Hi,
Thanks for providing the indexes via rsync::
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
We've, noticed that despite soft links pointing to it, there are no .fa
files for example in hg19/seq/
However there are 2bit files.
Would you guys recommend we convert them from 2bit to fasta?
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/ subdirectory
to start Galaxy. The log file
--log-file
Hi,
I have a question regarding the param tag. I would like to pass on the
user email to a external python script. I tried to use it like this:
param name=email type=hidden value=$__user_email__ /
param name=experiment type=select label=Experiment help=select
Experiment
Kevin,
Correct, converting from 2bit to fasta shouldn't cause any problems.
--Dave B.
On 9/25/12 03:20:14.000, Kevin Y wrote:
Hi,
Thanks for providing the indexes via rsync::
http://wiki.g2.bx.psu.edu/Admin/Data%20Integration
We've, noticed that despite soft links pointing to it, there
Liisa,
My best guess is that this is fixed in the most recent distribution. Can you
please update your Galaxy instance to the Sept. 20 distribution and see if that
fixes the problem. If not, please let us know.
Thanks,
J.
On Sep 24, 2012, at 11:57 AM, Liisa Koski wrote:
Hello,
After
I'm sorry I wasn't more clear. I do believe that those links explain
the behavior I am seeing. However, let me try to describe it a different
way. It seems that there will, at most, be one installable revision of
a given version of a tool. Here I use revision to denote a mercurial
revision
Hi Lance,
I need to figure out precisely what steps you are taking to produce this
behavior, as I have not been able to do so. Please see my inline comments, and
let me know more information about each step you are taking to produce this
behavior.
On Sep 25, 2012, at 10:24 AM, Lance Parsons
Galaxy should probably be shutdown with --stop-daemon (depending on
how you are running it).
In the future we can look at making the logging handle the HUP signal.
-- jt
On Tue, Sep 25, 2012 at 11:40 AM, Scott McManus scottmcma...@gatech.edu wrote:
Lukasz-
How are you stopping the process?
I use start-stop-daemon that sends SIGTERM (which is a default signal sent to a
service that is being asked to stop) to Galaxy to let Galaxy store all
information in a database, close files, etc., and terminate itself. When Galaxy
process is terminated, both shell and python scripts (Galaxy
On Sep 25, 2012, at 6:57 AM, Lukasz Lacinski wrote:
On 9/24/12 12:40 PM, Nate Coraor wrote:
On Sep 19, 2012, at 9:50 AM, Jennifer Jackson wrote:
repost to galaxy-dev
On 9/7/12 6:39 PM, Lukasz Lacinski wrote:
Dear All,
I use an init script that comes with Galaxy in the contrib/
On Sep 25, 2012, at 12:35 PM, Lukasz Lacinski wrote:
I use start-stop-daemon that sends SIGTERM (which is a default signal sent to
a service that is being asked to stop) to Galaxy to let Galaxy store all
information in a database, close files, etc., and terminate itself. When
Galaxy
Hello,
I followed the instructions below to manually install the blast_datatypes:
Manual Installation
===
Normally you would install this via the Galaxy ToolShed, which would move
the provided blast.py file into a suitable location and process the
datatypes_conf.xml entry to be
Sorry, forgot to CC the list.
-- Forwarded message --
From: *Peter Cock*
Date: Tuesday, September 25, 2012
Subject: [galaxy-dev] problem installing blast_datatypes manually
To: Liisa Koski liisa.ko...@basf.com
On Tuesday, September 25, 2012, Liisa Koski wrote:
Hello,
I
Kourosh,
My first guess would be a misconfiguration of the security groups or the like
-- are you launching the instance using the regular AWS console?
If so, it might be worth it to try using Galaxy's Cloud Launch at
https://main.g2.bx.psu.edu/cloudlaunch which will help you format any
I just recently updated to the latest version of galaxy-central, and when
I started galaxy, the tools were not listed on the left panel. I could
rerun old jobs from my history, however. Why are the tools not listed?
David Hoover
Helix Systems Staff
Hi all,
I've been poking around with the Admin Manage jobs functions - Stop Jobs
does not seem to be working.
I looked at the code and added some debug prints. When I submit a Stop Jobs
in the manager, I don't think the job is making its way to the
stop_jobs_queue in the handler Are others
I recently installed Galaxy on Ubuntu 12.04.1 LTS. Bowtie, SAMtools, and
Tophat all run fine with my small subset of paired-end Illumina reads.
Unfortunately, it seems to only partially work when I run Cufflinks v2.0.2.
Three entires in my history appear (gene expression, transcript
I recently installed Galaxy on Ubuntu 12.04.1 LTS. Bowtie, SAMtools, and
Tophat all run fine with my small subset of paired-end Illumina reads.
Unfortunately, it seems to only partially work when I run Cufflinks v2.0.2.
Three entires in my history appear (gene expression, transcript
Try updating again and see if that fixes the issue. We've been refactoring
JavaScript dependencies, which may have caused some temporary problems.
In general, if you're going to use/track galaxy-central, you'll need to be both
persistent and patient because, as a development repository, things
The Cufflinks wrapper doesn't support v2.0 or greater yet. Please use v1.3.0
for now.
We expect to update the Cufflinks wrapper to support v2.0+ in the next couple
weeks.
Best,
J.
On Sep 25, 2012, at 5:34 PM, wormbuff wrote:
I recently installed Galaxy on Ubuntu 12.04.1 LTS. Bowtie,
Please help!
I'm new to sys admin and I've really messed up.
On our server we have a development instance and a production instance of
Galaxy. Both run under the same user (galaxy) and each has its own
postgresql table (galaxydb_dev and galaxydb_prod).
I was testing the ability to backup and
Thanks Dave,
A question before we go ahead, why are they missing in the first place?
Does the main galaxy not actually need them? are the tools moving away from
fa?
Cheers,
Kevin.
On Tue, Sep 25, 2012 at 11:12 PM, Dave Bouvier d...@bx.psu.edu wrote:
Kevin,
Correct, converting from 2bit to
Hi,
I am working on a wrapper that has multiple combinations of switches that lead
to the creation of the output files. For instance, one of the files can be
generated by conditions A and B and also by A and C. FIrst, I tried the xml
and and or elements, but that didn't work. Next, I tried
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