eventually we can get back to tool shed deps.
DT
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
Lyda Hill Department of Bioinformatics
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833
From: Nicola Soranzo [mailto:nicola.sora...@gmail.com] On Behalf Of Nicola
for reproducibility, rebuilding
them against updated (but compatible) libraries when there's a security issue,
perhaps?
Glad to know that my idea of the workflow isn't totally wrong though.
Thanks,
DT
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
Lyda Hill Department of Bioinformatics
to install that package.
Thanks,
DT
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
Lyda Hill Department of Bioinformatics
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833
From: Bjoern Gruening [mailto:bjoern.gruen...@gmail.com]
Sent: Wednesday, April 13, 2016 8:46 AM
'requirements' in its XML file and shows 'Missing repository/tool dependencies'
in the Admin. Has anyone had any experience of dealing with this kind of
situation?
Many thanks!
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
Lyda Hill Department of Bioinformatics
UT Southwestern Medical
Hi John,
No need to apologise!
This isn't really a priority for me as I can fix it with ACLs. Using a lot of
those lately - so another few won't hurt :-)
DT
-Original Message-
From: John Chilton [mailto:jmchil...@gmail.com]
Sent: Tuesday, November 17, 2015 2:10 PM
To: David Trudgian
what policies will
enable access:
cat /var/log/audit/audit.log | audit2allow -v
Then you can use setsebool (temporary) and setsebool -P (permanent) to enable.
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833
From
into Galaxy at some point. Not sure whether this has/is happening, but
it’d make these situations easier:
https://trello.com/c/4YwVZBtq/1865-embedded-pulsar-job-runner
DT
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833
https://wiki.galaxyproject.org/ToolShedApi
From: galaxy-dev [mailto:galaxy-dev-boun...@lists.galaxyproject.org] On Behalf
Of CHELSEA JU
Sent: Thursday, July 30, 2015 1:32 PM
To: galaxy-dev
Subject: [galaxy-dev] Galaxy Resource
Dear Galaxy Developer,
As one of our data mining projects, we are
. Having write
open to anyone when a tool is installed is then pretty nasty as in theory
someone could maliciously modify something.
Wondering if I'm missing some setting in Galaxy somewhere that would result in
775 all the time for newly installed tools and their deps?
--
David Trudgian Ph.D
/__init.py__ checks used, and when is it framework/webapp.py? I
couldn't work that out by looking.
Thanks,
DT
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833
UT Southwestern
Medical Center
,
--
David Trudgian Ph.D.
Computational Scientist, BioHPC
UT Southwestern Medical Center
Dallas, TX 75390-9039
Tel: (214) 648-4833
Please contact biohpc-help@utsouthwestern with general BioHPC inquries.
UT Southwestern
Medical Center
The future of medicine
?
Hi Carlos,
We're running Galaxy on CentOS 6.6, so that in itself shouldn't be a problem.
Most of the effort was sorting out shared storage with the cluster, which in
our case is managed with SGE (fairly commonly used with Galaxy).
In reply to your thread last month David Trudgian said he
. Some notes on that in a GitHub issue here:
https://github.com/galaxyproject/pulsar/issues/65
Cheers,
DT
-Original Message-
From: Carlos Lijeron [mailto:clije...@hunter.cuny.edu]
Sent: Tuesday, May 05, 2015 11:18 AM
To: David Trudgian; Peter Cock
Cc: galaxy-dev@lists.galaxyproject.org
Carlo,
We have Bright Cluster Manager in use on our cluster for node provisioning etc.
but the actual job scheduler in use in our case is SLURM, which we use directly.
Are you using one of the integrated workload managers such as SLURM / SGE /
TORQUE directly, or indirectly via cmsub?
I guess
InnoDB can be set as default:
http://serverfault.com/questions/93559/how-do-i-set-the-default-table-type-as-innodb-in-my-cnf
It should also be the default storage engine if you are using MySQL 5.5 or
higher:
http://dev.mysql.com/doc/refman/5.6/en/innodb-default-se.html
Which version of MySQL
[mailto:jmchil...@gmail.com]
Sent: Wednesday, April 08, 2015 8:12 AM
To: David Trudgian
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] DRMAA chmod to world-writable if to user chown fails
should not be default?
Yeah - I am with you on this. It is definitely less than ideal that any
Dannon, thanks,
This is on dev at commit 43a94ada37124dde5759b0c94bf25a97ff4da17a
Am running nginx 1.6.2 on RedHat EL 6.6
Python 2.7.8 with uWSGI 2.0.10
I can send my galaxy.ini and nginx.conf to you separately off list.
DT
--
David Trudgian Ph.D.,
Computational Scientist
UT Southwestern
?
Thanks,
--
David Trudgian Ph.D.,
Computational Scientist
UT Southwestern BioHPC
--
David Trudgian Ph.D.,
Computational Scientist
UT Southwestern BioHPC
UT Southwestern
Medical Center
The future of medicine, today
.
Thanks again,
DT
-Original Message-
From: Dave Bouvier [mailto:d...@bx.psu.edu]
Sent: Monday, March 30, 2015 8:03 AM
To: David Trudgian; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Safe / possible to sync toolshed tools and deps from
another machine?
Dave
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