3.0 just want stable and is not compatible with the current stable embassy-hmmer.
I just learned 3.0 is a testing release. Some binaries disappeared and some functionality is still not available: http://hmmer.janelia.org/software/archive . I posted upstream with the following email right now: <quote> I have just realized I need hmmer-2.3 because some application uses hmmpfam. So far I had hmmer-3.0 installed. Would you mind changing the libhmmer.a to libhmmer3.a in the hmmer-3.x branch and also append the '3' to the name of the binaries so that one could install both version together? Please let me know what is possible to for you. </quote> Unless they can be installed concurrently I propose masking 3.0 even for `~' arches.
It's not a testing release, and we won't mask it. Feel free to supply a patch to slot HMMER 2 and 3 properly, though. An eselect module might be necessary.
hmmer should either be slotted or hardmasked as explained in bug 414997
Yes, they should use SLOT. Quoting from http://hmmer.org/download.html <quote> The 1992-1998 HMMER1 lineage was closer to the original Krogh/Haussler conception of profile HMMs. It includes a feature that is missing in HMMER2 and HMMER3: the hmmt program for training HMMs from initially unaligned sequences (and hence creating multiple alignments). The final stable release of HMMER1 was 1.8.5 (Feb 2006). The 1998-2003 HMMER2 lineage introduced the "Plan 7" profile HMM architecture (which HMMER3 still largely shares), and was the long-time foundation for Pfam and other protein domain databases. It still included glocal and global alignment modes that HMMER3 lacks, because HMMER3 currently implements only fully local/local alignment; HMMER2 lacks DNA-DNA comparison that was present in HMMER1, and has returned in HMMER3.1. The final stable release of HMMER2 was 2.3.2 (Oct 2003). </quote> I just put hmmer-3.1_beta2.ebuild to science overlay but cannot help with SLOTs. Seems current Pfam-A.hmm files cannot be indexed using hmmpress from 3.0 package. The error message was "... does not appear to be in a recognized HMM format".
hmmer-2.3.2 is now SLOTed properly (which required renaming the hmm* binaries and man pages). commit 895b3abfbdacf52dbd7a0e817eb7ebf101ce55a7 Author: David Seifert <soap@gentoo.org> Date: Sun Oct 9 16:52:52 2016 +0200 sci-biology/hmmer: Properly SLOT=2 hmmer-2.3.2 Gentoo-bug: 328911, 586960 * EAPI=6 * Introduce SLOT=2 and rename binaries and static libraries
