On Fri, Oct 11, 2013 at 9:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Oct 10, 2013 at 8:20 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi all,
The recent changes to the DRMAA runner are for better handling
of job-ending conditions under slurm, but it looks like SGE has
different
Hello imon,
You are correct - this feature is not yet available on the main tool shed.
I'll add some code to handle this issue in a better way. However, the fact
that the main tool shed is not currently handles in a better way doesn't really
cause any problems in this case. So if you wanted
Hi,
I'm interested in a wrapper for SeqPrep:
https://github.com/jstjohn/SeqPrep
Anyone preparing one/aware of someone preparing one? Otherwise I'll put
one together.
From its description: SeqPrep is a program to merge paired end
Illumina reads that are overlapping into a single longer read.
Hi Brad,
(cc-ing the list)
I'm more interested in the merging part, and after a quick search on the
toolshed, there are no tools to merge reads. Seems that there is a need for a
read merger wrapper then...
Lionel
On 14 Oct 2013, at 13:46 , Langhorst, Brad langho...@neb.com wrote:
I would
Ian,
To help track down this issue, could you provide the revision of Galaxy
you're running?
--Dave B.
On 10/14/2013 08:09 AM, UMD Bioinformatics wrote:
Hello all,
I'm still dealing with an error regarding Fastx toolkit. I all of the
fastx commands in my /usr/local and I have installed
Dave,
Here is my information on the revision.
$ hg heads | more
changeset: 10421:a477486bf18e
branch: stable
tag: tip
user:Nate Coraor n...@bx.psu.edu
date:Thu Sep 26 11:02:58 2013 -0400
summary: Bugfix for tool-to-destination mapping, tool ids are lowercased
Hello Simon,
On Oct 14, 2013, at 6:26 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Oct 13, 2013, at 5:13 PM, Simon Guest simon.gu...@agresearch.co.nz wrote:
I've recently upgraded to the
development branch, and I'm getting HTTP 404 errors from the new
function
Dear all,
I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman
distribution (ami-118bfc78). The instatiated Galaxy however does not contain
Bowtie2 and Tophat2, even after updating through the Cloudman Admin section.
Although the wrappers are there in the tools directory,
Hi
Stanislas,
Please check the PATH variable and make sure that you can access bowtie2
from command line and then restart the Galaxy service through cloudman
interface. I think that should work.
Vipin
I'm trying to run Galaxy on an Amazon AWS cloud using the normal Cloudman
distribution
On Oct 14, 2013, at 6:07 AM, Peter Cock wrote:
On Fri, Oct 11, 2013 at 9:12 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
On Thu, Oct 10, 2013 at 8:20 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi all,
The recent changes to the DRMAA runner are for better handling
of job-ending conditions
- bowtie2 does not show any built-in reference genomes
by default Cloudman didn't ship the genome index for bowtie2. Bowtie2 use
its own index set.
Usage: bowtie2-build [option] genome.fa index_basename
and add the entries in bowtie2_indices.loc. Please make sure that the fields
are tab
Hello,
My account is under rrdatta@gmail.com.
I have been able to successfully transfer files and performed FTP uploads
using Filezilla in the past. However in the last few days I have been
consistently denied server access. The report I get is:
Status: Connection attempt failed with
On Oct 14, 2013, at 9:16 PM, Brad Chapman chapm...@50mail.com wrote:
Ian;
I have my PATH set as well as the env.sh and my ./bash_profile. Again
this all works fine from the command line. I don't know where else
Galaxy is trying to find the fastx commands.
I know zero about setting up
At Mon, 14 Oct 2013 20:22:06 -0500,
John Chilton wrote:
Simon,
Very cool! I have two concerns. Rather than adding a new
configuration option I think I would prefer to just check the
configured dependency resolvers and then infer from them if the tool
shed will be used. The configuration
Hi,
I'm getting this error when trying to restart a previously used cluster:
InvalidVolume.ZoneMismatchThe volume '' is not in the same
availability zone as instance
I did a search and I could only find this previous email in galaxy-user:
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