[galaxy-dev] shared TEMP directory location

2011-05-09 Thread Shantanu Pavgi
I am configuring galaxy to use a shared filesystem location as it's TEMP directory. I have modified $TEMP variable with the necessary path. Are there any other changes that I need to make? The cluster config page https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster mentions about

[galaxy-dev] galaxy with SGE cluster

2011-05-12 Thread Shantanu Pavgi
I need some help in configuring galaxy with SGE scheduler using unified method. The galaxy is running on a system distinct from SGE scheduler install. The cluster nodes can access galaxy install, galaxy-tools and dataset files using NFS. I am not sure how drmaa works and how galaxy submits

Re: [galaxy-dev] galaxy with SGE cluster

2011-05-13 Thread Shantanu Pavgi
On May 12, 2011, at 3:43 PM, Nate Coraor wrote: Shantanu Pavgi wrote: I need some help in configuring galaxy with SGE scheduler using unified method. The galaxy is running on a system distinct from SGE scheduler install. The cluster nodes can access galaxy install, galaxy-tools

Re: [galaxy-dev] galaxy with SGE cluster

2011-05-16 Thread Shantanu Pavgi
On May 12, 2011, at 3:43 PM, Nate Coraor wrote: Shantanu Pavgi wrote: I need some help in configuring galaxy with SGE scheduler using unified method. The galaxy is running on a system distinct from SGE scheduler install. The cluster nodes can access galaxy install, galaxy-tools

[galaxy-dev] galaxy doesn't start with drmaa job runner

2011-05-17 Thread Shantanu Pavgi
I am trying to configure galaxy with sge/drmaa scheduler. The galaxy process is starting up fine without any drmaa configuration. However the galaxy daemon doesn't start properly when I add drmaa configuration lines as shown below. I have set SGE_ROOT and DRMAA_LIBRARY_PATH variables

Re: [galaxy-dev] galaxy doesn't start with drmaa job runner

2011-05-17 Thread Shantanu Pavgi
On May 17, 2011, at 11:35 AM, Nate Coraor wrote: Shantanu Pavgi wrote: I am trying to configure galaxy with sge/drmaa scheduler. The galaxy process is starting up fine without any drmaa configuration. However the galaxy daemon doesn't start properly when I add drmaa configuration lines

[galaxy-dev] restarting galaxy while tools/jobs are running

2011-05-19 Thread Shantanu Pavgi
If we restart galaxy server then would it disturb galaxy-tools jobs that are running? e.g. I want to restart galaxy server while a user is running bowtie job/process. Will galaxy lose any context of this job/process after restart? -- Thanks, Shantanu.

Re: [galaxy-dev] restarting galaxy while tools/jobs are running

2011-05-19 Thread Shantanu Pavgi
On May 19, 2011, at 2:55 PM, Nate Coraor wrote: Shantanu Pavgi wrote: If we restart galaxy server then would it disturb galaxy-tools jobs that are running? e.g. I want to restart galaxy server while a user is running bowtie job/process. Will galaxy lose any context of this job/process

[galaxy-dev] cluster files directory configuration

2011-05-19 Thread Shantanu Pavgi
I have configured custom cluster_files_directory in universe_wsgi.ini file. The cluster jobs are running fine, however job scripts, stdout and stderr are being written in default database/pbs location. Am I missing something in the configuration here? -- Thanks, Shantanu.

Re: [galaxy-dev] multiple cluster job runners?

2011-05-24 Thread Shantanu Pavgi
On May 24, 2011, at 4:49 AM, Nate Coraor wrote: Shantanu Pavgi wrote: I am looking at options to configure settings such as wall-time, memory, and number of cores etc. for each tool and wondering if this can be done using multiple cluster job runner configurations. Is it possible

Re: [galaxy-dev] cluster files directory configuration

2011-05-24 Thread Shantanu Pavgi
On May 19, 2011, at 4:05 PM, Shantanu Pavgi wrote: I have configured custom cluster_files_directory in universe_wsgi.ini file. The cluster jobs are running fine, however job scripts, stdout and stderr are being written in default database/pbs location. Am I missing something

