R-2.13.1. I found this guide, which is about the same problem of mine: http://gmod.827538.n3.nabble.com/Rpy-1-0-3-and-R-2-13-1-td3359590.html

[galaxy-dev] Job runner out of memory problem

2011-12-14 Thread Oleksandr Moskalenko
It seems that even under very light i.e. just a couple of long-running jobs present load the job runner slowly, but steadily (1-3Mb per sec) grows its memory consumption until it's killed by linux OOM killer. My job runner config: http://pastebin.com/vMWDHAQm I'm currently restarting the

[galaxy-dev] 01/27 galaxy-dist startup problem (toolshed/pgsql related)

2012-02-07 Thread Oleksandr Moskalenko
I've upgraded my developmental Galaxy instance to the latest galaxy-dist release with a transplanted the drmaa.py patch from galaxy-central. All .conf files have been updated. However, I can't start the instance now The error listed below is generated. I tried enabling/disabling the toolshed

Re: [galaxy-dev] 01/27 galaxy-dist startup problem (toolshed/pgsql related)

2012-02-07 Thread Oleksandr Moskalenko
your database was migrated from version 85 to 90? Thanks, Greg On Feb 7, 2012, at 3:32 PM, Oleksandr Moskalenko wrote: I've upgraded my developmental Galaxy instance to the latest galaxy-dist release with a transplanted the drmaa.py patch from galaxy-central. All .conf files have been

Re: [galaxy-dev] 01/27 galaxy-dist startup problem (toolshed/pgsql related)

2012-02-07 Thread Oleksandr Moskalenko
INFO 2012-02-07 15:58:56,273 At database version 91 On Feb 7, 2012, at 3:55 PM, Oleksandr Moskalenko wrote: $ sh manage_db.sh -c ./dev_universe_wsgi.runner.ini upgrade 85 - 86... Migration script to add the metadata, update_available and includes_datatypes columns

Re: [galaxy-dev] Garli and Tandem Repeats Finder wrappers

2012-02-08 Thread Oleksandr Moskalenko
On Feb 8, 2012, at 10:07 AM, Jennifer Jackson wrote: Hello Alex, Both of these tools are in the Tool Shed. An easy way to locate these (and to search for tools/wrappers related to Galaxy in general) is: http://galaxy.psu.edu/search/getgalaxy/ More about the Tool shed:

[galaxy-dev] Trackster traceback on C. Cerevisiae mapped data

2012-03-01 Thread Oleksandr Moskalenko
Hello, I am getting consistent breakage for a C. Cerevisiae reference and mapped dataset when trying to visualize the mapped data in Trackster. I'm running the latest galaxy-dist and Trackster appears to be generally working since I added a couple of reference genomes and users were able to

[galaxy-dev] Default annotation track

2012-04-19 Thread Oleksandr Moskalenko
I needed to add a genome to the tracks in our local instance. However, the only available genome is a multi-fasta file of about 1800 supercontigs. I preserve the sanity of my clients I concatenated the fasta file and provided both versions. The unfortunate part is that the contig annotation

[galaxy-dev] Spaces in uploaded dataset filenames

2012-04-19 Thread Oleksandr Moskalenko
Hi, I have a problem with a tool wrapper I wrote handling input files with spaces in their names. If a user uploads a dataset that has spaces in the file name, e.g. foo bar.xml file then even though my tool, which uses the last tmp directory method of handling multiple output files is

[galaxy-dev] Is there a bowtie2 wrapper

2012-04-30 Thread Oleksandr Moskalenko
I wonder if someone has a functional bowtie2 wrapper that they can share. Thanks, Alex ___ 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

Re: [galaxy-dev] About Galaxy Configuration

2012-05-24 Thread Oleksandr Moskalenko
On May 23, 2012, at 11:42 PM, Ciara Ledero wrote: I didn't know that. Thanks for the reply! Now I have a new set of questions. First, how do I list myself as an admin? Should I just literally add my login detail in the config file? Second, my colleague would like to be able to edit and

