Re: [galaxy-dev] using drmaa-python

2011-01-03 Thread Nate Coraor
David Hoover wrote: Hi, I've gotten drmaa-python working for PBS Pro. Is there a resource somewhere that describes how to configure a tool for queues, node properties, etc., in the [galaxy:tool_runners] section? Hi David, It's explained at the bottom of the cluster configuration page

Re: [galaxy-dev] Recommendation for Grid/Cluster management ?

2011-01-10 Thread Nate Coraor
Assaf Gordon wrote: Slightly off-topic, but for a new Galaxy installation - What would you recommend for a free (FOSS) Grid/Cluster management product ? SGE is not free any more (Oracle Grid Engine is 90-days evaluation, binaries only free, starting 6.2u6). Ease of administration is

Re: [galaxy-dev] [patch] Job Runner Eggs

2011-01-12 Thread Nate Coraor
John Chilton wrote: Hello, Currently lib/galaxy/config.py requires that custom job runners be paired with exactly one egg for fetching, this seems less than ideal since runners may need 0 eggs (as is the case for a runner I am implementing) or multiple eggs. Attached is a minor patch

Re: [galaxy-dev] API connection error

2011-01-19 Thread Nate Coraor
Paszkiewicz, Konrad wrote: Dear all, I'm getting the following error when trying to follow the instructions in the API README file. Universe_wsgi.ini is pasted below. [galaxy@zeus api]$ ./display.py c43c7605ba60633a2ed60f46c12f354e http://zeus.ex.ac.uk:4000/api/libraries urlopen

Re: [galaxy-dev] API connection error

2011-01-20 Thread Nate Coraor
of universe_wsgi.ini: host = 0.0.0.0 I hope this helps. --nate All the best! Konrad. -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: 19 January 2011 16:43 To: Paszkiewicz, Konrad Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] API connection

Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster

2011-01-27 Thread Nate Coraor
Hi Sonali, Since this is a local installation question, I have moved the discussion to galaxy-dev. Further responses are inline below. Sonali Amonkar wrote: Hi, First of all I would like to appreciate the clean and neat documentation written for the Galaxy setup for Cluster. I am

Re: [galaxy-dev] unable to log out of galaxy

2011-02-02 Thread Nate Coraor
Nicki Gray wrote: Hello When trying to logout from our local instance of Galaxy I get the error message This link may not be followed from within Galaxy. and cant log out. I see this using Firefox, Chrome and Camino How do I fix this so I can log out? Hi Nicki, Are you using

Re: [galaxy-dev] unable to log out of galaxy

2011-02-02 Thread Nate Coraor
authentication system is being used at your site. Since that's specific to each implementation I am not sure what it should be for your site. For straight HTTP Basic Authentication, it's not actually possible to log out. --nate Nicki On 2 Feb 2011, at 14:31, Nate Coraor wrote: Nicki Gray

Re: [galaxy-dev] Galaxy integration with LSF: seg fault: update

2011-02-08 Thread Nate Coraor
My thanks as well, since we don't really have a way to debug LSF here. Platform only granted us a 1 month license for the development, so I'd have to get another license to debug it. --nate Leandro Hermida wrote: Hi Marina, Thanks for posting updates and information... we've moved from SGE

Re: [galaxy-dev] Installation Issue on Centos/python 2.4

2011-02-09 Thread Nate Coraor
:54 AM 2/9/2011, Nate Coraor wrote: Pieter Neerincx wrote: Hi John and Nate, But to make the tool search work in the web interface you'll need Python 2.5 or higher, so it's probably a better idea to get a newer version of Python anyway. (We have Galaxy on two CentOS servers, installed

Re: [galaxy-dev] Inquiring

2011-02-10 Thread Nate Coraor
Yan Luo wrote: Dear Nate, Please find the following errors, it is the newest, and our restart is stopped. I hope we can get the solution from you as soon as possible. Hi Yan, Your last 4 messages included 3 different paths to Galaxy. It seems as though there are quite a few copies of

Re: [galaxy-dev] Inquiring

2011-02-11 Thread Nate Coraor
pull -u http://bitbucket.org/galaxy/galaxy-central/ --nate Looking forward to hearing from you. Thanks, Yan On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Please find the following errors, it is the newest, and our restart

