On Tue, Jul 26, 2011 at 8:16 PM, Luobin Yang yangl...@isu.edu wrote:
I benchmarked MrBayes 3.1.2 program on my cluster for two cases:
1. use local /tmp for temporary files
2. use the network shared /home/galaxy/galaxy-dist/database/tmp
MrBayes is about 10 times slower for case 2 than for case
On Wed, Jul 27, 2011 at 9:06 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Tue, Jul 26, 2011 at 8:16 PM, Luobin Yang yangl...@isu.edu wrote:
I benchmarked MrBayes 3.1.2 program on my cluster for two cases:
1. use local /tmp for temporary files
2. use the network shared
Hi Ka Ming,
Thanks for your answer, but I already checked this for my galaxy user (and
for root) on both the galaxy frontend node and on each node all over the
cluster. It's the same path as yours for me.
If you have any other idea It would be great ! :)
Regards,
Remy
2011/7/26 Ka Ming
Hi ALL,
I want to delete some data from history_dataset_association. Will it
effect any other tables.and I want to delete records for last 3 days by
sqlite query manually.How may tables will be effected by this and provide me
tables name .How can i delete the records.
Regards
shashi shekhar
Hi all,
I am working on a way to add/install tools to galaxy in a more automated way.
I need that for the galaxy-taverna interoperability work we are doing
(https://trac.nbic.nl/elabfactory/wiki/eGalaxy). The generator
produces a galaxy tool (.zip or an .xml + .rb) that I want to install
as
Hi Kostas,
I recently talked with Bodo Vossen from MPI who has created this
functionality and made available:
https://bitbucket.org/Bodolski/galaxy-central-adding-tools
He added this functionality to the Admin page of Galaxy which allows to add
tools without restarting the server. Unfortunately
Hi all,
I have added separate job runner in my galaxy instance. So far it was
running successfully from many months.
Now its giving error as below and i am unable to trace it. Please suggest.
Traceback (most recent call last):
File /home/gwadmin/galaxy-central/lib/galaxy/jobs/__init__.py,
Helo Jelle,
I've taken a look at your patches and the code looks good.
However, I'm wondering why you find it necessary to upload image files to
Galaxy. Do tools exist that take image files as input? If the Galaxy
community finds this feature as a good addition to Galaxy, we can probably
On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar meshash...@gmail.com wrote:
Hi all,
I have added separate job runner in my galaxy instance. So far it was
running successfully from many months.
Now its giving error as below and i am unable to trace it. Please suggest.
Traceback (most
On Wed, Jul 27, 2011 at 2:28 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Helo Jelle,
I've taken a look at your patches and the code looks good.
However, I'm wondering why you find it necessary to upload image files to
Galaxy. Do tools exist that take image files as input? If the Galaxy
On Wed, Jul 27, 2011 at 2:14 PM, shashi shekhar meshash...@gmail.com
Hi all,
I have added separate job runner in my galaxy instance. So far it was
running successfully from many months.
Now its giving error as below and i am unable to trace it. Please
suggest.
Traceback (most recent
Hi Peter,
On Jul 27, 2011, at 9:34 AM, Peter Cock wrote:
On Wed, Jul 27, 2011 at 2:28 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Helo Jelle,
I've taken a look at your patches and the code looks good.
However, I'm wondering why you find it necessary to upload image files to
Galaxy. Do tools
Hello all,
I'm working on a local instance of Galaxy at George Mason University. We'd
been looking into integrating Qiime and I've found the toolkit very helpful,
thanks! I did have one question, though: would you mind uploading the
tool_conf file or chunk of text with the qiime functions in it?
Hi,
On Jul 27, 2011, at 3:34 PM, Peter Cock wrote:
On Wed, Jul 27, 2011 at 2:28 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Helo Jelle,
I've taken a look at your patches and the code looks good.
However, I'm wondering why you find it necessary to upload image files to
Galaxy. Do tools exist
Hi Greg,
I do see the concern of uploading data through the api but I don't think
filtering on file types is the right solution. It seems to be an issue with
allowing everyone to register. Wouldn't it be better to at least validate
e-mail addresses of new users on the main instance? This would
On Wed, Jul 27, 2011 at 3:26 PM, Jelle Scholtalbers
j.scholtalb...@gmail.com wrote:
Hi Greg,
I do see the concern of uploading data through the api but I don't think
filtering on file types is the right solution. It seems to be an issue with
allowing everyone to register. Wouldn't it be better
Well I got all the rw permissions changed correctly except for the metadata
files written to the temp directory (new_file_path). I still can't seem to
track down where those are written. Any help would be greatly appreciated.
Best,
Ilya
From: galaxy-dev-boun...@lists.bx.psu.edu
No, data does not require a login to view if the dataset permissions
are set permissively. This allows users to share direct links to
datasets (which is meant to be a good feature ;).
On Jul 27, 2011, at 11:45 AM, Paul Gordon wrote:
On the other hand, isn't user data supposed to require a
Hi.
I'm still searching for a solution to this problem.
Currently we have to implement a tool to read the GTF file selected
via a from_data_table parameter and output a list of feature types.
Secondly we have a second tool that reads this file using a
from_dataset parameter so the user
Hi,
I am trying to create a form where there are two select menus, both using
dynamic_options, where one is the parent menu that is chosen first and based
on the selection(s) there is a refresh and the second menu gets populated
based on the first menu's choice(s).
param name=names type=select
I should preface this by saying we are running a galaxy-dist that is a couple
months old now (we are planning on updating soon), but here is an annoying
issue we are seeing managing data library permissions:
The Roles not associated lists are filtered so it shows only roles associated
with
Answering myself here...
I don't see the error anymore after adding -w n:
[galaxy:tool_runners]
...
mytoolname = drmaa://-w n -l mem_free=1G -l mem_token=1G -l h_vmem=1G/
...
Is this what other Galaxy admins do when using drmaa native options for their
SGE?
Ka Ming
Glen, the behavior you see is undoubtedly the same in the development repo, so
feel free to open a ticket if you want. In any case, this is now on my list,
although several tasks down in it. I should be able to look into it some time
within the next 2 weeks though.
Thanks for pointing it
Jelle,
I've added support for uploading image datatypes based on your patches in
change set 5833:e7214c69ed7d, but with some changes. There is a new
image_util.py file in ~/lib/galaxy/datatypes/util which allows for detecting
image data types without having to create a new Image() class.
I completed the changes to galaxy to submit DRMAA jobs (SGE) as the actual
galaxy user. You can see the code at the fork below. Below is a brief
description of how to turn it which is also described in the
universe_wsgi.ini.sample.
https://icho...@bitbucket.org/ichorny/galaxy-central
#
here's what i have; i started categorizing the tools under labels but hadn't
finished. i'm also working on getting these tools working in galaxy (albeit
slowly as we won't need them until we get a miseq machine in oct), but maybe
we can be in communication with each other and jjohnson.
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