Hi Dave,
You are right that on closer inspection I've mixed tool_dependencies.xml
and repository_dependencies.xml *again*. Evidentially my mental model
does not match Greg's here:
(*) I need to define a tool installation recipe for something not in the
Tool Shed -- write an install script called
Hi Peter,
2014-07-31 10:57 GMT+02:00 Peter Cock p.j.a.c...@googlemail.com:
Hi Dave,
You are right that on closer inspection I've mixed tool_dependencies.xml
and repository_dependencies.xml *again*. Evidentially my mental model
does not match Greg's here:
(*) I need to define a tool
On Thu, Jul 31, 2014 at 5:21 PM, bjoern.gruen...@googlemail.com
bjoern.gruen...@gmail.com wrote:
Hi Peter,
2014-07-31 10:57 GMT+02:00 Peter Cock p.j.a.c...@googlemail.com:
Hi Dave,
You are right that on closer inspection I've mixed tool_dependencies.xml
and repository_dependencies.xml
First time posting so I hope I do this correctly.
I am using galaxy locally and installed the ea-utils fastq-mcf (FastqMcf). When
using the trimming options (not defaults) the -C option gets set to the -s
option. I checked the fastq-mcf.xml wrapper and indeed there is an mistake on
line 42.
Bjoern,
FYI, I found that package_gatk_1_4 from the main Galaxy toolshed
produces Rscript files for VariantRecalibrator and other commands that
require ggplot_0.8.8 and reshape_0.8.4. This applies to GATK versions
1.4-20 and 1.4-37.
The magic incantation to get a systemwide R v3.1 setup properly
Hi Evan,
unfortunately I have no access to this repository. I'm only the
maintainer of the galaxytools in github. But I have CC'ed Dave, he is
responsible for the devteam packages!
Cheers and thanks for sharing your information!
Bjoern
Am 31.07.2014 um 20:47 schrieb Evan Bollig:
Bjoern,
Btw, I forgot: plyr_1.7.1 is also required for package_gatk_1_4. Hence
the install_url call for it below.
-E
-Evan Bollig
Research Associate | Application Developer | User Support Consultant
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On
A security vulnerability was recently discovered by Inge Alexander Raknes that
would allow a malicious person to execute arbitrary code on a Galaxy server.
The vulnerability was in a method that uses Python pickle functionality to
decode state information from tool forms. Because pickles can be
