Hi all, I've recently written an ebuild for a statistical genetics program I use called Merlin (see http://www.sph.umich.edu/csg/abecasis/Merlin/). The program does not have any licence (see FAQ section), so I don't think there should be any issues with regards to the legality of including it in portage. Details of what the program actually does can be found in... Abecasis GR, Cherny SS, Cookson WO and Cardon LR (2002). Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30:97-101 ...but basically it a program (plus a few ancillary utility programs) for carrying out parametric, non-parametric, variance components, genotyping error detection and haplotyping analyses in (human) genetic linkage studies. I'd suggest adding it to the sci-biology/merlin since it is used with biological data. I update this when new versions come out, and would be happy to maintain the ebuild for portage. Regards Neil
Created attachment 79083 [details] Ebuild for statistical genetics program merlin ebuild for merlin (see comment in bug for more detail)
- merlin-1.0.1.tar.gz should be ${P}.tar.gz - for the correct license have a look at /usr/portage/licenses or attach the license if it's a special one - cd ${WORKDIR}/merlin-1.0.1 is superfluous - src_compile() is superfluous
(In reply to comment #2) Thanks for the comments... > - merlin-1.0.1.tar.gz should be ${P}.tar.gz Changed. > - for the correct license have a look at /usr/portage/licenses or attach the > license if it's a special one From the web-site.... 1. How do I reference MERLIN? To reference MERLIN, please cite: Abecasis GR, Cherny SS, Cookson WO and Cardon LR (2002). Merlin-rapid analysis of dense genetic maps using sparse gene flow trees. Nat Genet 30:97-101. 2. Why should I register my copy of MERLIN? Well, all software programs are buggy... and MERLIN is probably no exception. If we find something wrong, we need your e-mail address to let you know. This information is also used to gauge the level of interest in the project and helps decide whether to invest time making MERLIN even better or, perhaps, go back to the lab and do some real work. 3. Do I need a license to use MERLIN? MERLIN is available free for both commercial and non-commercial use, no license is required. However, note that no redistribution of the MERLIN source code or binaries is allowed. If you do use MERLIN, please register. So I've rehashed this and added it as an attachment to the bug. (I don't see using an ebuild as redistribution of source code, since it is simply a script to download the source, but if you think I should contact the author please let me know). > - cd ${WORKDIR}/merlin-1.0.1 is superfluous Changed. > - src_compile() is superfluous > I tried removing this, but then had failures when I tried to create a digest. I checked with the docs at http://dev.gentoo.org/~plasmaroo/devmanual/ebuild-writing/ but couldn't see how to exclude src_compile() Any pointers/examples? slack---line
Created attachment 79653 [details] Proposed Licence for Merlin ebuild Rehashed from the web-site FAQ, see http://www.sph.umich.edu/csg/abecasis/Merlin/FAQ.html for original.
Created attachment 79655 [details] merlin-1.0.1-r2.ebuild Revised ebuild after comments
Hi Neil. Thank you for your interest. Did you actually attach the right ebuild? The points raised in comment #2 are not addressed here in fact. I'll pinpoint them in a bit more detail: >DESCRIPTION="Gentoo ebuild for merlin-1.0-alpha" This is not really descriptive. Would you be happy with such text personally? >P=merlin-1.0.1 $P, $PN and other vars should *not* be set in ebuild. Besides, what is the point of this, it will be set to this very value by portage.. SRC_URI="http://www.sph.umich.edu/csg/abecasis/Merlin/download/merlin-1.0.1.tar.gz" here "merlin-1.0.1" part should be ${P} instead KEYWORDS="x86" this should be ~x86. It is not going to be stable right away. src_compile() { make all || die "emake failed" } Portage tries to detect standard installation procedures, as such src_compile having just this is not necessary. In general you can test your ebuilds with this function commented and add it only if necessary.. Please read the Gentoo Developer Handbook: http://www.gentoo.ro/proj/en/devrel/handbook/handbook.xml Especially sections "Ebuild howto": http://www.gentoo.ro/proj/en/devrel/handbook/handbook.xml?part=2&chap=1 and common mistakes: http://www.gentoo.ro/proj/en/devrel/handbook/handbook.xml?part=2&chap=3 George
Sorry about links (although they should work, you can just hit non-English text occasionally), for some reason I dug up slightly wrong references. Please replace .ro with .org in the domain names to get to the official pages.. George
Created attachment 84706 [details] Revised ebuild adressing correct structure. I've attempted to address comments on the ebuild (thanks George), and have the read documentation again and have hopefully understood more about the process. I tried a few trial and errors removing some of the lines from src_install{} but this resulted in errors. The attached compiles and installs to /usr/bin/merlin without any problems. If anyone has any comments on the ebuild please leave them below.
Taking bug.
Created attachment 187424 [details] Version bump Most recent ebuild for newest version in light of assignment of bug.
In Science overlay.
*** Bug 527966 has been marked as a duplicate of this bug. ***