Re: [galaxy-dev] Inquiring

2011-02-11 Thread Nate Coraor
Wishes, Yan On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Why did you say we have 3 paths? We have a link from /home/kangtu/Downloads/galaxy-dist lrwxrwxrwx 1 kangtu admin36 2010-11-01 17:07 galaxy-dist - /home

Re: [galaxy-dev] file upload speeds

2011-02-11 Thread Nate Coraor
Glen Beane wrote: On Feb 9, 2011, at 9:44 AM, Glen Beane wrote: I've been doing some testing with a Galaxy instance running on my laptop for some tools we are developing. I am uploading a file into Galaxy from a URL to use as test input (~1.5GB tabular) I can download this file to my

Re: [galaxy-dev] Inquiring

2011-02-11 Thread Nate Coraor
nate@weyerbacher% sh run.sh -- Looking forward to hearing from you. Best Wishes, Yan On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Why did you say we have 3 paths? We have

Re: [galaxy-dev] Inquiring

2011-02-11 Thread Nate Coraor
Yan Luo wrote: Dear Nate, I just run the first step and must use sudo to wget and it is ok. Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).) I would strongly advise against using sudo for any part of this, since this is how permissions get screwed up. If you don't

Re: [galaxy-dev] Inquiring

2011-02-11 Thread Nate Coraor
pip-2.6 kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ Could you please let me know if you have any suggestion? Best WIshes, Yan On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, I just run the first step

Re: [galaxy-dev] Inquiring

2011-02-11 Thread Nate Coraor
. Best Wishes, Yan On Fri, Feb 11, 2011 at 10:31 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, When I run . /home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate directly, kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ . /home

Re: [galaxy-dev] file upload speeds

2011-02-11 Thread Nate Coraor
Glen Beane wrote: On Feb 11, 2011, at 9:32 AM, Nate Coraor wrote: Glen Beane wrote: On Feb 9, 2011, at 9:44 AM, Glen Beane wrote: I've been doing some testing with a Galaxy instance running on my laptop for some tools we are developing. I am uploading a file into Galaxy from

Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster

2011-02-11 Thread Nate Coraor
Sonali Amonkar wrote: I am currently facing another issue. When I run my Workflow, I am seeing the following error on the server log. This error is not consistent, and occurs in an erratic manner. galaxy.jobs INFO 2011-02-03 05:17:03,522 job 151 dispatched galaxy.jobs.runners.pbs

Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster

2011-02-11 Thread Nate Coraor
Nate Coraor wrote: Sonali Amonkar wrote: I am currently facing another issue. When I run my Workflow, I am seeing the following error on the server log. This error is not consistent, and occurs in an erratic manner. galaxy.jobs INFO 2011-02-03 05:17:03,522 job 151 dispatched

Re: [galaxy-dev] python2.6 UserWarning: Unbuilt egg for pytz

2011-02-11 Thread Nate Coraor
Vipin TS wrote: Hi all, Last day we upgraded our galaxy service computing cluster nodes operating system from Ubuntu hadry to lucid 10.4. We updated python eggs and now getting an Warning message, it apparently kills the galaxy jobs. Warning message as follows:

Re: [galaxy-dev] Inquiring

2011-02-15 Thread Nate Coraor
nothing else has changed, it sounds like your NFS server is having some performance problems. --nate Thanks, Yan On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Thanks for your quick response, I got sever error. and just killed

Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster

2011-02-15 Thread Nate Coraor
Sonali Amonkar wrote: On further digging, we found that the script is failing in the following part of $GALAXY_HOME/lib/galaxy/jobs/runners/pbs.py: # submit galaxy_job_id = job_wrapper.job_id log.debug((%s) submitting file %s % ( galaxy_job_id, job_file ) )

Re: [galaxy-dev] Configuration of galaxy, metada values are missing

2011-02-16 Thread Nate Coraor
Christian Dreischer wrote: Hello community, I'm new to Galaxy and are currently trying to install a new instance on a debian system. So far I installed postgres and created a user and a database for galaxy. In the universe_wsgi.ini file I did the recommended changes and set this entry:

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Nate Coraor
Tena Sakai wrote: Hi I am a developer for a group. I am having a problem with local installation of galaxy. The platform I am using is: $ uname -o GNU/Linux $ uname -i x86_64 $ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008 $ uname -r 2.6.9-78.0.1.ELsmp

