(Sachit, please don't cross-post to the dev and user lists?)
There's a beta version of an edgeR/deseq/voom wrapper and a companion htseq
based count matrix maker in the test toolshed statistics section owned by
me - fubar. Definitely not quite ready for production but installable and
I'd
Hi, Galaxy Developers,
I have what I'm hoping is a fairly simple inquiry for the Galaxy community;
basically, our production Galaxy server processes appear to be dying off over
time. Our production Galaxy instance implements apache web scaling features so
I have a number of server processes,
Sorry about that Ross. I would try your wrapper of edgeR and would
happily report you the bug. Can you make me the link of Galaxy Test
Toolshed?
Thanks,
Sachit
On Mon, Jul 8, 2013 at 11:51 AM, Ross ross.laza...@gmail.com wrote:
(Sachit, please don't cross-post to the dev and user lists?)
Hi Sachit,
It's packaged up so it installs from the test toolshed directly via the
admin interface of your test instance, but you'll need a good reliable
network as there is a lot that gets downloaded and installed.
Like other toolshed tools, it would be possible but not advisable to
download
Hi Sachit,
we are working currently on a DESeq2 wrapper. Not yet finised sorry.
There is also a edgeR Test repository from Ross Lazarus under:
http://testtoolshed.g2.bx.psu.edu/view/fubar/edger_test
Work is in progress, help is welcome!
Ciao,
Bjoenr
Hi,
These are the R libraries. Have
Thank you Björn and Ross. I will install the tools from the admin
interface.
On Mon, Jul 8, 2013 at 12:35 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Sachit,
we are working currently on a DESeq2 wrapper. Not yet finised sorry.
There is also a edgeR Test
Hi Dan,
That's old code. Updating will probably help.
Logging level just takes disk space, but just in case you haven't followed
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer?action=showredirect=Admin%2FConfig%2FPerformance
leaving
debug = True uncommented used to fill
On Thu, Jul 4, 2013 at 9:49 PM, Robert Baertsch
robert.baert...@gmail.com wrote:
Dan,
Do these readers support gzip files?
reader = fastqVerboseErrorReader
reader = fastqReader
Presumably you are writing a Python script using this library?
The answer is a qualified yes.
Week 3 and Week 4 Plans:
http://galaxy-gsoc2013.blogspot.in/2013/07/week-3-accomplishments-and-week-4-plans.html
On 6 July 2013 16:46, Saket Choudhary sake...@gmail.com wrote:
Here is a short post explaining the data model. Not ver elaborately
written, so incase you you find a mistake or
Hi guys,
Any thoughts on this? I'm kind of stuck.
(Even some pointers on where to look for more clues would be extremely helpful.)
Thanks,
Greg
On Fri, Jul 5, 2013 at 11:10 AM, greg margeem...@gmail.com wrote:
Hi guys,
I'm hitting an error using CloudMan using the Share-an-Instance
It probably makes sense to specify the template type in this case.
Maybe an additional attribute, language='cheetah' ?
On Sun, Jul 7, 2013 at 1:19 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
action type=template_command
#if env.get('X11_LIB_DIR', False) and
Hi James,
It probably makes sense to specify the template type in this case.
Maybe an additional attribute, language='cheetah' ?
My first suggestion was action type=cheetah_command to reflect the
template engine. I'm fine with both.
On Sun, Jul 7, 2013 at 1:19 PM, Björn Grüning
liftOver files come from the UCSC genome browser, derived from
pairwise alignments.
A variety of tools can create nib files from fasta, however we prefer
the use of the twoBit format now, which can be created using
faToTwoBit from the UCSC utilities.
--
James Taylor, Assistant Professor,
I'll soon be committing a slightly altered version of your patch which includes
a language attribute for the template_command action type.
On Jul 8, 2013, at 10:02 AM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi James,
It probably makes sense to specify the template
Hi,
Our lab recently installed a local version of Galaxy on a mid-2012 Mac
Pro computer. We can access the Galaxy server and sign in as an
administrator. Today we tried creating a Data Library, adding a
dataset to it, and uploading a directory of files. We followed this
Galaxy documentation (
On Mon, Jul 8, 2013 at 3:36 PM, Nicholas Kline nx...@case.edu wrote:
Hi,
Our lab recently installed a local version of Galaxy on a mid-2012 Mac
Pro computer. We can access the Galaxy server and sign in as an
administrator. Today we tried creating a Data Library, adding a
dataset to it, and
Hi Greg,
Previously my workflows had hard coded dependencies on the main
Tool Shed, which currently is a bit of a problem on the Test Tool Shed.
Therefore I'm update my Tool Shed workflows using a
repository_dependencies.xml with implicit repository and revision fields
(i.e. the latest revision
Hello Björn,
Thanks very much for the patch - I've committed alsightly alterered verson of
it in changetset 10204:afec613d77fa which is currently running on the test tool
shed.
Greg Von Kuster
On Jul 7, 2013, at 6:59 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi
Hi,
I am running an instance of Galaxy that I setup using Cloudman.
We are trying to use the GATK Unified Genotyper, but we are missing the
reference genomes.
I saw in your website instructions on how to setup reference genomes for
some other tools, but not for the Unified Genotyper.
Where can I
Hi Nicholas,
as pointed out by Peter and here:
http://www.biostars.org/p/76021/
please check your white spaces and provide a little bit more
information.
Btw. what is wrong with biostar? Why the double post?
Cheers,
Bjoern
Hi,
Our lab recently installed a local version of Galaxy on a
Hello Peter,
Thanks for reporting this - I have committed a fix in changeset
10206:86efa5ac1fae, which is currently running on the test tool shed.
Greg Von Kuster
On Jul 8, 2013, at 11:35 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Hi Greg,
Previously my workflows had hard coded
Hi,
I am having trouble setting up a FTP connection with the recently released
version of Galaxy Cloudman (ami-118bfc78).
I have instantiated the new version of Galaxy Cloudman with
CloudLaunchhttp://usegalaxy.org/cloudlaunch and
also through the AWS EC2 wizard (using the same security group
On Mon, Jul 8, 2013 at 10:24 PM, Robert Baertsch
robert.baert...@gmail.com wrote:
Peter and Dan,
I like the idea of replacing all open() with galaxy_open() in all tools. You
can tell the format by looking at the first 4 byes (see C code below from
the UCSC browser team). Is there some pythonic
On Mon, Jul 8, 2013 at 11:21 PM, Robert Baertsch rbaer...@ucsc.edu wrote:
I respectfully disagree, If you want an extensible system, you should
always wrap primitive system level calls.
Any tools that opens a file that could be compressed would be affected.
That is a huge number of tools. Do
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