Re: [galaxy-dev] cluster files directory configuration

2011-05-26 Thread Shantanu Pavgi
On May 25, 2011, at 8:18 AM, Nate Coraor wrote: Shantanu Pavgi wrote: On May 19, 2011, at 4:05 PM, Shantanu Pavgi wrote: I have configured custom cluster_files_directory in universe_wsgi.ini file. The cluster jobs are running fine, however job scripts, stdout and stderr are being

[galaxy-dev] listing universe_wsgi.ini configuration

2011-06-01 Thread Shantanu Pavgi
Hi, I have started galaxy daemon using 'reload' option. I am wondering if there is a command to print currently used configuration values in the universe_wsgi.ini file. It may help verify that configuration changes were reloaded. -- Thanks, Shantanu.

[galaxy-dev] galaxy deployment workflow or best-practices

2011-06-01 Thread Shantanu Pavgi
I looked at the Galaxy deployment presentation from the Galaxy Community Conference ( http://wiki.g2.bx.psu.edu/GCC2011?action=AttachFiledo=viewtarget=GalaxyDeploymentandAPI.pdf ) and it was really helpful. I am wondering if you could share any details or best practices for maintaing the

[galaxy-dev] separate galaxy tools directory

2011-06-01 Thread Shantanu Pavgi
I am wondering if galaxy tools directory structure can be changed so that tool configurations resides outside galaxy code base. Right now the galaxy code comes with some default/pre-installed tools in the $GALAXY_DIST/tools directory. Any additional tool configurations are also defined in the

Re: [galaxy-dev] galaxy with SGE cluster

2011-06-17 Thread Shantanu Pavgi
:44 AM, Shantanu Pavgi pa...@uab.edu wrote: Just want to confirm SGE configuration again. As mentioned earlier we started with a separate galaxy VM without any SGE installation. The SGE master node is installed on a separate system altogether. As I understand from your reply, we will need

[galaxy-dev] public datasets/histories with external auth

2011-06-20 Thread Shantanu Pavgi
Hi, We have a galaxy server setup using external shibboleth authentication. While we would like to have site behind authentication realm, there are instances when our galaxy datasets/histories need to be accessible publicly from other websites. We tried adding an exception to auth rule for

Re: [galaxy-dev] public datasets/histories with external auth

2011-06-20 Thread Shantanu Pavgi
On Jun 20, 2011, at 2:40 PM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, We have a galaxy server setup using external shibboleth authentication. While we would like to have site behind authentication realm, there are instances when our galaxy datasets/histories need to be accessible

Re: [galaxy-dev] public datasets/histories with external auth

2011-06-22 Thread Shantanu Pavgi
On Jun 20, 2011, at 4:10 PM, Shantanu Pavgi wrote: On Jun 20, 2011, at 2:40 PM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, We have a galaxy server setup using external shibboleth authentication. While we would like to have site behind authentication realm, there are instances

[galaxy-dev] user_library_import_dir configuration

2011-06-22 Thread Shantanu Pavgi
Hi, I have setup 'user_library_import_dir' to allow non-admin users to import data libraries. The configured directory contains subdirectories with galaxy-login (email) name. I couldn't figure out how to view these files in galaxy web interface though. Any help? Also, what filesystem

[galaxy-dev] number of dataset files within 000

2011-06-22 Thread Shantanu Pavgi
Hi, The galaxy dataset files (file_path) are arranged within a subdirectory '000' (database/files/000). Will galaxy create a new subdirectory for storing datasets files after certain file count value is reached(say ~ 1000)? It may not be a problem while using web interface, but I am wondering

Re: [galaxy-dev] user_library_import_dir configuration

2011-06-23 Thread Shantanu Pavgi
On Jun 22, 2011, at 4:41 PM, Shantanu Pavgi wrote: Hi, I have setup 'user_library_import_dir' to allow non-admin users to import data libraries. The configured directory contains subdirectories with galaxy-login (email) name. I couldn't figure out how to view these files in galaxy

