[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 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 prevent

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

or details. The -l options (complex configuration options) can be found here: http://linux.die.net/man/5/sge_complex . Hope this helps you. -- Shantanu. From: galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> [galaxy-d

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

quot; was not in the DRMAA URLs. Ka Ming From: galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu> [galaxy-dev-boun...@lists.bx.psu.edu<mailto:galaxy-dev-boun...@lists.bx.psu.edu>] On Behalf Of Shantanu Pavgi [pa...@uab.edu<mailto:pa...

Re: [galaxy-dev] exporting environment variables to SGE in galaxy

On Jul 29, 2011, at 11:28 PM, Chaolin Zhang wrote: > Hi, > > I am setting up SGE in our galaxy mirror. One problem I have is that I > cannot export environment variables of the specific users running the galaxy > service. On command line, I did this by qsub -V script.sh. or add a line > #$

[galaxy-dev] set metadata step

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 by

Re: [galaxy-dev] set metadata step

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 &g

[galaxy-dev] handling galaxy updates

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 ga

Re: [galaxy-dev] handling galaxy updates

st release so we are > generally confident that it will be stable. > > Thanks, > > K > > On Fri, Sep 2, 2011 at 2:22 PM, Shantanu Pavgi wrote: > > Hi, > > I am curious to know which revision of galaxy code gets deployed in the main > ( http://main.g2.bx.psu.edu/ )

[galaxy-dev] displaying dataset paths in the UI

I am trying to display dataset paths in the UI when user clicks on the 'view details' icon in the history panel. I was able to display it by adding 'hda.file_name' field in the show_params.mako template file and it seems to be working. Following is a diff for it: {{{ diff --git a/templates/sh

[galaxy-dev] galaxy citation_url setting

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

[galaxy-dev] getting job's index position in the history from database

I am trying to get job's index in the history panel using SQL query (index number shown in the history when a job is submitted). I am unable to locate the necessary table-column for it. Any pointers in which table-column it is located will be really helpful. -- Thanks, Shantanu.

Re: [galaxy-dev] galaxy citation_url setting

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 >> s

Re: [galaxy-dev] galaxy citation_url setting

On Nov 3, 2011, at 8:36 AM, Nate Coraor wrote: Shantanu Pavgi wrote: 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 G

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

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 Tr

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

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] [galaxy-user] enabling regular users to upload large data volumes to a local Galaxy server

Moving this to galaxy-dev list. Just wanted to share my notes on both upload options. Although both ftp_upload_dir and 'user library import' options help in getting data into the galaxy there are some differences in both options: 1. ftp upload option deletes original copies of files after ga

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

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 whe

Re: [galaxy-dev] Galaxy Hang after DrmCommunicationException

18, 2012 at 1:07 PM, Edward Kirton mailto:eskir...@lbl.gov>> wrote: excellent, thanks for the correction! On Wed, Jan 18, 2012 at 8:59 AM, Shantanu Pavgi mailto:pa...@uab.edu>> wrote: Ed, I think you may want to add job with DrmCommunicationException error back into t

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

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 G

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

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 "/projects/galaxy/galaxy-165/lib/galaxy/j

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

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 Pyth

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

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 galaxy.j

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

On Feb 2, 2012, at 8:21 AM, Peter Cock wrote: On Thu, Feb 2, 2012 at 1:54 PM, Langhorst, Brad mailto: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 logs there - cou

[galaxy-dev] GALAXY_LIB path in job scripts

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"

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

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 st

[galaxy-dev] database engine pool size

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, connecti

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

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 a

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

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%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=9e40c73c79ff0c9ab6620433692

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

axy/galaxy-central > > Greg Von Kuster > > > 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. >>

[galaxy-dev] managing external dependency eggs

Hi, At the risk of exposing of my Python ignorance, here is a doubt regarding galaxy deployment. The galaxy application manages external dependency eggs through it's custom ini specification file and eggs installation scripts. I was wondering if this could be managed through pip using a requir

Re: [galaxy-dev] Galaxy server configuration question

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 permis

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

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 datatypes_c

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

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 fil

[galaxy-dev] Tool migration error

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 app

[galaxy-dev] human genome variation tool error

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( to

Re: [galaxy-dev] Tool migration error

f the following: > > hg status > > And finally, the results of the following: > > hg diff > > Thanks! > > Greg Von Kuster > > > On Jun 1, 2012, at 5:12 PM, Shantanu Pavgi wrote: > >> >> I am trying to migrate EMBOSS tools from core ga

Re: [galaxy-dev] Tool migration error

ng 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 wa

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

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

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 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 the

[galaxy-dev] Picard Reorder tool's reference genome box

Our local Galaxy instance doesn't have an auto-fill option working with Picard-Reorder-SAM/BAM tool's 'select a reference genome' box. We do have a 'tool-data/picard_index.loc' file with genome build-ids for picard tools. Do we need to configure anything else to get reference genome field worki

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

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 Gala

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

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 siz

[galaxy-dev] shared TEMP directory location

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 r

[galaxy-dev] galaxy with SGE cluster

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 jobs

Re: [galaxy-dev] galaxy with SGE cluster

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 g

Re: [galaxy-dev] galaxy with SGE cluster

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 g

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

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 properly.