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Nate Coraor
Nate Coraor wrote: $ uname -v #1 SMP Tue Jul 22 18:01:05 EDT 2008 $ uname -r 2.6.9-78.0.1.ELsmp RHEL 4, I believe? $ cd galaxy-dist $ sh run.sh ...lots of lines here... Fetch successful. ...more lines here... ysam/csamtools.py, line 6

Re: [galaxy-dev] installation and configuring galaxy

2011-02-17 Thread Nate Coraor
Pauras P Patil wrote: Hello, I am currently working on a project related to bioinformatics here at Purdue University and we wanted a tool that could create a workflow for the data that we collect. I have downloaded the source code for galaxy, but have no idea on how to integrate galaxy

Re: [galaxy-dev] upload directory of files error

2011-02-17 Thread Nate Coraor
David Hoover wrote: This used to work. Now when I try to upload a directory of files, it gives this error: URL: https://galaxy.cit.nih.gov/library_common/ldda_info?library_id=a799d38679e985dbshow_deleted=Falsecntrller=libraryfolder_id=0a248a1f62a0cc04use_panels=Falseid=dff4190d282fb07a

Re: [galaxy-dev] local galaxy display problem

2011-02-17 Thread Nate Coraor
Ryan Golhar wrote: I've set up a local instance of Galaxy following the instructions in the wiki for a production instance. I'm running on CentOS with Apache, and a mysql database server. Everything looks great when viewed directly through the Galaxy web server on port 8080. I've

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-17 Thread Nate Coraor
of the options near the top of the file is 'port ='. This can be changed to whatever you prefer. --nate Thank you! Regards, Tena Sakai PS: Thank you for updating the link on wiki page. On 2/17/11 9:57 AM, Nate Coraor n...@bx.psu.edu wrote: Nate Coraor wrote: $ uname -v #1 SMP

Re: [galaxy-dev] Local galaxy installation problem. Please help.

2011-02-18 Thread Nate Coraor
universe_wsgi.ini in the root of the Galaxy directory, one of the options near the top of the file is 'port ='. This can be changed to whatever you prefer. --nate Thank you! Regards, Tena Sakai PS: Thank you for updating the link on wiki page. On 2/17/11 9:57 AM, Nate Coraor

Re: [galaxy-dev] local galaxy display problem

2011-02-18 Thread Nate Coraor
Ryan Golhar wrote: I've implemented the Serving Galaxy at a sub directory (such as /galaxy), made the change to Apache, and the universe_wsgi.ini. When I view the page through Apache using http://server.name/galaxy, the page is garbled like something didn't take. Hi Ryan, Did you

Re: [galaxy-dev] local galaxy display problem

2011-02-18 Thread Nate Coraor
Ryan Golhar wrote: SOLVED. I copied/paste the Rewrite rules for apache from the wiki without updating the paths to my installation...once I did that, all worked well. Whoops, I should read ahead before I reply. Glad it's working! --nate On 2/17/11 5:07 PM, Ryan Golhar wrote: I've

Re: [galaxy-dev] Torque drmaa egg

2011-02-18 Thread Nate Coraor
Ryan Golhar wrote: Nevermind (once again). I figured out I need to compile it from the torque... You can also use the 'pbs' job runner, which wraps the PBS C API directly instead of using DRMAA. --nate On 2/17/11 10:30 PM, Ryan Golhar wrote: I'm configuring my local install of galaxy to

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Nate Coraor
Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs? Hi Ryan, Whatever

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Nate Coraor
Ryan Golhar wrote: Ryan Golhar wrote: I'm setting up Galaxy to run on my cluster using drmaa. I can see jobs getting submitted to Torque however the jobs keep failing, because the tools are in the default system path. How do I tell galaxy to append a directory to the path used by jobs?

Re: [galaxy-dev] cluster path question

2011-02-18 Thread Nate Coraor
Ryan Golhar wrote: It turns out the user's environment is not set up for batch jobs, only the system environment. I too added . ~/.bashrc to lib/galaxy/jobs/runners/drmaa.py. I'm afraid this is a kludgy fix that will break if/when the drmaa.py file gets updated. It'll work for now, but

Re: [galaxy-dev] pbs_python vs drmaa

2011-02-21 Thread Nate Coraor
Ryan Golhar wrote: I've configured my local instance of galaxy to run with drmaa. Unfortunately, there is a problem that after some time, galaxy loses its ability to talk to Torque, hence Galaxy thinks long-running jobs have failed and its unable to submit new jobs. I have no idea how this

Re: [galaxy-dev] Problems with run_functional_tests.sh and history?