Re: [galaxy-dev] user_library_import_dir configuration

2011-06-23 Thread Shantanu Pavgi
Shared Data - Data libraries from the top Galaxy menu bar. Go to the library to which you have permission to add, and upload files from your configured directory. Let us know if you bump into additional questions. Greg Von Kuster On Jun 22, 2011, at 5:41 PM, Shantanu Pavgi wrote

Re: [galaxy-dev] number of dataset files within 000

2011-06-23 Thread Shantanu Pavgi
, Shantanu Pavgi pa...@uab.edu wrote: Hi, The galaxy dataset files (file_path) are arranged within a subdirectory '000' (database/files/000). Will galaxy create a new subdirectory for storing datasets files after certain file count value is reached(say ~ 1000)? It may not be a problem while

Re: [galaxy-dev] public datasets/histories with external auth

2011-06-29 Thread Shantanu Pavgi
On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote: Leandro Hermida wrote: Hi Shantanu, In your Apache configuration exactly how did you set up an anonymous REMOTE_USER just for specific locations like the /datasets/ path? I'm just looking at the Apache docs and the RequestHeader directive has a

Re: [galaxy-dev] public datasets/histories with external auth

2011-06-29 Thread Shantanu Pavgi
On Jun 28, 2011, at 2:15 PM, Nate Coraor wrote: Shantanu Pavgi wrote: I did a test by excluding following URLs from Apache-Shibboleth external authentication and it seems to be working: - /datasets/ - /u/username/h/history-name - /static/ (css and javascript) Do I need to exclude any other

Re: [galaxy-dev] public datasets/histories with external auth

2011-06-30 Thread Shantanu Pavgi
On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote: Hi Nate and Shantanu, Thanks so much for the clear guidance, this works and sorry I didn't read the Apache docs properly best, Leandro On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi pa...@uab.edu wrote: On Jun 29, 2011, at 12:21

[galaxy-dev] empty status for non-empty datasets

2011-07-11 Thread Shantanu Pavgi
Hi, In our local galaxy install (currently revision 50e249442c5a) we are seeing few output datasets as 'empty' in the galaxy web interface. The actual file size on the filesystem is ~ 4GB. These 'empty' files can be downloaded by clicking on download/view icons, however they can't be imported

Re: [galaxy-dev] Best location for galaxy environmental variables

2011-07-21 Thread Shantanu Pavgi
We are using environment modules ( http://modules.sourceforge.net/ ) on the cluster and took same approach for the galaxy install. The module files are loaded using .bashrc file of galaxy user. It's also useful for non-galaxy users/admins for running galaxy-tools from command-line by simply

[galaxy-dev] TEMP variable in cluster install

2011-07-21 Thread Shantanu Pavgi
We have configured galaxy to work with our SGE cluster using drmaa job runner interface. We are using 'unified method' for this install and both TEMP environment variable and new_file_path in universe_wsgi.ini file have been configured correctly. However, we are seeing some errors where local

Re: [galaxy-dev] TEMP variable in cluster install

2011-07-26 Thread Shantanu Pavgi
On Jul 21, 2011, at 6:24 PM, Shantanu Pavgi wrote: We have configured galaxy to work with our SGE cluster using drmaa job runner interface. We are using 'unified method' for this install and both TEMP environment variable and new_file_path in universe_wsgi.ini file have been configured

[galaxy-dev] debugging jobs in 'new' state

2011-07-28 Thread Shantanu Pavgi
We experienced an issue where some of the galaxy jobs were sitting in the 'new' state for a quite long time. They were not waiting for cluster resources to become available, but haven't been even queued up through DRMAA. We are currently using non-debug mode and following were my observations:

Re: [galaxy-dev] debugging jobs in 'new' state

2011-07-28 Thread Shantanu Pavgi
Biswas, University of Otago Department of Biochemistry, Dunedin, New Zealand, Tel: +64(22)0855647 Fax: +64(0)3 479 7866 On Fri, Jul 29, 2011 at 10:03 AM, Shantanu Pavgi pa...@uab.edumailto:pa...@uab.edu wrote: We experienced an issue where some of the galaxy jobs were sitting in the 'new' state

