Hi,
I'am trying to set up ProFTP on Debain to enable FTP upload on Galaxy
installed locally? I followed the instructions on this link (
http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't
work.
When I restart proftpd i get this message :
mod_tls_memcache/0.1: notice: unable
On Fri, May 25, 2012 at 4:54 PM, Peter Cock wrote:
> I ran into some similar problems wrapping other tools giving table based
> output, and used a wrapper script to make them into tab separated tables
> for use in Galaxy. e.g. SignalP 3 (spaces), EffectiveT4 (semi-colons).
>
Sorry, that was a typ
On Wed, Feb 29, 2012 at 6:12 PM, Edward Kirton wrote:
> great suggestion; i'll make those changes
>
>
Hi Edward,
It has taken me a while but I'm how trying to use HMMER3, and do so
from within Galaxy.
I've realised that the per sequence and per domain tables from hmmscan
and hmmsearch (via the
Jason,
Is there a possibility that the jobs failing to submit because there is no
valid input detected (because of a write cache delay perhaps)?
Sorry I do not know PBS. We use LSF and we have ended up increasing the
“retry_job_output_collection” entry to 30 to catch these falsely “failed” jobs
Hi Hermant,
Thanks for the suggestion. I've tried setting that parameter to 5, but it has
not helped. I've noticed in the galaxy server output that I'm getting the
following error:
galaxy.jobs.runners.pbs DEBUG 2012-05-25 08:13:17,957 (96) pbs_submit failed,
PBS error 15031: Protocol (ASN.1) e
It works !!!
I've changed the extension of output file of an application.
But in Galaxy, it's referenced over the old file with .dat in history, so
if we want to re-use this file with other tool it's not the best way to
change this extension after the run of tool.
If I could change the extension be
I'm looking for a workflow of :
Forward reads.fastq =>
> QC => map => etc
Reverse reads.fastq =>
and would like to specify pairs of files (from MiSeq) in the batch
workflow interface. I'm currently looking into interlacing the files
outside of galaxy before uploading. Then I can de-interlace a
On Fri, May 25, 2012 at 12:03 PM, Greg Von Kuster wrote:
> Hi Peter,
>
> The tool shed should be functional now. Thanks for reporting this!
>
> Greg
It was working again when I got your email, but while I was out to
lunch it has gone back to Error 502 Bad Gateway :(
Peter
_
Batch mode is currently only allowed for a single input dataset step, so the
others are intentionally disabled upon toggling the first one on. We do,
however, plan to eventually expand this to allow for pairwise/etc input sets.
Out of curiosity, which behavior is it that you're looking for?
-
Is it possible to use multiple 'input dataset' steps in a single
workflow in batch? If I have two, I can only select batch input on one
of them. If one is open, the other toggle button does not respond.
Thanks,
Geert
On 02/14/2012 09:55 PM, Petit III, Robert A. wrote:
Thats it! Consider thi
Yes a follow this wiki but it doesn't work. I've tried to post too in
apache forum because may be it's simply a problem with apache.
thank you for your help.
Julie
2012/5/24 Carlos Borroto
> Glad it helped.
>
> About configuring Galaxy to use port 8080, other than what you are
> already doing, c
Jason,
Are the affected workflow steps actually failing or are they falsely being
reported as “failed” (have you checked if correct output exists for the
affected step)? Once a step/job is marked “failed’ you can’t use the output
(even if it exists) for any subsequent step.
If you are using a
Working fine as of now.
--hk
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Peter Cock
Sent: Friday, May 25, 2012 6:09 AM
To: galaxy-dev@lists.bx.psu.edu
Subject: [galaxy-dev] http://toolshed.g2.bx.psu.edu/ 502 Bad G
Hi Peter,
The tool shed should be functional now. Thanks for reporting this!
Greg
On May 25, 2012, at 6:08 AM, Peter Cock wrote:
> Hi,
>
> Could someone take a look at the Tool Shed server please?
> I'm getting this for http://toolshed.g2.bx.psu.edu/
>
> 502 Bad Gateway
> nginx/1.1.4
>
> Th
Hi,
Could someone take a look at the Tool Shed server please?
I'm getting this for http://toolshed.g2.bx.psu.edu/
502 Bad Gateway
nginx/1.1.4
Thanks,
Peter
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