2011-02-21 Thread Nate Coraor
Revival! (This thread was sitting flagged in my mailbox since November) Peter wrote: Hi all, I've since restarted with a clean clone of the repository, and see the same problems. See: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003625.html

Re: [galaxy-dev] Import files from local file system

2011-02-21 Thread Nate Coraor
Steve Taylor wrote: I think so. Just to double check is there a definitive way I can tell? In ./tools/data_source/upload.xml param name=ftp_files type=ftpfile label=Files uploaded via FTP/ So I got this to work by hacking basic.py. def visible( self ):

Re: [galaxy-dev] [galaxy-user] Galaxy does not find my executables

2011-02-21 Thread Nate Coraor
/11 05:58, Nate Coraor wrote: Hi Florent, et. al., I've moved the discussion over to galaxy-dev since it pertains to local instances. Florent Angly wrote: Indeed, this workaround works! Thank you. I added these lines to the beginning of my run.sh: PATH=/opt/local/bin:/opt/local/sbin

Re: [galaxy-dev] [galaxy-user] Galaxy does not find my executables

2011-02-21 Thread Nate Coraor
Marina Gourtovaia wrote: Hi In a bash shell, I define the path (needed both by Galaxy to find the right version of python and by tools that run on a cluster to find the executables) and some other global variables on the command line. The cluster jobs (LSF) inherit all these values. This

Re: [galaxy-dev] Problems with run_functional_tests.sh and history?

2011-02-21 Thread Nate Coraor
Peter wrote: On Mon, Feb 21, 2011 at 2:43 PM, Nate Coraor n...@bx.psu.edu wrote: Revival! (This thread was sitting flagged in my mailbox since November) I guess I should try and file issues for things which don't get a prompt resolution on the mailing list, but its good to know it hadn't

Re: [galaxy-dev] [galaxy-user] operating on, and getting at, large files in galaxy...

2011-02-21 Thread Nate Coraor
Nick Schurch wrote: Hi all, I've recently encountered a few problems when trying to use Galaxy which are really driving me away from using it as a bioinformatics platform for NGS. I was wonderinf if there are any simple solutions that I've missed... Hi Nick, We've had some internal

Re: [galaxy-dev] config files

2011-02-23 Thread Nate Coraor
Glen Beane wrote: We run a local galaxy instance with multiple galaxy web servers and a job runner. Per the wiki suggestion we have two config files: universe_wsgi.webapp.ini and universe_wsgi.runner.ini. I've noticed that we still need universe_wsgi.ini or else galaxy will not start Hi

Re: [galaxy-dev] Trouble compiling SAMtools

2011-02-23 Thread Nate Coraor
Zachariah K Zachariah wrote: Hello, I am having some trouble compiling SAMtools on a Solaris10 X86 p latform using gcc compiler version 3.4.6. Using the Makefile I get some link errors and have not been successful in creating the binary or the associated libraries. It seemed to me that

Re: [galaxy-dev] Configuring remote galaxy job runners

2011-02-23 Thread Nate Coraor
Ry4an Brase wrote: I'm working on getting more of our jobs offloaded to other machines, and I'm getting job failures I'm not able to debug. When running a simple tool like 'cut', submitted over qsub, I'm getting STDERR output like this: WARNING:galaxy.datatypes.registry:Error loading

Re: [galaxy-dev] maximum value for local_job_queue_workers

2011-02-24 Thread Nate Coraor
hari krishna wrote: Hi, What is the difference between threadpool_workers and local_job_queue_workers*.* Hi, threadpool_workers is the number of threads which will be available to serve web requests. This means the number of possible concurrent browser connections, but this value

Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster

2011-02-25 Thread Nate Coraor
, Sonali -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Tuesday, February 15, 2011 10:30 PM To: Sonali Amonkar Cc: Galaxy Dev Subject: Re: [galaxy-dev] Error with setuptools version in Galaxy installation on Cluster Sonali Amonkar wrote

Re: [galaxy-dev] Only use filepaths and Copy data into Galaxy?