[galaxy-dev] job status when SGE kills/aborts job

2011-07-29 Thread Shantanu Pavgi
We are using SGE cluster with our galaxy install. We have specified resource and run-time limits for certain tools using tool specific drmaa URL configuration, e.g.: - run-time (h_rt, s_rt) - memory (vf, h_vmem). This helps scheduler in submitting jobs to an appropriate node and also

Re: [galaxy-dev] job status when SGE kills/aborts job

2011-07-29 Thread Shantanu Pavgi
-dev-boun...@lists.bx.psu.edu] On Behalf Of Shantanu Pavgi [pa...@uab.edu] Sent: July 29, 2011 1:56 PM To: galaxydev psu Subject: [galaxy-dev] job status when SGE kills/aborts job We are using SGE cluster with our galaxy install. We have specified resource and run-time limits for certain tools using

Re: [galaxy-dev] job status when SGE kills/aborts job

2011-07-29 Thread Shantanu Pavgi
From: galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edumailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Shantanu Pavgi [pa...@uab.edumailto:pa...@uab.edu] Sent: July 29, 2011 1:56 PM To: galaxydev psu

[galaxy-dev] set metadata step

2011-08-30 Thread Shantanu Pavgi
Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? -- Thanks, Shantanu. ___ Please keep all replies on the list

Re: [galaxy-dev] set metadata step

2011-08-30 Thread Shantanu Pavgi
On Aug 30, 2011, at 9:16 AM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, There is a 'set_metadata_externally' setting in universe_wsgi.ini file. What is involved in this step? Is it run for every dataset/output being generated in the galaxy? Hi Shantanu, Metadata is always

[galaxy-dev] handling galaxy updates

2011-09-02 Thread Shantanu Pavgi
Hi, I am curious to know which revision of galaxy code gets deployed in the main ( http://main.g2.bx.psu.edu/ ) and test ( http://test.g2.bx.psu.edu/ ) instances of galaxy. I was thinking active development repository galaxy-central code gets deployed in the test galaxy instance and stable

Re: [galaxy-dev] handling galaxy updates

2011-09-02 Thread Shantanu Pavgi
confident that it will be stable. Thanks, K On Fri, Sep 2, 2011 at 2:22 PM, Shantanu Pavgi pa...@uab.edu wrote: Hi, I am curious to know which revision of galaxy code gets deployed in the main ( http://main.g2.bx.psu.edu/ ) and test ( http://test.g2.bx.psu.edu/ ) instances

[galaxy-dev] galaxy citation_url setting

2011-10-31 Thread Shantanu Pavgi
Hi, It seems like modification of 'citation_url' in the universe_wsgi.ini config file has no effect in the UI (Help -- How to Cite Galaxy). Is it something hard-coded in the source? -- Thanks, Shantanu. ___ Please keep all replies on

Re: [galaxy-dev] galaxy citation_url setting

2011-11-02 Thread Shantanu Pavgi
On Nov 2, 2011, at 3:39 PM, Nate Coraor wrote: Shantanu Pavgi wrote: Hi, It seems like modification of 'citation_url' in the universe_wsgi.ini config file has no effect in the UI (Help -- How to Cite Galaxy). Is it something hard-coded in the source? Hi Shantanu, Whoops

[galaxy-dev] error in downloading bai files using shared history link

2011-11-18 Thread Shantanu Pavgi
Hi, We are getting following error when a user tries to download bam index file (bai) files using a shared history link of following pattern - ' https://galaxy.mydomain/u/user1/h/awesome-analysis '. We are using external authentication and latest galaxy-dist code in our set up. {{{ Error

Re: [galaxy-dev] error in downloading bai files using shared history link

2011-11-18 Thread Shantanu Pavgi
Thanks for the fix Jeremy. -- Shantanu. On Nov 18, 2011, at 12:58 PM, Jeremy Goecks wrote: Shantanu, This is a bug and is fixed in galaxy-central changeset ccbee8d11a6a : https://bitbucket.org/galaxy/galaxy-central/changeset/ccbee8d11a6a/ Best, J. On Nov 18, 2011, at 12:37 PM, Shantanu

