On Mon, Feb 21, 2011 at 9:48 AM, Peter pe...@maubp.freeserve.co.uk wrote:
On Fri, Feb 18, 2011 at 3:13 PM, Kanwei Li kan...@gmail.com wrote:
All:
I retested under IE7 and found the bugs you were mentioning. This has all
been fixed on trunk by using a newer local storage library. The only IE7
Ryan Golhar wrote:
I've configured my local instance of galaxy to run with drmaa.
Unfortunately, there is a problem that after some time, galaxy loses
its ability to talk to Torque, hence Galaxy thinks long-running jobs
have failed and its unable to submit new jobs.
I have no idea how this
Steve Taylor wrote:
I think so. Just to double check is there a definitive way I can tell? In
./tools/data_source/upload.xml
param name=ftp_files type=ftpfile label=Files uploaded via FTP/
So I got this to work by hacking basic.py.
def visible( self ):
Hi All,
My group is trying to create some custom sections in the Tools pane,
and have run into an issue. We have a custom section, within which
there are three different labels and several tools under each label. We
are trying list the same tool under two different labels within the same
Florent Angly wrote:
I understand that it is best to flow with the logic of the
underlying OS and not too make too many platform-dependent
assumptions about what files should be read.
Perhaps, it seems like the best way to go would be to have a setting
in universe_wsgi.ini to specify a file
Hi
In a bash shell, I define the path (needed both by Galaxy to find the
right version of python and by tools that run on a cluster to find the
executables) and some other global variables on the command line. The
cluster jobs (LSF) inherit all these values. This is my line
Hi there, is there a way to undelete a folder within a data library? I've
deleted one (with some files) by mistake :-(
d
/*
Davide Cittaro, PhD
Cogentech - Consortium for Genomic Technologies
via adamello, 16
20139 Milano
Italy
tel.: +39(02)574303007
e-mail: davide.citt...@ifom-ieo-campus.it
Hi Davide,
Yes, in the Library actions popup menu you should see an option labeled Show
deleted items. If you select that, it will display the folder you deleted,
and you'll be able to undelete it via the Undelete option in it's own pop-up
menu.
Greg
On Feb 21, 2011, at 10:32 AM, Davide
Hi Greg
On Feb 21, 2011, at 4:36 PM, Greg Von Kuster wrote:
Hi Davide,
Yes, in the Library actions popup menu you should see an option labeled
Show deleted items. If you select that, it will display the folder you
deleted, and you'll be able to undelete it via the Undelete option in it's
What version of Galaxy are you running. I believe this issue was corrected a
while back, so can you update to the latest version?
On Feb 21, 2011, at 10:41 AM, Davide Cittaro wrote:
Hi Greg
On Feb 21, 2011, at 4:36 PM, Greg Von Kuster wrote:
Hi Davide,
Yes, in the Library actions popup
On 02/21/2011 04:05 PM, Branden Timm wrote:
Hi All,
My group is trying to create some custom sections in the Tools pane, and
have run into an issue. We have a custom section, within which there are
three different labels and several tools under each label. We are trying
list the same tool
On Feb 21, 2011, at 4:52 PM, Greg Von Kuster wrote:
What version of Galaxy are you running. I believe this issue was corrected a
while back, so can you update to the latest version?
I've pulled r ca0c4ad2bb39 this morning...
d
/*
Davide Cittaro, PhD
Cogentech - Consortium for Genomic
George Marselis, systems administrator
Building #2, Level 4, room 4327
Computational Bioscience Research Center, KAUST
Land: +966-2-808-2944, Mobile: +966-56-321-7714, Skype: project2501a
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On Mon, Feb 21, 2011 at 2:43 PM, Nate Coraor n...@bx.psu.edu wrote:
Revival! (This thread was sitting flagged in my mailbox since
November)
I guess I should try and file issues for things which don't get a prompt
resolution on the mailing list, but its good to know it hadn't been
forgotten.
Marina Gourtovaia wrote:
Hi
In a bash shell, I define the path (needed both by Galaxy to find
the right version of python and by tools that run on a cluster to
find the executables) and some other global variables on the
command line. The cluster jobs (LSF) inherit all these values. This
Peter wrote:
On Mon, Feb 21, 2011 at 2:43 PM, Nate Coraor n...@bx.psu.edu wrote:
Revival! (This thread was sitting flagged in my mailbox since
November)
I guess I should try and file issues for things which don't get a prompt
resolution on the mailing list, but its good to know it hadn't
On 21/02/2011 16:20, Nate Coraor wrote:
Marina Gourtovaia wrote:
Hi
In a bash shell, I define the path (needed both by Galaxy to find
the right version of python and by tools that run on a cluster to
find the executables) and some other global variables on the
command line. The cluster jobs
On Feb 21, 2011, at 4:55 PM, Davide Cittaro wrote:
On Feb 21, 2011, at 4:52 PM, Greg Von Kuster wrote:
What version of Galaxy are you running. I believe this issue was corrected
a while back, so can you update to the latest version?
I've pulled r ca0c4ad2bb39 this morning...
It
Nick Schurch wrote:
Hi all,
I've recently encountered a few problems when trying to use Galaxy which are
really driving me away from using it as a bioinformatics platform for NGS. I
was wonderinf if there are any simple solutions that I've missed...
Hi Nick,
We've had some internal
Branden,
we have also customised the tol menu and added a university specific section on
top just beneath Get data.
We have also listed tools twice for convenience. I do not see the need t list a
tool twice in the same expanding section. But in another section it should work
flawlessly.
Having
Hi Nick,
If you're running your own local instance, then nothing is impossible - it's
just a bit ugly...
Nate Coraor wrote, On 02/21/2011 12:36 PM:
[...] many tools that operate on these files produces multiple,
uncompressed large files which quickly eat up the disk allocation.
[...] With no
Hello Davide,
Sorry about the delay - I'm at a conference and can only connect while
in-between sessions. This problem should be fixed in change set
5099:ca53c664778e, whicl should be available in the distribution within the
next several weeks. If you need it sooner, you can pull from our
Hi Peter,
The changes are on tip, which aren't in galaxy-dist or on main yet. I will
look into the other issues when I get access to my IE7 VM tomorrow.
Thanks!
K
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I am trying to use galaxy for the first time and am running into some early
problems. While trying to upload my file which is basically an fq containing
illumina short reads, the file won't upload. When I try the fastq extension of
the same file, it does but then the file isn't recognized by
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