Count me in. I'm more of an "arch-engineering" than science. But I can give some love to packages like ElmerFEM, I compiled it myself under Arch and worked well... Unfortunately I lost he PKGBUILDs but I can rewrite them again (like most of the times ).
elmerfem-svn is still in the AUR. I adopted it a couple of weeks ago (and still haven't touched it). It currently works but some files are installed under /usr/local despite the prefix option. The PKGBUILD needs an overhaul. If you're up to the task I can orphan it for you. I don't have time to fiddle with it right now.
There is room for making some noise about this? I would really like a lot of AUR packages related to science in the official repos.
This may well happen given that there are at least 2 TUs involved so far, but I think the initial goal should be to establish an independent binary repo before pushing everything into [community]. I have begun discussing some ideas of how to manage PKGBUILDs and repos on the other forum.
Anyway... out of curiosity here.. what thoughts on projects which are binary and/or commercial then?
You could provide incubation packages which include a custom installer/uninstaller in the install-script. In this case I would propose an interactive setup script when necessary with automation support with a configfile in e.g. /etc/autoinstall/{PKGNAME}.cfg
Or just distribute PKGBUILD templates where the user has to fill in his license information.
Templates will probably be easier to manage. I have a script that might be useful for this. It can interpolate arbitrarily defined variables in any text file by prompting the user. I wrote it to generate wpa_supplicant files with passwords (there is a way to mark variables as passwords and the output is sent to a fifo to avoid writing to disk). That could be easily adapted to generate PKGBUILDs after prompting the user.
I might just package that script right now.
]]>Anyway... out of curiosity here.. what thoughts on projects which are binary and/or commercial then?
You could provide incubation packages which include a custom installer/uninstaller in the install-script. In this case I would propose an interactive setup script when necessary with automation support with a configfile in e.g. /etc/autoinstall/{PKGNAME}.cfg
Or just distribute PKGBUILD templates where the user has to fill in his license information.
I'm not joining the other forum... but I can supply a bunch of genetic software - all of which is probably not in the AUR now I think about it.
Edit: pedfiddler is not as bad as it sounds!
Allan.. all I can say is OMG!!! I certainly hope not
I had an online name eons ago; moon fiddler... and I was often referred to by my chaps, as something else due to the name hehe.
Anyway... out of curiosity here.. what thoughts on projects which are binary and/or commercial then?
eg. Maple, Mathematica, Matlab and so on.
If one does set up such a targeted section, I wouldn't mind seeing sanitising such solutions which are intended for linux to being installed on arch. Even if it's not open source, many scientists would be happy to have it still easier obtained and configured through the 'science' repo as you put it with interaction for registering/licensing?
[science-oss]
bla bla
[science-prop]
bla bla
Needless to say.... the oss step is of course a more prudent and pressing issue (centralising maintenance/collaboration and so forth) but just thought I'd chuck in my tuppence.
]]>There is room for making some noise about this? I would really like a lot of AUR packages related to science in the official repos.
]]>Concerning the access to MUMPS: some distributions, e.g., Ubuntu, provide binary packages, some toolkits like petsc can provide the package themselves (petsc-3.3-p5/config/PETSc/packages/MUMPS.py: self.download = ['http://ftp.mcs.anl.gov/pub/petsc/extern … -p3.tar.gz']), and the current PKGBUILD downloads directly the package from the MUMPS website... The MUMPS people appreciate to know who use the code and in what context, so that's why there's this form system, that's all.
]]>> ls -1 /var/abs/local/genetics/
crimap
haploview
mendel-bin
merlin
ms
pap
pedcheck
pedfiddler
pedstats
plink
plink-seq
qtdt
tabix
vcftools
Edit: pedfiddler is not as bad as it sounds!
]]>It sounds like would have a lot to offer the group. MUMPS is one of the packages that I consider problematic to package due to the need to register to access the source code (via email). If you can sort that out and help with some related packages, it would be great!
Packaging it relatively simple. A PKGBUILD is just a simple Bash file with some metadata and build instructions. Open up the PKGBUILD wiki article and use it to make sense of some existing PKGBUILDs. There are also several tools to facilitate PKGBUILD retrieval for existing packages. I'm understandably biased towards pbget.
I hope to see you on the other forum.
]]>I've been using Linux for quite a few years, and I switched to Arch a few months ago. I've been looking for a way to contribute to the project, and Xyne's idea sounds great.
I'm a contributor to the MUMPS project, a linear algebra package. There's a package on AUR but it is orphaned, and I plan to update it. I also know my way around other related packages, like Scotch/PT-Scotch, Metis/ParMetis, Scalapack, BLAS, and other (parallel) linear algebra and scientific computing packages.
However, I have no experience on packaging for Arch or any other distro, but I'm willing to learn
PS: FYI, English is not my native language...
]]>I think registering is too easy: http://xyne.archlinux.ca/forum/viewtopic.php?id=8 (haven't registered yet myself).
Yeah, I noticed that, even with the VSABR (very simple anti-bot registration) plugin. Presumably spammers have already incorporated the default questions in their scripts. I've replaced the default questions with my own now. Hopefully that will work.
]]>Let me know if you have any trouble registering.
I think registering is too easy: http://xyne.archlinux.ca/forum/viewtopic.php?id=8 (haven't registered yet myself).
]]>Let me know if you have any trouble registering.
]]>-A list of packages and/or applications that will be part of the "arch-science" collection.
-A list of users who have decided to volunteer
-A few users who have taken the initiative to be the leaders of this project. De-facto leader right now, I think, is Xyne.
This information needs to exist in a centralized location, so I think that should go on Xyne's forum.
For the purposes of this thread, though, I think Xyne should append and regularly update a list of volunteers.
]]>