Re: [galaxy-dev] Setup galaxy to run on SGE cluster

2012-01-10 Thread Shantanu Pavgi
On Jan 9, 2012, at 7:45 PM, Derrick LIN wrote: Hi guys, I am trying to configure our test galaxy to run on our SGE cluster http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster. This is my first time to come across to drmaa, so a bit confused. I installed teh galaxy on a NFS location

Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException

2012-01-19 Thread Shantanu Pavgi
, Edward Kirton eskir...@lbl.govmailto:eskir...@lbl.gov wrote: excellent, thanks for the correction! On Wed, Jan 18, 2012 at 8:59 AM, Shantanu Pavgi pa...@uab.edumailto:pa...@uab.edu wrote: Ed, I think you may want to add job with DrmCommunicationException error back into the watched_jobs list

Re: [galaxy-dev] Status on importing BAM file into Library does not update

2012-01-20 Thread Shantanu Pavgi
Just wanted to add that we have consistently seen this issue of 'samtools index' running locally on our install. We are using SGE scheduler. Thanks for pointing out details in the code Nate. -- Shantanu. On Jan 20, 2012, at 9:35 AM, Nate Coraor wrote: On Jan 18, 2012, at 11:54 AM, Ryan

[galaxy-dev] DRMAA error with latest update 26920e20157f

2012-01-29 Thread Shantanu Pavgi
I am getting following error with the latest galaxy-dist revision '26920e20157f' update. The Python version is 2.6.6. {{{ galaxy.jobs.runners.drmaa ERROR 2012-01-29 21:00:28,577 Uncaught exception queueing job Traceback (most recent call last): File

Re: [galaxy-dev] DRMAA error with latest update 26920e20157f

2012-01-30 Thread Shantanu Pavgi
Figured it out. It was an error introduced while resolving version control conflicts. -- Shantanu On Jan 29, 2012, at 9:12 PM, Shantanu Pavgi wrote: I am getting following error with the latest galaxy-dist revision '26920e20157f' update. The Python version is 2.6.6

[galaxy-dev] job cleanup files drmout and drmerr not found

2012-01-30 Thread Shantanu Pavgi
I see following warning messages in galaxy logs after a job finishes up. Does it mean something is misconfigured or a tool did not generate stdout and stderr files? {{{ galaxy.datatypes.metadata DEBUG 2012-01-30 11:52:07,345 loading metadata from file for: HistoryDatasetAssociation 7

Re: [galaxy-dev] Missing stdout and stderr files from SGE cluster

2012-02-02 Thread Shantanu Pavgi
On Feb 2, 2012, at 8:21 AM, Peter Cock wrote: On Thu, Feb 2, 2012 at 1:54 PM, Langhorst, Brad langho...@neb.commailto:langho...@neb.com wrote: Peter: I have a working sge setup. Two ideas: 1 - look in the sge logs on the worker node (on my system they are in /var/spool...) No sign of any SGE

[galaxy-dev] GALAXY_LIB path in job scripts

2012-02-02 Thread Shantanu Pavgi
The job scripts generated by galaxy contain following code. I was wondering what's the purpose of if-block after setting 'GALAXY_LIB=None' assignment. {{{ GALAXY_LIB=None if [ $GALAXY_LIB != None ]; then if [ -n $PYTHONPATH ]; then PYTHONPATH=$GALAXY_LIB:$PYTHONPATH else

Re: [galaxy-dev] Running Galaxy on Rocks Cluster

2012-02-02 Thread Shantanu Pavgi
On Feb 1, 2012, at 9:13 PM, Derrick LIN wrote: Hi guys, Is there anyone has actually setup galaxy on a Rocks based cluster? I know that galaxy should be hosted on a submission host so that it can submit jobs to the cluster. Rocks provides preconfigured DRM such as SGE, so I start

[galaxy-dev] database engine pool size

2012-03-26 Thread Shantanu Pavgi
I would like to get some idea about 'database_engine_option_pool_size' and 'database_engine_option_max_overflow' settings. We seem to hit both of these limits whenever a user runs a large workflow with following error: {{{ TimeoutError: QueuePool limit of size 40 overflow 50 reached,

Re: [galaxy-dev] Interested in speaking with other institutions deploying Galaxy locally?