2011-02-25 Thread Nate Coraor
Jean-Baptiste Denis wrote: Hello everybody, i've got one galaxy server running. The ressource on the wiki are very useful for that purpose, thank you. I've got one question regarding data library when using upload files from filesystem paths. There is a checkbox, unchecked by default,

Re: [galaxy-dev] Local Galaxy implimentation

2011-02-25 Thread Nate Coraor
Conference as they will be able to interact with key Galaxy Team members such as Nate Coraor, who runs Penn State instance here. Thanks! anton On Feb 25, 2011, at 6:14 AM, Lee Hazelwood wrote: Dear Prof Nekrutenko, The university where I work is looking to locally implement

Re: [galaxy-dev] stagingin and stagingout at DRMAA

2011-02-25 Thread Nate Coraor
hari krishna wrote: Hi , Can any one help me how to transfer files from head node to remote location by using DRMAA job template attributes with example will DRMAA supports staging in and staging out of files,... Hi, You can use the drmaa_transfer_files job template attribute,

Re: [galaxy-dev] unable to login user to local instance

2011-02-25 Thread Nate Coraor
Peter Cock wrote:  File /home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py, line 29    return (content if len(content) = length else content[:length].rsplit(' ', 1)[0]+suffix)                     ^ SyntaxError: invalid syntax I deduce you're using Python 2.4,

Re: [galaxy-dev] How to retain files compressed

2011-02-28 Thread Nate Coraor
Christian Hundsrucker wrote: Hi all! I want to load a R-workspace within a galaxy module (.rdat-file, R-Project) and therefore built the galaxy-.rdat datatype (binary). .rdat-files are gzipped and are only recognized within R if they are still zipped. However, the corresponding .dat-file

Re: [galaxy-dev] uploading gzip compressed datasets

2011-02-28 Thread Nate Coraor
Ryan Golhar wrote: Hi all - I'm uploading datasets into my local instance by importing from the filesystem w/o copying into Galaxy. Importing of uncompressed files works properly. The files I'm importing are owned by user1 and a read-able by everyone, including the galaxy user. The galaxy

Re: [galaxy-dev] Galaxy static assets and redirect woes

2011-03-01 Thread Nate Coraor
Paul-Michael Agapow wrote: This is not a Galaxy problem per se, but a problem during Galaxy setup so maybe others will have an insight. So we're installing our own Galaxy for production / general use. I've been following the config and advanced config guides and installed Galaxy in its

Re: [galaxy-dev] rpy and R

2011-03-03 Thread Nate Coraor
Sarah Diehl wrote: Hi all, I'm currently working on setting up a fresh Galaxy server at our institute. I'm going through the tool dependencies list and install everything on it. I installed the latest R version (2.12.2) and now I'm trying to install rpy. With some workarounds I managed to

Re: [galaxy-dev] file upload

2011-03-07 Thread Nate Coraor
Musa A. Hassan wrote: I am trying to use galaxy for the first time and am running into some early problems. While trying to upload my file which is basically an fq containing illumina short reads, the file won't upload. When I try the fastq extension of the same file, it does but then the

Re: [galaxy-dev] Inquiring

2011-03-07 Thread Nate Coraor
-in limitations on file size/count. --nate Please find the attached screenshoots for your reference. Looking forward to hearing from you. Best Wishes, Yan On Tue, Feb 15, 2011 at 9:08 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Yes, you are right

Re: [galaxy-dev] upload large data file

2011-03-07 Thread Nate Coraor
Yanji Xu wrote: Dear Sir/Madam, I installed galaxy in my local server, then I tried to upload a 4.7 Gb fastq file into galaxy, but failed. Below is the error message. OverflowError: signed integer is greater than maximum How could I upload large data files into galaxy and process the

Re: [galaxy-dev] possible bug - user log in / browser cache

2011-03-07 Thread Nate Coraor
Ryan Golhar wrote: I have a local instance running. When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's cache is retaining some information. To get around this, after I log out as user1, I have to

Re: [galaxy-dev] possible bug - user log in / browser cache

2011-03-07 Thread Nate Coraor
Peter Cock wrote: On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor n...@bx.psu.edu wrote: Ryan Golhar wrote: I have a local instance running.  When I'm logged in as user1, log out, then try to log in as user2, I keep getting the You have been logged out message. Its as if the browser's

Re: [galaxy-dev] parallel computing

2011-03-15 Thread Nate Coraor
Yanji Xu wrote: Dear Sir/Madam, Does Galaxy support parallel computing? Yes, please see the information about using a cluster at: http://usegalaxy.org/production --nate Thanks, Yanji ___ Please keep all replies on the list by

Re: [galaxy-dev] Login problem.

