galaxy-proteomics

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galaxy-proteomics@lists.galaxyproject.org

April 2016

2 participants
2 discussions

Mailing list moved, but not to Google Groups
by Dave Clements 29 Aug '25

29 Aug '25

Hello all, This mailing list has a new home! But it isn't Google Groups. Yesterday Nate moved this list from the lists.bx.psu.edu domain to the lists.galaxyproject.org domain. This gives us better control over the list, including spam. This transition should be largely transparent to you, but there are a few things to be aware of: - List sender addresses and headers will change to reflect the updated domain: from bx.psu.edu togalaxyproject.org. Existing email filters you have set up may require adjustments. - Posts from lists.galaxyproject.org could be categorized as spam until you train your filtering method. - Mailing list archives and posting functionality will be briefly inaccessible during the migration. - The prior bx.psu.edu list posting email addresses will continue to accept email, which will be forwarded to the new list addresses. What happened to the Google Groups plan, you might ask. Well, we used Google Groups for the GCC2014 mailing lists and they were problematic. It turns out that many people's work email servers periodically identify Google Groups as a spammer and then just block it causing emails from the list to silently stop being delivered. Not exactly the behavior you want in a mailing list. Please let us know if you have any questions. Thanks, Dave C and Nate On Thu, May 22, 2014 at 12:17 PM, Dave Clements <clements(a)galaxyproject.org> wrote: > Hello Galaxy Proteomicists! > > The Galaxy Project has started to create new mailing lists using a Google > Groups infrastructure. The new lists still work like mailing lists (plus > other stuff). We are hoping that Google Groups proves to be less > maintenance than Mailman. We are also considering moving our established > lists to Google too. > > Since this is the smallest and least active of the Galaxy community's > mailing lists, this is the first established list we are going to move. > Look for this to happen before GCC2014. > > If anyone has any requests or questions about the move, please let us know. > > Thanks, > > Dave C > > PS: John Chilton originally wanted this list set up on Google Groups. I > talked him out of it. There can't possibly be a lesson for me in that > experience, can there? ;-) > -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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toolshed
by Jorrit Boekel 07 Apr '16

07 Apr '16

Hi Galaxy-P, I would like to package some tools for the toolshed and include them in the Galaxy-P github repo. The tools are: - percolator and pout2mzid - hardklor/kronik - msstitch (aka my own tool) And maybe some isobaric protein quant R script, and/or updates to MSGF+. Anyway, I have poked around a little and have no problems creating and testing tools. However the toolshed syntax is a bit confusing. I understand I have to specify a package definition (tool_dependencies.xml) which installs the tool. And then the tool itself, which seems easy enough. My questions about this: - Is there any doc on the toolshed XML that defines how you install your binaries? I am planning to build from source, since percolator has binaries for different linuxes. (If it is not possible to specify which one of those to use.) - what is in the admin-scripts directory? Static data? Hoping to submit pull requests soon! cheers, — Jorrit Boekel Proteomics systems developer BILS / Lehtiö lab Scilifelab Stockholm, Sweden

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