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

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&

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

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

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 l

[galaxy-dev] cluster files directory configuration

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. __

[galaxy-dev] multiple cluster job runners?

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 to define multiple cluster job runner configurations for each tool? In the universe

[galaxy-dev] debugging tools - print environment variables

Hi, I am writing a simple tool (env command!) for debugging environment/path related issues. Attached below is the xml config file. I noticed that inputs tag is necessary for getting 'execute' button. Is there any way to execute commands that have no input file/data? Also, can we have a simila

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

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 r

Re: [galaxy-dev] cluster files directory configuration

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 some

Re: [galaxy-dev] cluster files directory configuration

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 a

[galaxy-dev] listing universe_wsgi.ini configuration

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

I looked at the Galaxy deployment presentation from the Galaxy Community Conference ( http://wiki.g2.bx.psu.edu/GCC2011?action=AttachFile&do=view&target=GalaxyDeploymentandAPI.pdf ) and it was really helpful. I am wondering if you could share any details or best practices for maintaing the g

[galaxy-dev] separate galaxy tools directory

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 s

Re: [galaxy-dev] listing universe_wsgi.ini configuration

On Jun 1, 2011, at 11:30 AM, Nate Coraor wrote: > Shantanu Pavgi wrote: >> >> 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 >>

Re: [galaxy-dev] galaxy with SGE cluster

. > > On Mon, May 16, 2011 at 10:44 AM, Shantanu Pavgi 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 underst

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

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 /dat

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

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 gal

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

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 l

[galaxy-dev] user_library_import_dir configuration

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 permissi

[galaxy-dev] number of dataset files within 000

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 i

Re: [galaxy-dev] user_library_import_dir configuration

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 figu

Re: [galaxy-dev] user_library_import_dir configuration

To use the > feature, select 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

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

> > Regards, Hans > > > On 6/23/11 5:44 AM, "Shantanu Pavgi" wrote: > >> Hi, >> >> The galaxy dataset files (file_path) are arranged within a subdirectory '000' >> (database/files/000). Will galaxy create a new subdirectory f

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

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 c

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

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//h/ - /static/ (css and javascript) Do I need to exclude any other URLs so that

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

Thanks for pointing it out Nate. I had missed that in the docs. -- Shantanu. On Jun 30, 2011, at 8:51 AM, Nate Coraor wrote: > Shantanu Pavgi wrote: >> >> On Jun 28, 2011, at 2:15 PM, Nate Coraor wrote: >> >> Shantanu Pavgi wrote: >> >> I did

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

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 wrote:

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

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] empty status for non-empty datasets

or histories? > > -K > > On Mon, Jul 11, 2011 at 3:07 PM, Shantanu Pavgi wrote: >> >> Hi, >> >> In our local galaxy install (currently revision 50e249442c5a) we are seeing >> few output datasets as 'empty' in the galaxy web interface. The actual f

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

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 loa

[galaxy-dev] TEMP variable in cluster install

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

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

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

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

arish 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 mailto:pa...@uab.edu>> wrote: We experienced an issue where some of the galaxy jobs were sitting in the 'n

[galaxy-dev] Error resolving Emboss tool dependencies

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

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 Grünin

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

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 foun

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

t sure how this mismatch happened though. How do I fix this issue now? Should I update installed_changeset_revision entry in the database or migrated tool XML file or re-install emboss using tool-shed? Any help? -- Thanks, Shantanu On Aug 15, 2013, at 3:33 PM, Shantanu Pavgi (Campus) wrot

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

ories page to find the uninstalled repository. > - Select "activate or reinstall" from the dropdown. > - Proceed with the installation process. > > > --Dave B. > > On 8/16/13 15:45:11.000, Shantanu Pavgi (Campus) wrote: >> >> The installed depend

[galaxy-dev] ncbi_blast_plus - tool shed updates

I am trying to get repository updates for the ncbi_blast_plus tool which is making following request to the toolshed site:

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

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 m

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

-shed migration 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 faile

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

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)? -- Thanks

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

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 we

[galaxy-dev] changing datasets file_path storage location

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 s

[galaxy-dev] counting number of dataset files on the file system

I am recovering lost dataset files from the file system and I need to verify number of recovered files with corresponding dataset records count in the database. Should number of dataset files on the file system match count obtained using following query? $ select count(*) from dataset where d

[galaxy-dev] FTP and data library uploads

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 m

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

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] galaxy from subdirectory - new history with a page refresh

I have setup a galaxy instance from the root host (without sub-directory) and it's working fine. I have setup another galaxy instance on the same system, but it's being served from a sub-directory using the same front-end Apache. The sub-directory instance creates a new history on every visit o

[galaxy-dev] download URLs limited to twelve?

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 Galaxy instance as well. I

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

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

[galaxy-dev] uninstalling migrated tool

It seems like if we uninstall a migrated tool then it's entry in the migrated_tools_conf.xml file doesn't get deleted. Does it need to be removed manually? -- Thanks, Shantanu ___ Please keep all replies on the list by using "reply all" in

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

. 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 m