2011-03-15 Thread Nate Coraor
CHAN Chee Seng wrote: Hi Ryan, Thanks for sharing the work around. I had the same problem. I am running galaxy with mysql server. I tested on 1. Firefox on a linux box 2. IE and firefox on a windows box. I tried restarting galaxy and the apache httpd server and my client machines

Re: [galaxy-dev] Problem upgrading DB from 73 to 75 (on SQLite)

2011-03-17 Thread Nate Coraor
Peter Cock wrote: $ python -ES ./scripts/fetch_eggs.py Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.2.5-py2.6.egg Fetched http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-macosx-10.6-universal-ucs2.egg Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg

Re: [galaxy-dev] Can't save BAM file from Galaxy

2011-03-22 Thread Nate Coraor
Liisa Koski wrote: Hello, I have a local instance of galaxy and after successfully running an NGS analysis I am trying to save my BAM file to my local machine. When I click on the save icon my Galaxy instance crashes with the following error. This also happens when I try to save the SAM

Re: [galaxy-dev] new_file_path vs $TMP

2011-03-29 Thread Nate Coraor
Louise-Amélie Schmitt wrote: 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

Re: [galaxy-dev] Wiki bug for updating local galaxy?

2011-03-30 Thread Nate Coraor
Ryan Golhar wrote: Hi all - I was about to update my local Galaxy installation, and went back to the wiki to refer to how to do this (https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy), and noticed a mistake. Step 1 says to use hg clone https://bitbucket.org/galaxy/galaxy-dist/;

Re: [galaxy-dev] Can't save BAM file from Galaxy

2011-03-31 Thread Nate Coraor
Ryan Golhar wrote: Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off? I'm running into this same problem but still prefer to have the job scripts kept in case something goes wrong. Not without modifying the call to cleanup() in the job runner

Re: [galaxy-dev] Can't save BAM file from Galaxy

2011-03-31 Thread Nate Coraor
Assaf Gordon wrote: +1 Nate Coraor wrote, On 03/31/2011 12:34 PM: Ryan Golhar wrote: Nate - Is there a way to get the pbs job scripts to still get saved with debugging turned off? Not without modifying the call to cleanup() in the job runner (lib/galaxy/jobs/__init__.py). It'd

Re: [galaxy-dev] Inquiring

2011-04-01 Thread Nate Coraor
Yan Luo wrote: Dear Nate, I can't start my galaxy and got the following information, could you please let me know how we can fix it as soon as possible? We were running the system, it was down last night suddenly. Hope we can fix it today. File

Re: [galaxy-dev] Inquiring

2011-04-01 Thread Nate Coraor
interface, it's up. If you are worried about corruption, you can check the MySQL logs or use 'mysqlcheck'. --nate Best Wishes, Yan On Fri, Apr 1, 2011 at 10:48 AM, Nate Coraor n...@bx.psu.edu wrote: Yan Luo wrote: Dear Nate, Your suggestion is very important for us. You

Re: [galaxy-dev] How to control which nodes particular applications run on

2011-04-01 Thread Nate Coraor
Ryan Golhar wrote: Hi all - Is it possible to define in a tool's XML file specific nodes in a cluster that the tool should run on? I have a few machines in my cluster is lots of RMA that I need for a specific tool. However there is no way to guarantee the tool will execute on one of those

Re: [galaxy-dev] SGE and Galaxy (a different approach)

2011-04-05 Thread Nate Coraor
andrew stewart wrote: I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini, however what I want to do is a little different. Because I only want certain processes to be submitted to the queue, I'd rather control this at the tool configuration level (the xml wrapper). For

Re: [galaxy-dev] Trouble viewing interval files in UCSC with Apache+XSendFile

2011-04-06 Thread Nate Coraor
Assaf Gordon wrote: Until a better solution comes along, this tiny patch makes the temp files world-readable: http://cancan.cshl.edu/labmembers/gordon/files/apache_xsendfile_temp_files.patch We avoid this by running our webserver as the Galaxy user. Obviously not a solution for everyone

Re: [galaxy-dev] reason/advantages for making Galaxy proxy using mod_rewrite instead of mod_proxy

2011-04-08 Thread Nate Coraor
Leandro Hermida wrote: Sorry one more question... are these lines in the Galaxy wiki instructions still correct for the latest galaxy-dist? They should be, yes. RewriteRule ^/galaxy/static/style/(.*) /home/nate/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule

Re: [galaxy-dev] Recommended Specs for Production System

2011-04-08 Thread Nate Coraor
Assaf Gordon wrote: Forgot to mention SGE/PBS: you definitely want to use them (even if you're using a single machine), because the local job runner doesn't take into account multi-threaded programs when scheduling jobs. So another core is needed for the SGE scheduler daemons (sge_qmaster

Re: [galaxy-dev] DRMAA_python installation problem

2011-04-19 Thread Nate Coraor
Hi Johannes, Johannes Eichner wrote: Dear Galaxy Team, I just updated my local instance of galaxy, and now I have a problem with the DRMAA_python egg, which makes it impossible to run jobs on our SGE cluster. I get the following error message after executing run.sh: ... gcc -pthread

Re: [galaxy-dev] User Name not set with external LDAP authentication

2011-04-28 Thread Nate Coraor
Pieter Neerincx wrote: Hi Leandro, On Apr 27, 2011, at 6:08 PM, Leandro Hermida wrote: Hi Pieter, cut I have this *exact* same setup as you where I am authenticating with the LDAP user ID and returning a mail LDAP attribute as REMOTE_USER, but this sets the Galaxy user email

Re: [galaxy-dev] anyone actually properly implemented remote_user_logout_href with external HTTP authentication?

2011-04-28 Thread Nate Coraor
Leandro Hermida wrote: Hi everyone, Has anyone actually properly implemented remote_user_logout_href in Galaxy with external HTTP authentication? As probably those who have tried know, it is rife there doesn't seem to be a clean and robust way to do this? Hi Leandro, Other than loading in

Re: [galaxy-dev] problem running latest galaxy-central

2011-04-29 Thread Nate Coraor
Assaf Gordon wrote: I'll rephrase my question: Is cython going to be a standard requirement for Galaxy (and needs to be manually installed on our production servers), or is this just a temporary thing, or is it going to be an automatic egg thing ? No, that's a mistake. I should have a fix

Re: [galaxy-dev] connecting to a DB on a different host

2011-05-02 Thread Nate Coraor
Nikolai Vazov wrote: Hi, I am trying to connect my galaxy instance to a DB on a different host. This DB uses an SSL encryption and Auth method md5. I have no problems in connecting to the DB via the command line, but the line (in universe_wsqi.ini) : database_connection =

Re: [galaxy-dev] connecting to a DB on a different host

2011-05-02 Thread Nate Coraor
Nikolai Vazov wrote: Hi, Nate, Thanks a lot for the hint : I also had suspicions about the SSL and it seems to be working, well, I mean, failing, as you supposed because of my psycopg2 which was built without SSL. OperationalError: (OperationalError) sslmode value require invalid

Re: [galaxy-dev] [galaxy-user] Removing deleted datasets

2011-05-02 Thread Nate Coraor
Simon Lank wrote: Hi. Our current galaxy database is ~ 600 gb, most of which are user deleted datasets. I followed the instructions here: https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDatasets and ran the shell scripts in recommended order. One of them in

Re: [galaxy-dev] Question Regarding Local Galaxy Installation Uploading Files Error

2011-05-02 Thread Nate Coraor
George Yianni Michopoulos wrote: To any wonderful person that can help me: I recently uploaded a local instance of Galaxy on a new computer at the Fernald Lab at Stanford. I am not too familiar with Unix, but needed to install the local instance due to the high volume of genomic data

Re: [galaxy-dev] connecting to a DB on a different host

2011-05-03 Thread Nate Coraor
/galaxy/galaxy-dist 4. Given the above details, can I just execute 4? Yes, you should be able to. That version of postgres is rather old but psycopg2 should be backwards compatible. --nate Thank you Nikolay On Mon, 2 May 2011 10:27:41 -0400, Nate Coraor n...@bx.psu.edu wrote: Nikolai

Re: [galaxy-dev] connecting to a DB on a different host

2011-05-03 Thread Nate Coraor
Nikolai Vazov wrote: Hi again, The version of the PostgreSQL server I am trying to connect to is actually 8.3. The DB department say they will soon move to 9.0. The psycopg2 version in my eggs.ini for Galaxy is 8.4.2: psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg Do you

Re: [galaxy-dev] connecting to a DB on a different host

2011-05-03 Thread Nate Coraor
Nikolai Vazov wrote: Hi, Nate, When trying to execute PYTHONPATH=/home/galaxy/galaxy-dist/scripts/scramble/lib python26 setup.py egg_info --tag-build=_8.4.2_static bdist_egg I get Traceback (most recent call last): File setup.py, line 52, in module from scramble_lib import

