galaxy-dev October 2020

galaxy-dev@lists.galaxyproject.org

4 participants
5 discussions

Expose local filesystem to Galaxy?
by Sandra Maksimovic 16 Dec '20

16 Dec '20

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

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Galaxy Developer Round Table: Tool testing and deployment, Oct 29
by Dave Clements 28 Oct '20

28 Oct '20

Hi All, The next Galaxy Developer Round Table will be Thursday, October 29, at Noon US Eastern. It will be a roundtable discussion on tool testing and tool deployment issues. Links (including time zone conversion) are here: https://galaxyproject.org/events/2020-10-29-dev-roundtable/ Hope to see you there, Dave C (channelling actual developers!) -- https://galaxyproject.org/

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Galaxy Paper Cuts Day: Wednesday October 19
by Dave Clements 20 Oct '20

20 Oct '20

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/

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Segmentation fault
by James White 09 Oct '20

09 Oct '20

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.

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October Galaxy Newsletter
by Dave Clements 07 Oct '20

07 Oct '20

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/

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galaxy-dev October 2020