Expose local filesystem to Galaxy?
by Sandra Maksimovic
Hi there,
We are hosting an on-prem Galaxy instance in a HPC environment. Our research staff would like the ability to manipulate raw data that is located on the shared filesystem without having to manually upload it into Galaxy. Is this currently supported and would there be any related documentation?
Thanks,
Sandra
4 months
Galaxy Paper Cuts Day: Wednesday October 19
by Dave Clements
Hi all,
We are organising the Galaxy Paper Cuts contribution fest this Wednesday*:
https://galaxyproject.org/events/2020-10-papercuts/
Paper Cuts are small irritants that introduce friction when using or
administering Galaxy. We want to
1) get rid of them, thus improving Galaxy
2) grow the contributor community!
Want to help / learn / join? Please sign up. (You can also just show
up, but then you won't get a reminder email.)
Between now and the end of Wednesday, there are a couple of big ways
you can help:
1. Participate!
2. Create GitHub issues for things that you find irritating, in any
part of the Galaxy ecosystem
3. If you manage a Galaxy component (e.g., BioBlend, Planemo, ...)
create a tag for paper cuts, tag any appropriate issues with it, and
then let us know what tag you used.**
Hope to see you on Wednesday,
Dave C channeling Simon, Björn, and Dannon (in time zone order!)
* This Wednesday == 21 hours from now in Australia
** Or just update the paper cuts page in the hub directly.
--
https://galaxyproject.org/
6 months
Segmentation fault
by James White
We have installed Galaxy on a local server with these os and programs:
CentOS Linux release 8.1.1911
galaxy release_20.09
Python 3.6.8
When we configured object store for disk store it worked fine. We tried to
configure Google Compute Platform and followed the instructions to create
a bucket and install the .json key.
When we test it it starts for a short time and then fails.
/lib64/libpython3.6m.so.1.0(+0x1cd274) [0x7f1f5d9da274]
/lib64/libpthread.so.0(+0x82de) [0x7f1f5d5f52de]
/lib64/libc.so.6(clone+0x43) [0x7f1f5cb9ce83]
*** end of backtrace ***
run.sh: line 91: 18100 Segmentation fault (core dumped)
.venv/bin/uwsgi --yaml /usr/local/galaxy/config/galaxy.yml --static-safe
/usr/local/galaxy/client/src/assets
Will appreciate any suggestions.
Jim W
--
Programmer
Dept. of Entomology and Plant Pathology
N.C. State Univ.
Raleigh, N.C.
6 months, 1 week
October Galaxy Newsletter
by Dave Clements
Hello all,
The October Galaxy Newsletter is out.
https://galaxyproject.org/news/2020-10-galaxy-update/
News on
* Event news & JTech Scholarships
* Galaxy platform news: BRIDGE, BioCompute Object, French Galaxies,
PhagePromoter, and UseGalaxy.*
* Blog posts: Remote training, EOSC-Life calls
* Training material and doc updates: refgenie magic
* Publications
* Q: Who's hiring? A: Ten different groups
* New releases
* Other news too
If you have anything to include to next month's newsletter, then
please send it to outreach(a)galaxyproject.org.
Thanks,
Dave C and Bea
________________________________
--
https://galaxyproject.org/
6 months, 2 weeks