Re: [galaxy-dev] Different User with Torque

2012-08-06 Thread Oleksandr Moskalenko
On Aug 6, 2012, at 1:01 PM, Wood, James, D james.wo...@topper.wku.edu wrote: I am a systems administrator for a cluster, and we use Torque and Moab as the resource manager and scheduler. I read that you can use drmaa to submit jobs as a different user other than the 'galaxy' user using the

Re: [galaxy-dev] Different User with Torque

2012-08-06 Thread Oleksandr Moskalenko
runner as a native DRMAA option. The only remaining step is to populate the galaxy_user.username from our LDAP. All modified galaxy code has been provided to the core Galaxy Team by the way. Cheers, Alex On Aug 6, 2012, at 1:16 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: On Aug 6, 2012

Re: [galaxy-dev] Re-starting Galaxy

2012-08-28 Thread Oleksandr Moskalenko
On a related note, it's definitely nice to be able to consolidate the configuration into a single universe_wsi.ini, but --daemon and --stop-daemon are not sufficient for smooth operation of a multi web and job runner instance of Galaxy. I wonder if anyone's already adapted run.sh to restart the

[galaxy-dev] Boolean logic in filters for data in outputs

2012-09-25 Thread Oleksandr Moskalenko
Hi, I am working on a wrapper that has multiple combinations of switches that lead to the creation of the output files. For instance, one of the files can be generated by conditions A and B and also by A and C. FIrst, I tried the xml and and or elements, but that didn't work. Next, I tried

Re: [galaxy-dev] jobName lost when drmaa used with real user use

2012-10-03 Thread Oleksandr Moskalenko
David, For instances that run jobs under real user ids I think the job_name variable in drmaa.py does not need the username component in this case anymore as the batch system takes care of that and the resulting job name looks cleaner in the qstat output. I use @@ -184,10 +183,12 @@

[galaxy-dev] Velveth wrapper not working with real user jobs

2012-10-08 Thread Oleksandr Moskalenko
Velveth wrapper passes the location of the database/files/xxx/dataset_yyy_files to the velveth as an argument. Same paths are put into the output html file. This method can't work anymore when jobs are submitted under real user names as a real user doesn't have write permissions outside of the

Re: [galaxy-dev] Apache proxy to Galaxy: mod_rewrite or mod_proxy ?

2012-10-18 Thread Oleksandr Moskalenko
On Oct 18, 2012, at 12:28 PM, Christophe Antoniewski christophe.antoniew...@snv.jussieu.fr wrote: Hi, Currently, the guide lines for using Apache as a reverse proxy to galaxy are to use the mod_rewrite module and the rewrite rules as explained in the galaxy wiki. I was wondering

Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?

2012-10-29 Thread Oleksandr Moskalenko
On Oct 29, 2012, at 3:20 PM, Todd Oakley todd.oak...@lifesci.ucsb.edu wrote: Ann, Also to your request I'd appreciate any input about MrBayes or a similar kind of tool. We are developing a suite of tools for phylogenetics in Galaxy. We are calling the tool suite Osiris. We are

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

2012-11-02 Thread Oleksandr Moskalenko
On Nov 1, 2012, at 4:22 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Hi, I've been researching the possibility of using dynamic job runner in combination with job splitting for blast jobs. My main interest is to create a rule where both the size of the query and the database are

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

2012-11-02 Thread Oleksandr Moskalenko
On Nov 2, 2012, at 4:42 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Fri, Nov 2, 2012 at 3:58 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Fri, Nov 2, 2012 at 9:53 AM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: The dynamic runner is alive and well thanks

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

2012-11-02 Thread Oleksandr Moskalenko
On Nov 2, 2012, at 3:58 PM, Carlos Borroto carlos.borr...@gmail.com wrote: Please, could you share your rules related to blast. I would love to take a look at them. Thanks, Carlos Here is the blastn rule procedure code and the relevant snippet of the default runner procedure. I just

Re: [galaxy-dev] Dynamic job runner status? Could I use it in combination with job splitting?

