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
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
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)?
--
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
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:
.
- 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
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
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
. 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
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
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
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
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
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/
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
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
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(
, 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
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
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
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
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
I am getting following ValueError: too many values to unpack from Python
while trying to install a tool from toll_shed repository.
{{{
URL:
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
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
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,
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
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
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
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
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
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
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
, 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
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
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
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
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
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
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
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
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
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
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
-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
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
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:
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
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
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
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
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
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
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
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
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
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
, 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
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
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
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
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
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
: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
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.
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
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
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
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
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
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.
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
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
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
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
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