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

Package-Manager: portage-2.3.1

sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch

@@ -0,0 +1,22 @@
+Make the build system respect DESTDIR, in order to allow staged builds.
+
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -109,13 +109,13 @@
+ #          installs man pages in MANDIR/man1/  (e.g. if MANSUFFIX is 1)
+ #          Creates these directories if they don't exist.
+ install: 
+-	mkdir -p ${BINDIR}
+-	-mkdir -p ${MANDIR}/man${MANSUFFIX}
++	mkdir -p ${DESTDIR}${BINDIR}
++	-mkdir -p ${DESTDIR}${MANDIR}/man${MANSUFFIX}
+ 	for file in $(PROGS) $(PVMPROGS); do\
+-	   cp src/$$file $(BINDIR)/;\
++	   cp src/$$file ${DESTDIR}$(BINDIR)/;\
+ 	done
+ 	-for file in hmmer $(PROGS); do\
+-	   $(INSTMAN) documentation/man/$$file.man $(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
++	   $(INSTMAN) documentation/man/$$file.man ${DESTDIR}$(MANDIR)/man$(MANSUFFIX)/$$file.$(MANSUFFIX);\
+ 	done
+ 
+ # uninstall: Reverses the steps of "make install".

sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch

@@ -0,0 +1,108 @@
+* Fix ancient perl 4 modules that are long gone.
+* Fix perl shebangs to be portable and usable on Prefix.
+See also: https://blogs.gentoo.org/mgorny/2016/02/08/a-quick-note-on-portable-shebangs/
+
+--- a/squid/Testsuite/bug-1-sfetch-paths
++++ b/squid/Testsuite/bug-1-sfetch-paths
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test for bug #1: sfetch/SSI path bug.
+ # sfetch can't follow paths out of current directory if it's using
+--- a/squid/Testsuite/x-base-afetch
++++ b/squid/Testsuite/x-base-afetch
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-alistat
++++ b/squid/Testsuite/x-base-alistat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-seqstat
++++ b/squid/Testsuite/x-base-seqstat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-sfetch
++++ b/squid/Testsuite/x-base-sfetch
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-shuffle
++++ b/squid/Testsuite/x-base-shuffle
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-sindex
++++ b/squid/Testsuite/x-base-sindex
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/squid/Testsuite/x-base-sreformat
++++ b/squid/Testsuite/x-base-sreformat
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use testsuite;
+ 
+--- a/testsuite/sqc
++++ b/testsuite/sqc
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # sqc 
+ # quality control script for exercising code, regression testing, 
+@@ -176,12 +176,11 @@
+ # SRE, Tue Aug  6 11:16:39 2002
+ # CVS $Id: sqc,v 1.3 2003/01/05 23:40:57 eddy Exp $
+ 
+-require "getopts.pl";
+-require "importenv.pl";
++use Getopt::Std;
+ 
+ # Parse our command line
+ #
+-&Getopts('mp:r:v');
++getopts('mp:r:v');
+ if ($opt_m) { $do_memtest = 1;    }
+ if ($opt_p) { push @prepdirs, $opt_p; }
+ if ($opt_r) { push @olddirs,  $opt_r; }
+@@ -506,7 +505,7 @@
+ #
+ sub tempname {
+     my ($dir, $name, $suffix);
+-    if ($TMPDIR) { $dir = $TMPDIR."/"; } else {$dir = "";}
++    if ($ENV{TMPDIR}) { $dir = $ENV{TMPDIR}."/"; } else {$dir = "";}
+ 
+     foreach $suffix ("aa".."zz") {
+         $name = "$dir"."sre".$suffix.$$;
+--- a/testsuite/test1-conversion.pl
++++ b/testsuite/test1-conversion.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test hmmconvert.
+ #

sci-biology/hmmer/hmmer-2.3.2-r4.ebuild

@@ -0,0 +1,75 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Id$
+
+EAPI=6
+
+DESCRIPTION="Sequence analysis using profile hidden Markov models"
+LICENSE="GPL-2"
+HOMEPAGE="http://hmmer.org/"
+SRC_URI="http://eddylab.org/software/${PN}/${PV}/${P}.tar.gz"
+
+SLOT="2"
+IUSE="altivec test threads"
+KEYWORDS="~alpha ~amd64 ~ia64 ~ppc ~ppc64 ~sparc ~x86"
+
+DEPEND="test? ( dev-lang/perl )"
+RDEPEND=""
+
+PATCHES=(
+	"${FILESDIR}/${P}-fix-perl-shebangs.patch"
+	"${FILESDIR}/${P}-fix-build-system-destdir.patch"
+)
+
+src_configure() {
+	# prevent stray environmental variable
+	# from causing issues in the test phase
+	unset TMPDIR
+
+	econf \
+		--enable-lfs \
+		$(use_enable altivec) \
+		$(use_enable threads)
+}
+
+src_install() {
+	default
+
+	newlib.a src/libhmmer.a libhmmer2.a
+	insinto /usr/include/hmmer2
+	doins src/*.h
+
+	dobin squid/{afetch,alistat,compalign,compstruct,revcomp,seqstat,seqsplit,sfetch,shuffle,sreformat,sindex,weight,translate}
+	dolib.a squid/libsquid.a
+	insinto /usr/include/hmmer2
+	doins squid/*.h
+
+	dodoc NOTES Userguide.pdf
+	newdoc 00README README
+
+	# rename files due to collisions with hmmer-3
+	# in order to make SLOTing possible
+	local i
+
+	# first rename man pages...
+	pushd "${ED%/}"/usr/share/man/man1/ >/dev/null || die
+	for i in hmm*.1; do
+		mv ${i%.1}{,2}.1 || die
+	done
+	popd >/dev/null || die
+
+	# ... then rename binaries
+	pushd "${ED%/}"/usr/bin/ >/dev/null || die
+	for i in hmm*; do
+		mv ${i}{,2} || die
+	done
+	popd >/dev/null || die
+}
+
+pkg_postinst() {
+	elog "All ${P} binaries have been renamed, in order"
+	elog "to avoid collisions with hmmer-3. For instance"
+	elog
+	elog "    hmmalign -> hmmalign2"
+	elog
+}