Re: [galaxy-dev] Version Error and Python 2.7

2011-05-03 Thread Nate Coraor
Branden Timm wrote: Sorry to dig up this old thread, but how do you remove the check that prevents galaxy running on 2.7? One of my developers just updated his workstation to Ubuntu 11.04 (Py 2.7) which is preventing him from running Galaxy. I'm not sure whether it would be better to remove

Re: [galaxy-dev] connecting to a DB on a different host

2011-05-04 Thread Nate Coraor
Nikolai Vazov wrote: Hi, Nate, I followed your instructions and managed to compile the psycopg2. What I did: 1. Downloaded a tar.gz of psycopg2 2.0.13 to /home/galaxy/galaxy-dist and unpacked it there 2. cd into psycopg2, modified the setup.py according to your instructions (added

Re: [galaxy-dev] python2.6?

2011-05-04 Thread Nate Coraor
Yamshchikov, Vladimir wrote: Hello all, If this question is not for this list, please advise. Both my RHEL55 and SL55 are based on python 2.4.3 - how I can add python 2.6 support for Galaxy without screwing up OS? I had both 2.4 and 2.6 installed, by python -V returns only 2.4.3. When

Re: [galaxy-dev] Restoring galaxy database return few empty tables.

2011-05-06 Thread Nate Coraor
Vipin TS wrote: Dear Galaxy Team, I am switching our Galaxy production service to a new machine, We are using Postgres as database server. The existing database belongs to postgres version 8.3 and I took my instance's dump using postgres version 8.4. I am able to restore my database on

Re: [galaxy-dev] Problem downloading file from local Galaxy

2011-05-06 Thread Nate Coraor
Marco Moretto wrote: Hi all, I successfully installed a Galaxy instance locally. I use Galaxy with Apache. Every time I try to download a file from history (like Options - Export to file) the browser (Firefox 3.6) reply with the error /tmp/lFeL6erm.asc.part could not be saved, because the

Re: [galaxy-dev] Workflow steps stuck in job queue - since cleanup_datasets.py

2011-05-06 Thread Nate Coraor
Liisa Koski wrote: Hi, Yesterday I ran the cleanup_datasets.py scripts as follows.. Deleting Userless Histories python cleanup_datasets.py universe_wsgi.ini -d 10 -1 Purging Deleted Histories python cleanup_datasets.py universe_wsgi.ini -d 10 -2 -r Purging Deleted Datasets python

Re: [galaxy-dev] Question on setting metadata on upload via API

2011-05-06 Thread Nate Coraor
Duddy, John wrote: I'm looking at extending the metadata fields for one of the supported file types. The files can get VERY large, and since I'm creating those files, I'd like to save as metadata some of the information I have on the contents. Specifically, I'd like to tag the files with

Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

2011-05-06 Thread Nate Coraor
Peter Cock wrote: On Fri, May 6, 2011 at 8:18 AM, Hans-Rudolf Hotz h...@fmi.ch wrote: Hi Ed You can use the variable $userEmail in the 'command' tag of the tool definition file Regards, Hans That should probably be listed on the wiki,

Re: [galaxy-dev] typo in galaxy-dist/tool_conf.xml?

2011-05-06 Thread Nate Coraor
Marina Gourtovaia wrote: Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution downloaded yesterday tool file=indels/indel_table.xml / should be tool file=indels/indel_table.xml / ? Hi Marina, Indeed, thanks for catching this. It has been fixed and will go out in the

Re: [galaxy-dev] Question on setting metadata on upload via API

2011-05-06 Thread Nate Coraor
Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com -Original Message- From: Nate Coraor [mailto:n...@bx.psu.edu] Sent: Friday, May 06, 2011 8:12 AM To: Duddy, John Cc: galaxy-dev@lists.bx.psu.edu Subject

Re: [galaxy-dev] quick question: how can i supply the user's email address to a tool?

2011-05-06 Thread Nate Coraor
not, when in doubt, look in lib/galaxy/config.py. --nate Thanks! On Fri, May 6, 2011 at 9:06 AM, Nate Coraor n...@bx.psu.edu wrote: __tool_data_path__ = GALAXY_DATA_INDEX_DIR = universe_wsgi.ini tool_data_path value ___ Please

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