I wonder if someone has a functional bowtie2 wrapper that they can share.
Thanks,
Alex
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On Apr 23, 2012, at 4:55 AM,
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
> remove some data libraries,
> But until now, I
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 inst
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
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 https://bitbucket.org/galaxy/gal
I am getting following "ValueError: too many values to unpack" from Python
while trying to install a tool from toll_shed repository.
{{{
URL:
http://localhost:8080/admin_toolshed/install_repository?tool_shed_url=http%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F&repo_info_dict=9e40c73c79ff0c9ab6620433692
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
Yeah, I was using ['printenv| mail && 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 access samto
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
> serve
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
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 job_working
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
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
> touc
Hi Ann,
Count me in. Great idea!
-Dan
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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 Cock
>> wrote:
>>> On Mon, Feb 13, 2012 at 5:02 PM, Nate Coraor wrote:
On Feb 10, 2012, at 6:47 AM, Peter Cock wrote:
> Hello all,
>>
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 f
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
wrote:
> Hi Ryan, Ann, and everyone else
>
> I second what Nate says (I always do :-). I too like that it is user
>
On Apr 29, 2012, at 1:50 AM, Peter van Heusden wrote:
> Hey there
>
> The instructions on using REMOTE_USER with nginx are still a bit vague
> in the wiki, so let me share how I got this working with nginx's
> http_auth_pam module and our local Kerberos setup. Really simple actually:
>
> First,
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 Coll
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 = `/ho
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
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 = `/
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 w
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 ofte
On Thu, Apr 26, 2012 at 10:40 PM, Edward Kirton 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 the peek issue I
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 ple
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 bro
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