2012-04-27 Thread Shantanu Pavgi
We are interested too. Thanks Ann for taking the initiative. -- Shantanu On Apr 27, 2012, at 3:38 PM, Anne Pajon wrote: I'm interested too. On 27 Apr 2012, at 21:13, Ann Black-Ziegelbein wrote: Thanks everyone! Glad to find some common interest. I will see if I can arrange an

[galaxy-dev] installing tool from ToolShed - Python Error 'too many values to unpack'

2012-04-30 Thread Shantanu Pavgi
I am getting following ValueError: too many values to unpack from Python while trying to install a tool from toll_shed repository. {{{ URL:

Re: [galaxy-dev] installing tool from ToolShed - Python Error 'too many values to unpack'

2012-04-30 Thread Shantanu Pavgi
On Apr 30, 2012, at 2:46 PM, Shantanu Pavgi wrote: I am getting following ValueError: too many values to unpack from Python while trying to install a tool from toll_shed repository. {{{ URL: http://localhost:8080/admin_toolshed/install_repository?tool_shed_url=http%3A%2F

Re: [galaxy-dev] Galaxy server configuration question

2012-05-18 Thread Shantanu Pavgi
On May 18, 2012, at 1:37 AM, Huayan Gao wrote: Dear Nate, Thanks for checking. No, it is still not working. I tried all possible ways to fix it but still not working. Could it possible to send me your httpd.conf file for reference? Best, Huayan Huayan, The permission

[galaxy-dev] starting galaxy server - Paste/egg installation

2012-05-29 Thread Shantanu Pavgi
Hi, Has there been any change in the way galaxy-dist server is started up? I am getting following error after running 'run.sh --daemon' command after galaxy initializes config files from .sample files: {{{ Initializing community_wsgi.ini from community_wsgi.ini.sample Initializing

Re: [galaxy-dev] starting galaxy server - Paste/egg installation

2012-05-29 Thread Shantanu Pavgi
On May 29, 2012, at 5:46 PM, Shantanu Pavgi wrote: Hi, Has there been any change in the way galaxy-dist server is started up? I am getting following error after running 'run.sh --daemon' command after galaxy initializes config files from .sample files: {{{ Initializing

[galaxy-dev] Tool migration error

2012-06-01 Thread Shantanu Pavgi
I am trying to migrate EMBOSS tools from core galaxy code dir to shed_tools directory. I am getting following error with the migration script: {{{ sh ./scripts/migrate_tools/0002_tools.sh Traceback (most recent call last): File ./scripts/migrate_tools/migrate_tools.py, line 21, in module

[galaxy-dev] human genome variation tool error

2012-06-04 Thread Shantanu Pavgi
I am getting following errors in the galaxy log: {{{ Error reading tool from path: human_genome_variation/sift.xml Traceback (most recent call last): File /home/shantanu/galaxy/galaxy-uab/lib/galaxy/tools/__init__.py, line 315, in load_tool_tag_set tool = self.load_tool( os.path.join(

Re: [galaxy-dev] Tool migration error

2012-06-04 Thread Shantanu Pavgi
, 2012, at 5:12 PM, Shantanu Pavgi wrote: I am trying to migrate EMBOSS tools from core galaxy code dir to shed_tools directory. I am getting following error with the migration script: {{{ sh ./scripts/migrate_tools/0002_tools.sh Traceback (most recent call last): File ./scripts

Re: [galaxy-dev] Tool migration error

2012-06-04 Thread Shantanu Pavgi
in your environment since you have the mercurial package installed for your Python 2.6. Your environment probably results in a conflict that is not properly handled by the version_conflict() method in ~/lib/galaxy/eggs/__init__.py. On Jun 4, 2012, at 4:04 PM, Shantanu Pavgi wrote: Just want

