Hi Nikhil,
I've been using your Galaxy wrapper for deseq_and_sam2counts.
I fixed it up to run the R script from the tool install directory directly, so
no manual copying of the script is required after installation in the Galaxy
GUI.
I attach my patch (as a Mercurial export), and hope you will
At Thu, 19 Sep 2013 11:44:35 +0200,
Bjoern Gruening wrote:
> Hi Simon,
>
> it's just a guess but can you try the attached patch if you have a
> reproducible case. It is not tested, but at least it should point you in
> the right direction. If its working, I will create a pull request.
Hi Bjoern,
Jeremy,
We didn't have time to factor out to toolshed just now, so we took the
following approach
1. Take 1.3-compatible cuffdiff wrapper (0.0.5) and move it to
cuffdiff_1.3_wrapper.py/xml - and add a dependency on cufflinks verson=1.3.0
(and set that up).
2. Apply your patch, cha
Hello Rico,
This used to work, and I have no idea when it was broken, but it should now be
working again as of 10688:27a3c2f3fc20, which is currently running only on the
test tool shed. The main tool shed will be updated with this fix when the next
Galaxy release happens.
Thanks for reporting
Hi all,
I have a Mac OSX 10.8, python 2.7.5 and the newest version of mercury.
My local instance is working fine. I went to admin, toolshed, located
fastq groomer parallel, preview and install but it did not work at all.
Please help!
Di Nguyen, PhD
Postdoc, U of W, Seattle, WA
__
> Can you provide a usage scenario for including history_id in the tool
dict?
A simple example is the creation of a full history based log file.
My more detailed need is to parallel an existing analysis pipeline in
galaxy, using the same underlying code. Reusing the same code from within
galaxy ha
You have to determine if the old version of galaxy (
galaxylocal.genenetwork.org:8080/) and the new one, if any database changes
have occurred between them -- most likely. If not, and you can check, by
looking at the hg history changes via the bitbucket website:
https://bitbucket.org/galaxy/galaxy-
Howdy,
On our local galaxy cluster, I have gotten a report that the multiple
input files selection on workflows is missing. How do I enable it?
Looking at the past mailing list[1] this is the item that is missing
from our setup -- the tooltip icon. We are running a version of galaxy
that is rough
Hi Dave,
Mystery solved - although my revision numbers don't match yours,
if I look at the hashes this makes sense - I was unlucky in the timing:
$ hg heads
changeset: 11674:45abde58ef55
tag: tip
user:Dave Bouvier
date:Mon Sep 23 11:04:52 2013 -0400
summary: Upgrade
Peter,
Can you confirm that you are running 10639:8045e137464f or later when
this problem occurs? Fabric was upgraded in 10638, and the paramiko egg
was added in 10639.
--Dave B.
On 09/24/2013 12:21 PM, Peter Cock wrote:
Hmm.
This error message is unhelpful, no hint of if this is a loca
This should happen automatically at startup though, indicating a bug,
--
James Taylor, Associate Professor, Biology/CS, Emory University
On Tue, Sep 24, 2013 at 12:08 PM, Dave Bouvier wrote:
> Peter,
>
> We recently upgraded the Fabric egg, which now depends on paramiko. You
> should be able to
Hmm.
This error message is unhelpful, no hint of if this is a local configuration
error (like the egg paths) or remote (e.g. the Galaxy egg cache):
$ python ./scripts/fetch_eggs.py
Warning: paramiko (a dependent egg of Fabric) cannot be fetched
(Meanwhile working from the stable branch avoids th
Peter,
We recently upgraded the Fabric egg, which now depends on paramiko. You
should be able to resolve this issue by running
python ./scripts/fetch_eggs.py
--Dave B.
On 09/24/2013 11:42 AM, Peter Cock wrote:
Hi all,
Has something changed recently on galaxy-central with the fabric egg,
Hi all,
Has something changed recently on galaxy-central with the fabric egg,
and a possible missing dependency?
$ ./run.sh
...
galaxy.jobs.handler INFO 2013-09-24 16:40:21,849 job handler stop queue started
galaxy.jobs.handler INFO 2013-09-24 16:40:21,867 job handler queue started
galaxy.sample_
On Mon, Sep 23, 2013 at 3:41 PM, John Chilton wrote:
> So you want this:
> docopt==0.6.1
> python-levenshtein==0.10.2
> biopython==1.62
> ngs-tools==0.1.6
>
>
> Newline between dependencies, and no whitespace to the left of each package.
Hi John,
I can confirm this did the trick. It also solves
Dear James,
Thanks so much for your info.
Dumping database is a good idea. But the problem is that the two Galaxy are
running on different servers, and the Galaxy versions are very different.
Thanks again.
Lei Yan
Center for Integrative and Translational Genomics
UTHSC
On Mon, Sep 23, 2013 at
Peter,
The one on the main tool shed is due to an issue Greg and I are in the
process of resolving. As soon as we've tested the fix, I'll schedule a
re-test of that repository and update you on the status.
--Dave B.
On 09/24/2013 05:53 AM, Peter Cock wrote:
Thanks Dave,
Looks like the s
Hi all,
Some good news, the strange missing /bin/sh error has gone away
on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/aecdffbc08fc
The BLAST+ wrapper tests also look good on the main Tool Shed:
http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus /7
Thanks Dave,
Looks like the same thing happened again last night, but as this
is on the Main Tool Shed your fix wouldn't be included anyway:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90d552
Any clues about the installation failure would be useful, this is
working nice
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