Hi Nate,
I have used the local.py logic for submission of my jobs, for a grid based
architecture. But local.py does not have the recover() function so I was
trying to use the concept of recover() from other modules. My job submission
also uses the drmaa api's, so I thought of using the drmaa.py
Hi Kanwei,
I think we'll get more feedback once it when it is added to Galaxy. I
have run small tests (included in the functional tests) and real large
datasets and have had no issues with the scripts and wrappers.
Regards,
Florent
On 27/05/11 18:49, Kanwei Li wrote:
Has anyone on the list
On Tue, May 31, 2011 at 11:26 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi all,
As I mentioned on Twitter, at the end of last week I wrapped Blast2GO
for Galaxy, using the b2g4pipe program (Blast2GO for pipelines). See
http://blast2go.org/
Currently current code is on bitbucket under
Hi all,
I have a couple of minor suggestions for improving the website
http://galaxy.psu.edu/gcc2011/Home.html
First, please fill in a meaningful HTML titles since that will be used
as the default caption in a bookmark, tab or window title.
Second, please add a link to the presentation slides
Hi Harendra
I am not aware of anybody who made this kind of transition without
running into all kind of problems. I suggest the following workaround:
- set up a new, independent Galaxy server using PostgreSQL.
- transfer the histories you want to keep to the new server using the
'Export to
Matthew Conte wrote:
Hi Nate,
I was able to finally track down the login issue. It had to do with the
following setting in my universe_wsgi.ini:
*
*
*cookie_path = /galaxy*
Removing this out fixed the problem and I should be fine leaving it out out
since I don't need to run more than
Harendra chawla wrote:
Hi Nate,
I have used the local.py logic for submission of my jobs, for a grid based
architecture. But local.py does not have the recover() function so I was
trying to use the concept of recover() from other modules. My job submission
also uses the drmaa api's, so I
On Wed, Oct 6, 2010 at 11:16 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Tue, Sep 28, 2010 at 12:04 PM, Peter pe...@maubp.freeserve.co.uk wrote:
Hi all,
I'm wondering if there is any established way to share parameter
definitions between tool wrapper XML files?
For example, I am
Louise-Amélie Schmitt wrote:
Hello everyone
I have an issue when trying to import new datasets or when putting a
dataset into a history. I saw Edward Kirton had the same problem but he
got no answer:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-May/002732.html
Here is the error
Lewis, Brian Andrew wrote:
After following the instructions in the wiki for setting up scaling/load
balancing, I was testing out submitting a job and got this error when trying
to pull data from USCS Main:
Traceback (most recent call last):
File
Patch Imported in 5618:b9fdb88da530.
Thanks!
Dan
On Mar 16, 2011, at 11:50 AM, Jim Johnson wrote:
Request is issue#494
https://bitbucket.org/galaxy/galaxy-central/issue/494/support-sub-dirs-in-extra_files_path-patch
I'm finding that some qiime metagenomics applications build HTML
John Eppley wrote:
I had an error upgrading my galaxy instance. I got the following exception
while migrating the db (during step 64-65):
sqlalchemy.exc.ProgrammingError: (ProgrammingError) (1064, You have an error
in your SQL syntax; check the manual that corresponds to your MySQL
On Thu, 2 Jun 2011 11:48:55 -0400, Nate Coraor n...@bx.psu.edu wrote:
Greg Von Kuster wrote:
Hello Louise,
I've CC'd Nate on this as he may be able to help - although no
guarantees. I'm not expert enough in this area to know where to look
for
the cause. Perhaps someone in the community
Hi all,
Something I've not needed to do until now is define a new file format
in Galaxy. I understand the basic principle and defining a subclass in
Python... however, how does this work with new tools on the Tool Shed?
In particular, if an output format is likely to be used by more than
one
Lewis, Brian Andrew wrote:
Nate -
I checked and I still have a copy of universe_wsgi.ini within my galaxy-dist
directory. I did also make a change in
/usr/local/galaxy-dist/lib/galaxy/eggs/__init__.py according to the post
here:
Okay, yeah, when I changed it back to the original code it worked.
~ Brian
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Thursday, June 02, 2011 12:47 PM
To: Lewis, Brian Andrew
Cc: galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Error: unable to read Galaxy
For some odd reason, when I try to import data using the URL
http://localhost:8081 or http://localhost:8081/galaxy none of my jobs will even
show up. However if I go to http://127.0.0.1 or http://127.0.0.1/galaxy the
jobs run fine. Here's a snip from my httpd.conf file:
RewriteEngine on
On Jun 2, 2011, at 1:29 PM, Nate Coraor wrote:
Peter Cock wrote:
Hi all,
Something I've not needed to do until now is define a new file format
in Galaxy. I understand the basic principle and defining a subclass in
Python... however, how does this work with new tools on the Tool Shed?
In
Hi Marco,
Thanks for all of the details, they make a big difference when
troubleshooting. Sorry for the delay in response.
Can you ensure that you don't have any of the pbs_* options set in
universe_wsgi.ini? I noticed that there are stagein/stageouts
set on the job.
You may also need to set
(moved to galaxy-dev)
Nate Coraor wrote, On 06/02/2011 01:31 PM:
Peter Cock wrote:
On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor n...@bx.psu.edu wrote:
pbs.py then knows to translate 'resource type=cores8/resource' to
'-l nodes=1:ppn=8'.
Your tool can access that value a bunch, like
scott.cou...@monash.edu wrote:
Hi,
I'm a newbie when it comes to this kind of thing, so I was wondering whether
you can tell me the most appropriate place to ask questions about making some
modifications to your nglims extension for galaxy? Should they be posted to
the normal galaxy
Louise-Amélie Schmitt wrote:
On Thu, 2 Jun 2011 11:48:55 -0400, Nate Coraor n...@bx.psu.edu wrote:
Greg Von Kuster wrote:
Hello Louise,
I've CC'd Nate on this as he may be able to help - although no
guarantees. I'm not expert enough in this area to know where to look
for
the cause.
Just FYI,
With the recent version of cufflinks (at least 1.0.2), the developers added a
'feature' of automatic version check.
While the idea is nice, the implications are not:
cufflinks,cuffcompare and cuffdiff will connect to host
cufflinks.cbcb.umd.edu every time you run them.
I'm sure the
If you haven't already registered for BOSC, now is your chance--after
June 3, prices will go up!
Registration for BOSC is through the ISMB main conference website:
http://www.iscb.org/ismbeccb2011-registration#sigs . Since BOSC is a
two-day SIG, the price is 2x the one-day SIG price listed on
shashi shekhar wrote:
Hi All,
I am using standalone system for galaxy and am doing some modification
in galaxy .i need the all output file names in local.py .How can i get all
the output file names in local.py file.
From the job wrapper object in local.py,
Lewis, Brian Andrew wrote:
For some odd reason, when I try to import data using the URL
http://localhost:8081 or http://localhost:8081/galaxy none of my jobs will
even show up. However if I go to http://127.0.0.1 or http://127.0.0.1/galaxy
the jobs run fine. Here's a snip from my
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