Hi Greg,
Could there be some problems with https://toolshed.g2.bx.psu.edu/ I have
some troubles installing toolshed tools in our galaxy. When I try
installing for instance 'suite_samtools_0_1_19', I am presented with a 500
error.
I tried then pulling a new stable galaxy from bitbucket, which
Hi All,
I am playing around with putting a tool in testtoolshed. Now when changes
to dependency versions are detected, the toolshed detects a new version and
a dropdown is created.
but sometimes I do not want this behavior when the first version was
erroneous for example. I tried hg strip on the
Thanks! I think
http://gregvonkuster.org/galaxy-tool-shed-leveraging-community-contributions-repository-capsules/
will
solve my problem!
Because I want to use R which has multiple layers of dependencies
rebuilding it locally seemed a bit labor intensive but this capsule thing
sounds exactly
Hi Dannon,
could this still be existent in galaxy-dist?
Impersonate.makohttps://bitbucket.org/galaxy/galaxy-dist/src/29ce93a13ac7c4a5d2b54e5e2c10960f30a350b3/templates/admin/impersonate.mako?at=default
doesn't seem to have ${h.url_for(controller=/api/users, action=index)} in
its source and
Hi all,
At gcc2013 at the storage workshop I think I heard about a feature in
galaxy, where different users could be assigned to a specific object
store.
But I can't find any documentation on this subject. Is this possible
and how do I implement this?
Thanks,
--
Central Veterinary Institute
Ok thanks, I will vote it up, and for now try to manually edit
lib/tool_shed/util/shed_util_common.py
Thanks
On 20 January 2014 15:51, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi Eric,
please see the following ticket for it and vote it up :)
https://trello.com/c/dWvkfBKC
Sorry
Hi All,
We are having some problems serving our toolshed images. We are using
the notation below to embed images in our tools help tag set.
.. image:: some image file name
.. image:: $PATH_TO_IMAGES/some image file name
The problem is, is that our galaxy instance runs on a proxy prefix
while
Just the licence server was installed and not the actual genomics
workbench, so I couldn't do real testing yet.
I am now downloading 6-5-1 64bit.
I'll keep you noticed.
On 18 November 2013 16:37, Peter Cock p.j.a.c...@googlemail.com wrote:
On Mon, Nov 18, 2013 at 3:31 PM, Eric Kuyt erick
250 -q -i reads1.fq
reads2.fq
Version: 4.20.91522
On 18 November 2013 16:58, Eric Kuyt eric.ku...@wur.nl wrote:
Just the licence server was installed and not the actual genomics
workbench, so I couldn't do real testing yet.
I am now downloading 6-5-1 64bit.
I'll keep you noticed
Hi Peter,
After installing the clc testing galaxy wrapper I noticed there are still
some static paths in the wrapper.
I'm in favor of expecting binaries in the system path, but maybe that's a
matter of taste.
Greets,
Eric Kuijt
On 30 October 2013 17:03, Peter Cock p.j.a.c...@googlemail.com
.
-Dannon
On Fri, Sep 20, 2013 at 7:35 AM, Eric Kuyt eric.ku...@wur.nlmailto:
eric.ku...@wur.nl wrote:
Hi All,
I'm trying to do some cleanup in my test environment (galaxy-dist)
and pgcleanup.py ends with
Traceback (most recent call last):
File ./scripts/cleanup_datasets/pgcleanup.py
Hi All,
I'm trying to do some cleanup in my test environment (galaxy-dist)
and pgcleanup.py ends with
Traceback (most recent call last):
File ./scripts/cleanup_datasets/pgcleanup.py, line 773, in module
cleanup = Cleanup()
File ./scripts/cleanup_datasets/pgcleanup.py, line 55, in
will try to work on this more as I have time.
-John
On Mon, Sep 9, 2013 at 10:58 AM, Eric Kuyt eric.ku...@wur.nl wrote:
Hi all,
I'm using blend4j for some time now and I'm quite happy about it, but
now I run into some OutOfMemory issues.
When I try to upload large files to galaxy (I know http
, 2013 at 4:37 AM, Eric Kuyt eric.ku...@wur.nl wrote:
Hello all,
I'm trying to implement blend4j in a java application. for this I cloned
the
source, fetched the dependencies and added a maven assembly plugin to
assemble a jar file with dependencies.
This jar I put in my classpath
Hello all,
I'm trying to implement blend4j in a java application. for this I cloned
the source, fetched the dependencies and added a maven assembly plugin to
assemble a jar file with dependencies.
This jar I put in my classpath.
Now fetching histories works, but creating a new one fails. Online
Sorry forgot,
root cause = A message body writer for Java type, class
com.github.jmchilton.blend4j.galaxy.beans.History, and MIME media type,
application/json, was not found
On 11 July 2013 11:37, Eric Kuyt eric.ku...@wur.nl wrote:
Hello all,
I'm trying to implement blend4j in a java
Hi All,
I am Running my local galaxy instance in Eclipse - pydev to make debugging
somewhat easier, but now I run into loads of Code errors. It seems that
pydev doesn't understand the Bunch() Class frequently used in Galaxy.
But also code errors that maybe could be fixed. such as:
features in Eclipse.
Thanks again,
Eric
-Dannon
On Feb 5, 2013, at 5:29 AM, Eric Kuyt eric.ku...@wur.nl wrote:
Hi All,
I am Running my local galaxy instance in Eclipse - pydev to make
debugging somewhat easier, but now I run into loads of Code errors. It
seems that pydev doesn't
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