[galaxy-dev] import from FTP directories - ownership and copy/move operations

2012-08-24 Thread Shantanu Pavgi
I am seeing some odd behavior with BAM file import from FTP staging directory where ownership of imported file is retained instead of being changed to galaxy system user account. I should note that our site is not using galaxy specific FTP server configuration, but instead we have configured

Re: [galaxy-dev] [galaxy-user] git mirror

2012-09-05 Thread Shantanu Pavgi
On Sep 5, 2012, at 4:55 AM, Luca Pireddu wrote: On 09/05/2012 01:30 AM, Peter Cock wrote: On Tue, Sep 4, 2012 at 5:57 PM, Luca Pireddu pire...@crs4.it wrote: Hello list. A simple question: is there a git mirror of the Galaxy repositories? If not, what do git users here do to work with

Re: [galaxy-dev] How to rotate Galaxy log file

2012-09-25 Thread Shantanu Pavgi
On Sep 25, 2012, at 6:57 AM, Lukasz Lacinski wrote: On 9/24/12 12:40 PM, Nate Coraor wrote: On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote: repost to galaxy-dev On 9/7/12 6:39 PM, Lukasz Lacinski wrote: Dear All, I use an init script that comes with Galaxy in the contrib/

Re: [galaxy-dev] How to rotate Galaxy log file

2012-10-01 Thread Shantanu Pavgi
On Oct 1, 2012, at 2:57 PM, Lance Parsons wrote: I also use a logrotate script: '/etc/logrotate.d/galaxy' /path/to/galaxy/install/*.log { weekly rotate 52 copytruncate } The 'compress' options seems like it might be nice, and I'm not sure of the effect of size 1. I

[galaxy-dev] changing datasets file_path storage location

2012-11-29 Thread Shantanu Pavgi (Campus)
We are planning to change datasets directory location (file_path setting in universe_wsgi.ini) in our Galaxy installation. We will be moving existing datasets to the new directory location and updating XSendfile setting in Apache as well. I was wondering if there are any side effects that we

[galaxy-dev] FTP and data library uploads

2013-01-08 Thread Shantanu Pavgi (Campus)
I am trying to understand how FTP and data library upload options are working in Galaxy. When a non-binary file is uploaded through FTP option, it goes through three move operations: 1. First it is copied to a temporary namespace line-by-line converting newlines 2. Then the temporary file is

Re: [galaxy-dev] FTP and data library uploads

2013-01-14 Thread Shantanu Pavgi (Campus)
On Jan 9, 2013, at 12:41 PM, Nate Coraor wrote: On Jan 8, 2013, at 1:27 PM, Shantanu Pavgi (Campus) wrote: I am trying to understand how FTP and data library upload options are working in Galaxy. When a non-binary file is uploaded through FTP option, it goes through three move operations: 1

[galaxy-dev] download URLs limited to twelve?

2013-04-21 Thread Shantanu Pavgi (Campus)
One of our users is trying to download thousands of files by pasting their URLs in 'URL/Text' box of the upload tool. It seems like Galaxy selects only first 12 URLs and ignores rest of them. The issue can be reproduced on the main public Galaxyhttps://main.g2.bx.psu.edu/ instance as well. I

[galaxy-dev] BWA - failed to resolve dependency error

2013-07-11 Thread Shantanu Pavgi (Campus)
I had migrated BWA tool while at release_2013.02.08 revision. It was working fine, however, it fails to run with following warning message after updating Galaxy to release_2013.06.03. {{{ Building dependency shell command for dependency 'bwa' galaxy.tools WARNING 2013-07-11 17:16:28,429 Failed

Re: [galaxy-dev] BWA - failed to resolve dependency error

2013-07-12 Thread Shantanu Pavgi (Campus)
. It's hard to tell which revision is working as I see the same version tag for both revisions - https://www.dropbox.com/s/7ux0xafm9yb6s6h/bwa.png . Also, Galaxy updates are working fine now. -- Thanks, Shantanu On Jul 11, 2013, at 5:33 PM, Shantanu Pavgi (Campus) wrote: I had migrated BWA

