Greetings,
My name is Ravi Sanka. I have a question regarding Galaxy.
Recently, I had a local installation set up and am now trying to change the
location where the install stores imported and created files.
I opened the config file universe_wsgi.ini and did the following:
- Removed
- Bioinformatics Engineer
J. Craig Venter Institute
301-795-7743
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From: Enis Afgan [mailto:eaf...@emory.edu]
Sent: Wednesday, June 29, 2011 11:32 AM
To: Sanka, Ravi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] changing file storage location
Hi Ravi
Institute
301-795-7743
---
From: Enis Afgan [mailto:eaf...@emory.edu]
Sent: Wednesday, June 29, 2011 12:02 PM
To: Sanka, Ravi
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] changing file storage location
In order for Galaxy to acknowledge
Hello,
We have recently put a local installation of Galaxy on our network and
connected it to a MYSQL database. In order to have more space available for
uploaded and created files, we also changed the values of file_path and
new_file_path in the config file. The file_path field was changed
301-795-7743
---
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Wednesday, August 17, 2011 12:52 PM
To: Sanka, Ravi
Cc: galaxy-dev@lists.bx.psu.edu; Zhang, Haiyan; Singh, Indresh
Subject: Re: [galaxy-dev] Galaxy: self
Greetings,
We are trying to enable job-splitting and merging on our Galaxy blast tools. We
set the following parameters in the universe_wsgi.ini:
use_tasked_jobs = True
local_task_queue_workers = 2
Then we executed the tool NCBI BLAST+ blastn (from devteam's NCBI BLAST+) on
a query set of
--
On 2/25/14 6:21 PM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Feb 25, 2014 at 10:57 PM, Sanka, Ravi rsa...@jcvi.org wrote:
Greetings,
We are trying to enable job-splitting and merging on our Galaxy blast
tools.
We set the following parameters in the universe_wsgi.ini
do you have Ravi (i.e. what hg revision,
find out by running hg summary at the command line)?
Peter
On Wed, Feb 26, 2014 at 2:22 PM, Sanka, Ravi rsa...@jcvi.org wrote:
Hi Peter,
This galaxy instance is connected to our SGE, and all jobs get run on
it.
When we started this particular job
Greetings,
Since yesterday, I have been experiencing an unusual problem with Uploading
files.
Seemingly at random, an uploaded will finish successfully (history item in
green) but no preview is available. Under the title of the item, the keyword
empty is found and preview box says no peek.
Greetings,
I and another individual are attempting to test Galaxy's ability to share data.
We have attempted to share histories and workflows, selecting only each other's
user email address for people to allow sharing with.
All cases have failed, we go to the Shared Data section in both
under Shared Data “Items shared with me” or
similar though.
Thanks for using Galaxy,
Dan
On Mar 5, 2014, at 11:49 AM, Sanka, Ravi
rsa...@jcvi.orgmailto:rsa...@jcvi.org wrote:
Greetings,
I and another individual are attempting to test Galaxy's ability to share data.
We have attempted to share
Greetings,
Despite being an admin, I am unable to remove old datasets from our Galaxy
instance. I am following the procedure detailed in:
https://wiki.galaxyproject.org/Admin/Config/Performance/Purge%20Histories%20and%20Datasets
1. delete_userless_histories.sh
2. purge_histories.sh
3.
p.j.a.c...@googlemail.com wrote:
Have the owners of the old datasets marked them as permanently deleted?
Peter
On Thu, Mar 13, 2014 at 5:35 PM, Sanka, Ravi rsa...@jcvi.org wrote:
Greetings,
Despite being an admin, I am unable to remove old datasets from our
Galaxy
instance. I am following
I have now been able to successfully remove datasets from disk. After deleting
the dataset or history from the front-end interface (as the user), I then run
the cleanup scripts as admin:
python ./scripts/cleanup_datasets/cleanup_datasets.py ./universe_wsgi.ini -d 0
-1 $@
have then caused the
dataset to be deleted and purged, but this may not be the case if there is more
than one instance of the dataset you are trying to purge (either another copy
in a history somewhere, or in a library).
--nate
On Tue, Mar 25, 2014 at 5:12 PM, Sanka, Ravi
rsa
to deleted = true.
--nate
On Fri, Mar 28, 2014 at 1:52 PM, Sanka, Ravi
rsa...@jcvi.orgmailto:rsa...@jcvi.org wrote:
Hi Nate,
I checked the dataset's entry in history_dataset_association, and the value in
field deleted is true.
But if this does not enable the cleanup scripts to remove
Greetings,
I am trying to add a new datatype in our Galaxy install to represent a TAR file
(we are trying to add a custom tool that produces a tarball of its output).
Is it possible to create a datatype of a TAR file (or ZIP, BZIP, GZIP, or any
other type of compressed file)? If so, what
admin_cleanup_datasets.py only works on database times. The rest of
your assumptions are likely correct, although without looking at more details
of the database I can't confirm.
--nate
On Fri, Mar 28, 2014 at 5:12 PM, Sanka, Ravi
rsa...@jcvi.orgmailto:rsa...@jcvi.org wrote:
Hi Nate,
I checked
Greetings,
I am adding a new tool to our in-house Galaxy, which has a few string inputs. I
have made each one a text param in the XML, but want to ensure that the user
does not leave any empty when he executes the tool.
How can I do this? I tried setting the optional field of each text param
, Nicola Soranzo sora...@crs4.it wrote:
Il 2014-04-09 17:00 Sanka, Ravi ha scritto:
Greetings,
I am adding a new tool to our in-house Galaxy, which has a few string
inputs. I have made each one a text param in the XML, but want to
ensure that the user does not leave any empty when he executes
Greetings,
Currently my group has set our universe_wsgi.ini's cleanup_job to onsuccess,
allowing us to troubleshoot failed runs.
However, now failed job folders are beginning to accumulate in the
job_working_directory. Is there a way to clean this up? Preferably, a means
that can be
Greetings,
Just have a conceptual question regarding the dataset object's field update
time. What events trigger this field to get modified? For example, I know that
using admin_cleanup_datasets.py will update the dataset's update time if it
matches the given parameters.
What other triggers
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