moving to dev..
Hi Jen and Brandon
well, I don't agree (or maybe I misunderstood the question/answer):
we work a lot with compressed data (ie g'zipped fastq files from the
sequencer), and link them as a Galaxy data library. We preselect 'fastq'
as file format.
And then, the first
Hello Susan
The tool is using the identifier in the gene_id attribute from the
reference annotation GTF to name the output.
This link at the tool manual can help:
http://cufflinks.cbcb.umd.edu/howitworks.html#hdif
The iGenomes dataset may be what you are looking for. Shared Data -
Data
Hi all,
I am wondering what is the best way to dynamically update tool data files
without having to restart Galaxy.
The context is as follows. A cron job is regularly creating new blast databases
(or in general: e.g. tool data needed to fill a dropdown list). The same cron
job could be adapted
Hi all,
I'm having issues rsync'ing the reference data of Galaxy
$ rsync -avvvzP rsync://datacache.g2.bx.psu.edu/indexes/phiX .
opening tcp connection to datacache.g2.bx.psu.edu port 873
rsync: failed to connect to datacache.g2.bx.psu.edu (128.118.201.89):
Connection timed out (110)
rsync
A peculiar quirk - I'm configuring a new Galaxy system for production use and
can't get it to recognise my account as an admin, i.e. the admin menu doesn't
appear after I've added my email address to the admin_user line in the universe
file. Of course, I've restarted the instance multiple
On Tue, Aug 21, 2012 at 11:47 AM, Paul-Michael Agapow
paul-michael.aga...@hpa.org.uk wrote:
A peculiar quirk – I’m configuring a new Galaxy system for production use
and can’t get it to recognise my account as an admin, i.e. the admin menu
doesn’t appear after I’ve added my email address to the
Hi Paul
what version of Galaxy are you using? In older versions, it was
important, that there was no blanc space between the email adress'
(although, as far as IO know, this has been fixed).
Regards, Hans
On 08/21/2012 12:47 PM, Paul-Michael Agapow wrote:
A peculiar quirk – I’m configuring
Hi Clare,
If you use the system python, or a build from python.org, you should be fine.
It's Enthought python, which is only built for a single architecture, that's
the reason for having to do so much manual egg building.
--nate
On Aug 19, 2012, at 7:36 AM, Tomithy Too wrote:
Hi Clare,
On Aug 17, 2012, at 6:08 PM, Rodolfo Aramayo wrote:
Hi,
We are in the process of deploying a small Galaxy server here at Texas
AM University
I am a GNU/Linux kind of guy
My IT people want to use an SMB-mounted drive share as a backup destination
I am concerned that this might impact the
On 08/21/2012 04:23 PM, Carlos Borroto wrote:
Interesting...
Hans, could you specify what tools currently available in Galaxy
support gzip'd fastq files?
Any in this list?:
- Bowtie/Tophat
- FastQC
- FASTQ Groomer
I can't tell you, as we don't use any of these tools in Galaxy as
provided
On Tue, Aug 21, 2012 at 5:36 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
Not what I was hoping for.
I usually link without copying into galaxy, so it won't help me. I
also got excited because I thought there was the possibility of
working with fastq files without having to keep
On Tue, Aug 21, 2012 at 4:18 PM, Hans-Rudolf Hotz h...@fmi.ch wrote:
HI
We have been struggling with this problem since we updated to
changeset:6799:40f1816d6857 (March 12, 2012 release). We never had the
time to figure out whether it was a bug or whether we made a mistake.
Unfortunately,
Hello all,
With recent additions to lib/galaxy/util/__init__.py
I have started getting the following in the std out of bowtie and
cufflinks (and probably other tools as well):
ERROR: Unable to read builds file: [Errno 2] No such file or
directory:
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