I tested all versions of setuptools available in PyPI from 0.6c11 up
to 7.0. I found that galaxy fails to fetch eggs with the following
error when setuptools > 6.0.2 (i.e., 6.1 and 7.0).
#
* Creating directory in /mnt for galaxy data
Devteam:
The "cached" reference genome option on the variant_selector tool
(Main Toolshed) does not properly load reference options into the drop
down. Please comment out the following line to get it to work (the
same edit was already done in Unified Genotyper tool):
###
diff -r 135e8721f
Minnesota Supercomputing Institute
599 Walter Library
612 624 1447
e...@msi.umn.edu
boll0...@umn.edu
On Wed, Dec 3, 2014 at 8:01 AM, Evan Bollig PhD wrote:
> Devteam:
>
> The "cached" reference genome option on the variant_selector tool
> (Main Toolshed) does not properly load
I get this error occasionally:
"/bin/sh: 1:
/opt/galaxy/web/database/job_working_directory/000/100/galaxy_100.sh:
Text file busy"
When this occurs, the step fails outright. Resubmitting the step
resolves the issue and things run no problem. If this error appears
early in a long workflow, I have
Hey Bjoern,
I'm playing with your docker recipes
(https://github.com/bgruening/docker-recipes) today and I've been
waiting for the galaxyp image build to complete for about 3 hours. For
the majority of that time it has been stuck on
RUN install-repository "--url http://testtoolshed.g2.bx.psu.edu/
Not sure why, but these tools fail to install inside the
docker-galaxy-stable Dockerfile build:
indel_realigner
unified_genotyper
variant_select
package_bedtools_2_19
bedtools
I'm getting errors like these when executing "RUN install-repository":
[]
Galaxy is running.
Processing
anks for reporting!
> Bjoern
>
> Am 13.06.2015 um 10:59 schrieb Evan Bollig PhD:
>> Not sure why, but these tools fail to install inside the
>> docker-galaxy-stable Dockerfile build:
>>
>> indel_realigner
>> unified_genotyper
>> variant_select
>> packa
Hey Björn,
I'm using your galaxy-stable docker image to boot Galaxy on port 443
by default (i.e., with USE_HTTPS=True). Since the certificate is
self-signed, transactions with the URL (https://127.0.0.1) warn of
insecure SSL. Is it possible to force shed-install to use --insecure
and accept the SS
