On 04/27/2012 08:45 PM, Ann Black-Ziegelbein wrote:
Hi everyone -
Here at the University of Iowa we are working on deploying Galaxy
locally for campus wide access. I am interested in forming a
community of other institutions trying to deploy Galaxy locally and
mange/operate it on a broad
Hi,
I m running my own Galaxy instance and I would like to do some simple
customization of the web interface such as adding my logos in the header
frame, changing background colors, etc.
I am having a look to static/ folders but I can't see clearly where the
header frame is defined.
Could you
On Thu, Apr 26, 2012 at 10:40 PM, Edward Kirton eskir...@lbl.gov wrote:
your suggestion for blastdbn and blastdbp sounds fine.
it's okay if a few of our users need to edit the metadata of the dbs in
their history. thanks for asking and doing this.
Great.
Perhaps you can throw some light on
Hi Ann
I am definitively interested in any form of collaboration - thank you
very much for bringing up this idea!
However, I also share some of the concerns which have been raised by
others. Even in Europe, we sometimes struggle to coordinate a conference
call with the Americas and very
We get the following error when trying to run MACS in our local installation of
Galaxy:
INFO @ Mon, 30 Apr 2012 09:02:14:
# ARGUMENTS LIST:
# name = MACS_in_Galaxy
# ChIP-seq file = /proj/galaxy/000/dataset_552.dat
# control file = None
# effective genome size = 2.70e+09
# tag size = 36
# band
On Apr 29, 2012, at 9:19 PM, Ciara Ledero wrote:
This is my code for running a samtools command internally, via Galaxy:
open INP, $ARGV[0]
or die Cannot open file: $!;
$file = $ARGV[1];
open OUT, $file
or die Cannot open file: $!;
@out =
On Apr 29, 2012, at 9:26 PM, Ciara Ledero wrote:
Hi all,
Can I ask what this line of code does?
job_wrapper.finish( stdout, stderr )
It's the one from the local.py.
Hi Ciara,
This runs the JobWrapper.finish() method in
galaxy-dist/lib/galaxy/jobs/__init__.py, which performs all the
On Apr 29, 2012, at 9:19 PM, Ciara Ledero wrote:
This is my code for running a samtools command internally, via Galaxy:
open INP, $ARGV[0]
or die Cannot open file: $!;
$file = $ARGV[1];
open OUT, $file
or die Cannot open file: $!;
@out =
Hi,
We have two galaxy instances installed within our institute, and I am very
interested in communicating with other galaxy users. Please count me in.
Zhibin Lu
Bioinformatics Support: Databases Applications
Ontario Institute for Cancer Research
MaRS Centre, South Tower
101
Agreed. User driven is good. Having developer(s) available to answer
questions would be helpful...that's what I was alluding to...
On Sun, Apr 29, 2012 at 10:37 PM, Dave Clements
cleme...@galaxyproject.orgwrote:
Hi Ryan, Ann, and everyone else
I second what Nate says (I always do :-). I
I would like to thank everyone for their responses! I am working on a
few things to hopefully get us going in the right direction:
1) a brief online web survey for everyone to fill out that will help us
gauge the background of those interested in participation and help steer
content for the
On Apr 26, 2012, at 11:03 AM, Hans-Rudolf Hotz wrote:
On 04/26/2012 04:47 PM, Peter Cock wrote:
On Fri, Mar 16, 2012 at 11:00 AM, Peter Cockp.j.a.c...@googlemail.com
wrote:
On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraorn...@bx.psu.edu wrote:
On Feb 10, 2012, at 6:47 AM, Peter Cock
Hi Ann,
Count me in. Great idea!
-Dan
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On Apr 25, 2012, at 9:22 AM, Louise-Amélie Schmitt wrote:
Hi everyone,
I'm (still) having issues with running jobs as the real user on our PBS Pro
cluster. When I try running a job, it ends up in error state and displays
the following error message:
tou!
ch: cannot
touch
On Apr 25, 2012, at 9:39 AM, Louise-Amélie Schmitt wrote:
Hi everyone,
I just wanted to ask how the extra_file_path is handled in case of job
running as the real user since the file_path is only writable by the galaxy
user. Any clue?
Hi L-A,
There are actually two dataset attributes for
On Apr 25, 2012, at 8:25 AM, Louise-Amélie Schmitt wrote:
Hi,
Thanks a lot it actually helped. It is not exactly as straightforward in
drmaa.py but somehow I could manage.
However, it was not the problem. For some reason, the user needs to write
files from the node to
On Apr 24, 2012, at 8:36 PM, Michael Moore wrote:
There is apparently a persistent problem with samtools which normally lives
at /usr/bin/samtools. I encountered a similar problem in Python when
uploading BAM files.
I did not resolve the problem. I hacked for a while on binary.py in a
On Apr 23, 2012, at 10:31 PM, Ciara Ledero wrote:
Hi all,
According to Galaxy, uploading files larger than 2GB will surely fail. For
this reason, uploading via FTP is recommended. Unfortunately, I cannot
download/install an FTP server for Galaxy since I am working on a remote
server. I
Yeah, I was using ['printenv| mail myaddress samtools'] inside the
subprocess.Popen(['samtools'],... in upload.py.
Now right before in upload.py before the subprocess was called, I had
/usr/bin/ in my PATH, but inside the subprocess the story was different. I
just used the symbolic link to
Hi Kiran,
This is a question best directed to the galaxy-dev list, which I have CC'd.
On Apr 23, 2012, at 5:23 AM, Kiran Jaycee wrote:
Dear Nate,
Im deploying Galaxy in the cluster environment with 8 nodes and 96 cores. Im
particularly interested in running NGS tools
like BWA, BOWTIE etc
I am getting following ValueError: too many values to unpack from Python
while trying to install a tool from toll_shed repository.
{{{
URL:
Hi Shantanu,
Your Galaxy instance is not current with the Galaxy central repository - are
you tracking Galaxy dist? In order to use the features that provide
communication between Galaxy and a tool shed, you'll have use the latest code
from Galaxy central - see
Hi Tilahun,
This tool is in the Galaxy Tool Shed
(http://wiki.g2.bx.psu.edu/Tool%20Shed) so to use for now, use with a
local/cloud instance (http://getgalaxy.org) would be the best route:
http://galaxy.psu.edu/search/getgalaxy/
search for cutadapt
I will also forward this to the galaxy-dev
That's right Greg, I was using the latest revision from the galaxy-dist and not
the galaxy-central. It worked fine after using the latest code on from the
galaxy-central. Thanks for the help.
--
Shantanu
On Apr 30, 2012, at 1:54 PM, Greg Von Kuster wrote:
Hi Shantanu,
Your Galaxy
On Apr 23, 2012, at 4:55 AM, liram_va...@agilent.com
liram_va...@agilent.com wrote:
Hello,
I am using Galaxy API for some actions and I must say that this is indeed a
really great feature with a great power.
Anyway, I am trying to write a python script that one of its goals is to
I wonder if someone has a functional bowtie2 wrapper that they can share.
Thanks,
Alex
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