2012-11-05 Thread Oleksandr Moskalenko
On Nov 5, 2012, at 2:15 PM, Carlos Borroto carlos.borr...@gmail.com wrote: On Fri, Nov 2, 2012 at 6:03 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: Here is the blastn rule procedure code and the relevant snippet of the default runner procedure. I just added the database based multiplier

[galaxy-dev] Workflow extraction breaks on a bwa step

2012-11-06 Thread Oleksandr Moskalenko
Hi, I wonder if it's a known problem. I had a quick look through the mailing list, but didn't see any relevant messages: An extraction of a workflow from a history breaks on the bwa step: Error - type 'exceptions.ValueError': invalid literal for int() with base 10: 'False' URL:

Re: [galaxy-dev] Workflow extraction breaks on a bwa step

2012-11-06 Thread Oleksandr Moskalenko
This is a pre-migration bwa. I've not updated this Galaxy instance, yet. Here is a paste of used all options: Will you select a reference genome from your history or use a built-in index? history Select a reference from history 3: StaphAureus_USA300_FPR3757 .fasta Is this library

Re: [galaxy-dev] multithreaded tools

2012-11-27 Thread Oleksandr Moskalenko
On Nov 27, 2012, at 6:06 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Hi Peter, thanks for your replies. On 27.11.2012 11:44, Peter Cock wrote: On Tue, Nov 27, 2012 at 10:38 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: Dear Peter, As the author of several

Re: [galaxy-dev] multithreaded tools

2012-11-27 Thread Oleksandr Moskalenko
On Nov 27, 2012, at 9:37 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Tue, Nov 27, 2012 at 2:20 PM, Oleksandr Moskalenko o...@hpc.ufl.edu wrote: The Right Way (TM) I believe would be to have a universal resource request selector that could be plugged into any wrapper simply

Re: [galaxy-dev] Permission denied error for velveth

2012-12-04 Thread Oleksandr Moskalenko
On Dec 4, 2012, at 9:30 AM, Andreas Kuntzagk andreas.kuntz...@mdc-berlin.de wrote: I see that this issue came up before by Oleksandr Moskalenko in October but was unresolved then. Is there a workaround now? regards, Andreas The velvet wrapper is not going to be usable for real user jobs

Re: [galaxy-dev] How to refresh the tool panel in Galaxy?

2012-12-14 Thread Oleksandr Moskalenko
There's also a shortcut that avoids having to click through the menus every time. You can use a reload URL. For instance, if you were working with a local instance and developing the tool 'mytool'. You can open the following url, keep that page open and reload it when necessary to update the

Re: [galaxy-dev] Galaxy users on virtual machine

2012-12-18 Thread Oleksandr Moskalenko
On Dec 18, 2012, at 12:05 PM, Ganote, Carrie L cgan...@iu.edu wrote: Hi all, Right now I have drmaa running with Torque. I have a virtual machine with Galaxy installed on it, a filesystem mounted on the virtual machine that holds the dataset info, and a cluster that runs big jobs and

Re: [galaxy-dev] How to refresh static/welcome.html

2012-12-18 Thread Oleksandr Moskalenko
On Dec 18, 2012, at 12:51 PM, greg margeem...@gmail.com wrote: Hi guys, When I make a change to welcome.html how do I get galaxy to start displaying the new version? Thanks, Greg In my experience you have to restart all web server paster processes. Cheers, Alex

Re: [galaxy-dev] Galaxy users on virtual machine

2012-12-18 Thread Oleksandr Moskalenko
We're using ldap authentication on our cluster, so our /etc/passwd files don't have any user data and the credentials are returned by ldap. You will have to adjust this to your situation. You can rsync /etc/passwd from elsewhere or fiddle with PAM to work something out for your key-based setup.