Re: [galaxy-dev] Main Galaxy Tool Shed is running the next-stable branch

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 see

Re: [galaxy-dev] Control on versioning in toolshed tools

​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 what

[galaxy-dev] Control on versioning in toolshed tools

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

Re: [galaxy-dev] I can't impersonate an user

​Hi Dannon,​ could this still be existent in galaxy-dist? Impersonate.mako doesn't seem to have "${h.url_for(controller="/api/users", action="index")}" in its source

[galaxy-dev] object_store_conf.xml route users to different storage

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 o

Re: [galaxy-dev] toolshed image file location problem

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 wrote: > Hi Eric, > > please see the following ticket for it and vote it up :) > > https://trello.com/c/dWvkfBKC > > Sorry that there is no fix f

[galaxy-dev] toolshed image file location problem

Hi All, We are having some problems serving our toolshed images. We are using the notation below to embed images in our tools tag set. .. image:: .. image:: $PATH_TO_IMAGES/ The problem is, is that our galaxy instance runs on a proxy prefix while the link to the tool's help section doesn't inc

Re: [galaxy-dev] Galaxy wrappers for CLC Assembly Cell (CLCbio)

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 wrote: > Hello all, > > Th

Re: [galaxy-dev] Galaxy wrappers for CLC Assembly Cell (CLCbio)

fb ss 180 250 -q -i reads1.fq reads2.fq Version: 4.20.91522 On 18 November 2013 16:58, Eric Kuyt 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 ke

Re: [galaxy-dev] Galaxy wrappers for CLC Assembly Cell (CLCbio)

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 wrote: > On Mon, Nov 18, 2013 at 3:31 PM, Eric Kuyt wrote:

Re: [galaxy-dev] pgcleanup problem

13-09-26 10:04:10,476 Closing log file: > /opt/galaxy_testing/scripts/cleanup_datasets/delete_datasets.log > _run INFO 2013-09-26 10:04:10,476 Finished delete_datasets On 25 September 2013 17:45, Dannon Baker wrote: > Eric, > > What version of posgresql are you using? The sc

[galaxy-dev] pgcleanup problem

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 > cleanup = Cleanup() > File "./scripts/cleanup_datasets/pgcleanup.py", line 55, in __i

Re: [galaxy-dev] Large files in blend4j

conditionally somehow. Right now all requests are sharing the same > underlying client object. > > I will try to work on this more as I have time. > > -John > > On Mon, Sep 9, 2013 at 10:58 AM, Eric Kuyt wrote: >> Hi all, >> >> I'm using blend4j for s

[galaxy-dev] Large files in blend4j

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 might be not the best option) some byte array is getting to large. A possible solution would be file chunking in jersey, is

Re: [galaxy-dev] Implementing blend4j

n with, > so some of my terminology could be wrong there, but hopefully the idea > makes sense. Also happy to look at pull requests if it helps to push > changes upstream. > > Sorry if this response is not more helpful, let me know if there is > anything else I can do or answer. &g

Re: [galaxy-dev] Implementing blend4j

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 wrote: > Hello all, > > I'm trying to implement blend4j in a java ap

[galaxy-dev] Implementing blend4j

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

Re: [galaxy-dev] Fwd: Running galaxy from eclipse running PyDev

eah maybe it's better just to debug this way but it feels a bit low tech with all the nice PyDev features in Eclipse. Thanks again, Eric > -Dannon > > > On Feb 5, 2013, at 5:29 AM, Eric Kuyt wrote: > > > Hi All, > > > > I am Running my local galaxy instance in

[galaxy-dev] Fwd: Running galaxy from eclipse running PyDev

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: lib/galaxy/job