Alternative methods for external authentication
by Amelia Ireland
I'd like to set up a galaxy instance to use a custom external
authentication system. The documentation has examples of using LDAP and
Apache-based authentication, but I wondered if there was a more general
method for hooking up a login system.
Thanks!
Amelia Ireland
Integrated Microbial Genomics
5 years, 9 months
Missing modules after upgrade to 16.01
by C. Ch.
Hi,
I've upgraded to 16.01 and have error messages indicating missing modules. This produces problems while setting the metadata. The processes run, the results are there but the history entry is in red.
How can I trigger the installation of all the modules that galaxy needs with the new pip based mechanism?
Thanks for the help!Cristian
5 years, 9 months
Python 2.6 Support
by Dannon Baker
We're currently discussing when we should stop supporting Python2.6 and
it'd be useful to know how much this might impact local Galaxy
administrators. Does anyone on the list have strong feelings or concerns
about this and want to weigh in?
Here's the issue on GitHub for more information and discussion:
https://github.com/galaxyproject/galaxy/issues/1596
Thanks!
Dannon
5 years, 9 months
GATK problems with data manager
by Scott Szakonyi
Hi all,
Sorry to be repetitive, but this issue is really blocking our efforts to
develop the workflow that we need in our instance of Galaxy. If anyone has
any familiarity with the issue described below, please let me know. I
really need to get this solved.
One of my co-administrators is having some issues with data
indexed/processed with data managers in GATK. His email to me:
Currently there is no way to load a genome into versions of GATK above
version 1.4. No version seems to be able to load a reference from history
and only version 1.4 seems to work with the available picard-gatk data
manager. We need to be able to work with these later versions of GATK, 3.4
on the Galaxy tool shed is the latest.
Thanks!
Scott
--
Scott B. Szakonyi
Research Programmer
*Center for Research Computing*
107 Information Technology Center
Notre Dame, IN 46556
http://crc.nd.edu
5 years, 9 months
novoalign in Galaxy
by Peter van Heusden
Hi there
We're busy integrating novoalign in our local Galaxy - there doesn't seem
to be a tool around for this, but I recall some people saying they were
using (single threaded) novoalign with Galaxy. Does anyone know if tool XML
has already been written? If not, we'll just have to write it.
Peter
5 years, 9 months
Downgrade tool upload tool
by Makis Ladoukakis
Hello everyone,
I was wondering whether it's possible to downgrade the upload tool to the previous version(1.1.4).
I copied the upload.py and upload.xml scripts from a previous galaxy version to the tools/data_source/ directory and reloaded the tool as admin but it hasn't changed even when I restarted the server.
Do I have to change something else in addition?
Thank you,
Makis
5 years, 9 months
