Ok, thanks for the help Björn.
I finally got this built by doing two things:
1) I upgraded boot2docker and docker to 1.6.2, then deleted my existing boot2docker image and reinitialized (i.e, stop delete download init up).
2) Also added this line to the top of the Dockerfile (to enable testtoolshed):
ENV GALAXY_CONFIG_TOOL_SHEDS_CONFIG_FILE $GALAXY_HOME/tool_sheds_conf.xml
Now all packages install properly.
Cheers, -E -- Evan F. Bollig, PhD Scientific Computing Consultant, Application Developer | Research and User Services (RUS) Supercomputing Institute for Advanced Computational Research | msi.umn.edu University of Minnesota | umn.edu boll0107@umn.edu | 612-624-1447 | Walter Lib Rm 556
On Sat, Jun 13, 2015 at 4:13 AM, Björn Grüning bjoern.gruening@gmail.com wrote:
Hi Evan,
can you install other tools, or is this happening to all tools? Which version are you running?
Thanks 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 package_bedtools_2_19 bedtools
I'm getting errors like these when executing "RUN install-repository": ############ [....] Galaxy is running.
Processing: --url https://toolshed.g2.bx.psu.edu/ --name variant_filtration --revision da6e2503c62d --owner devteam
HTTP Error 500: Internal Server Error
{"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}
2015/06/13 03:56:34 The command [/bin/sh -c install-repository "--url https://toolshed.g2.bx.psu.edu/ --name variant_filtration --revision da6e2503c62d --owner devteam"] returned a non-zero code: 1 ############
Any thoughts?
Cheers, -E
-- Evan F. Bollig, PhD Scientific Computing Consultant, Application Developer | Research and User Services (RUS) Supercomputing Institute for Advanced Computational Research | msi.umn.edu University of Minnesota | umn.edu boll0107@umn.edu | 612-624-1447 | Walter Lib Rm 556 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/