[galaxy-dev] Error resolving Emboss tool dependencies

2013-08-15 Thread Shantanu Pavgi (Campus)
I have migrated Emboss tool from dist to tool-shed using the migration script and later updated it's revision. The tool was installed along with it's dependencies, but it's failing to find them during job run. It's logging following 'Failed to resolve dependency on 'emboss', ignoring' warning

Re: [galaxy-dev] Error resolving Emboss tool dependencies

2013-08-15 Thread Shantanu Pavgi (Campus)
Thanks for the reply Bjoern. It's installed correctly - green box. The emboss entries in tool_dependency and tool_shed_repository look fine as well. If I directly run an emboss command (e.g. antigenic) from CLI then it seems to be working. -- Shantanu On Aug 15, 2013, at 2:53 PM, Björn

Re: [galaxy-dev] Error resolving Emboss tool dependencies

2013-08-15 Thread Shantanu Pavgi (Campus)
There is only one EMBOSS suite in the tool panel. The EMBOSS tool repo is at revision c159a6ded912 and shows version 5.0.0 in the job panel. The tool was migrated using galaxy-dist provided migration script and later upgraded using the admin panel interface. The job fails with 'command not

Re: [galaxy-dev] Error resolving Emboss tool dependencies

2013-08-16 Thread Shantanu Pavgi (Campus)
or re-install emboss using tool-shed? Any help? -- Thanks, Shantanu On Aug 15, 2013, at 3:33 PM, Shantanu Pavgi (Campus) wrote: There is only one EMBOSS suite in the tool panel. The EMBOSS tool repo is at revision c159a6ded912 and shows version 5.0.0 in the job panel. The tool was migrated

Re: [galaxy-dev] Error resolving Emboss tool dependencies

2013-08-19 Thread Shantanu Pavgi (Campus)
. - Proceed with the installation process. --Dave B. On 8/16/13 15:45:11.000, Shantanu Pavgi (Campus) wrote: The installed dependencies is failing as following query in './lib/galaxy/tools/__init__.py' isn't returning any results. {{{ @property def tool_shed_repository( self

[galaxy-dev] ncbi_blast_plus - tool shed updates

2013-08-26 Thread Shantanu Pavgi (Campus)
I am trying to get repository updates for the ncbi_blast_plus tool which is making following request to the toolshedhttp://toolshed.g2.bx.psu.edu/repository/check_for_updates?galaxy_url=http://galaxydev.uabgrid.uab.edu/name=ncbi_blast_plusowner=devteamchangeset_revision=d375502056f1 site:

[galaxy-dev] tool-shed migration - dist version still shown in UI

2013-09-05 Thread Shantanu Pavgi (Campus)
I have migrated few tools from dist to tool-shed and I am seeing two version select options in the UI. Both option contain same version number though. One of them is linking to dist path (underneath tools directory) and other one is using tool-shed path. The dist path isn't in place after the

Re: [galaxy-dev] Error resolving Emboss tool dependencies

2013-09-07 Thread Shantanu Pavgi (Campus)
scripts. Has anyone else seen similar problem before? -- Thanks, Shantanu On Aug 19, 2013, at 2:26 PM, Shantanu Pavgi (Campus) wrote: Thanks for the reply Dave.The reinstallation process worked fine, but it gave couple of errors. Initially it failed with a JavaScript alert like

[galaxy-dev] Tool-shed: Migration scripts vs direct install

2013-09-07 Thread Shantanu Pavgi (Campus)
I was wondering if we can move dist installed tools to tool-shed version by installing them manually using the admin web interface. Do migration scripts provide any functionality that we would lose if we use admin web interface (dist_to_shed column in database and it's significance)? --

[galaxy-dev] Tool-shed - bowtie and tophat dependency

2013-09-10 Thread Shantanu Pavgi (Campus)
We have migrated bowtie tool wrapper from dist to tool-shed using migration script # 7 with install_dependencies option. We removed our locally installed bowtie binaries so that install_dependencies option would work fine. I think an earlier release would skip dependency installation if they