reinit the tree, so we can have metadata

8 files changed, 691 insertions, 0 deletions

diff --git a/sci-biology/hmmer/Manifest b/sci-biology/hmmer/Manifest
new file mode 100644
index 000000000000..0483bcfe2070
--- /dev/null
+++ b/sci-biology/hmmer/Manifest
@@ -0,0 +1,11 @@
+AUX hmmer-2.3.2-fix-build-system-destdir.patch 825 SHA256 d1d2dd37606e512016a2e36cb1869433162b937e2a01d7d32ec755b913f3fc27 SHA512 f7eb3de5cbb1bf58b4ae4514e020ea059ad6a267e6f425494d8b444ac1bab056bc4709fed7f2793e68720b057ca1ac8c6dbca907125712d18dc05b77e37b1c3f WHIRLPOOL bfd161f040aed24b327f1ce9a5f90a02bc79baf0c114819964c6f687a2602df98b8eab5e0471c75af8d58084da58b705b2398fc7ef8023b8b3002758dcfa0c69
+AUX hmmer-2.3.2-fix-perl-shebangs.patch 2457 SHA256 9c3b581704d410a2ac25b31816c179388092c04f034afcf4dbd59216951bdc00 SHA512 9597d77b3101c091bb1d005f36229cb6bedaf496a15da472495bb688fdb2750c94a38adc1236f3d90b0085caa78f61bddb350d51e0d3cc8dfa96edcdd5e2e5b9 WHIRLPOOL 68f3ad01d6f91a1d26ffaaf0e6af299cb35181f7576eb9431a7b6aa7b5e9558c482d2cca47177fa21bef59b00ed7f06b5085109f57552bd844097d42bfbd0d82
+AUX hmmer-3.1_beta2-fix-header-install-path.patch 3202 SHA256 4d27d42010878a6cd21ea04921c85ea4ee08c1a21da68dc0b7a1fafbfaf3c6c5 SHA512 ccaaff25a50a60526d0a16196b2b1d8cd57a7e9d016ce2b6b36ba1c0123966113b10965303dceb494810cd17a802514bba3a49d010ee6bbdc039715b84524d9a WHIRLPOOL 8d909ebd0445d6f2fb75c7b71df942fdb5631b75602ac44840c632e5ccd9c7b4cc47172f4b3c8223fa9ee44e995233b93b8c0e1b55f5770cc268b29091e8ab45
+AUX hmmer-3.1_beta2-fix-perl-shebangs.patch 8605 SHA256 a0cc39baaf73280585ecf98b950fc96a432a0fbf956cbcbe60557c23b9d97d61 SHA512 ce2c91c2d34d49dd5082a97ca0543bf3a176c792b4efd0cb37561114fc572b41d6cd546e16267283d33138ad54e2bb0c9c912c8fa1142e558a5452e9e72da2ff WHIRLPOOL df90c8d77165ccf529917003236c831826757927ae23b730411f29d5e7e1e48b9af6c94b56007c836be9f7cb744a6ef0f2fcb2d3141a4673155983f1469040b5
+DIST hmmer-2.3.2.tar.gz 1024933 SHA256 d20e1779fcdff34ab4e986ea74a6c4ac5c5f01da2993b14e92c94d2f076828b4 SHA512 5abf9c304de38b183a5beab7a5cfc75c3774ff6e161b7b8e55a0eae9fd156dbb7ed95d216c16d3c585c494bb69e3a9fdfabfb5dc729b7050a4d1be95c74df7d7 WHIRLPOOL 604cc3f532d6eae3fbca893d991d0714a5a897fbac3059d63fdbebc6221e9321c2b444db2700e7068a11c043c0a7f9f3935617a3aa1878ca06ba18c558d55d40
+DIST hmmer-3.1b2.tar.gz 5965253 SHA256 dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536 SHA512 64c8a840cb62160a1c13a20e64f42d297edb7969425d5047eefd8ee9f992d66612d62843523e8f33a2c38568ce1b0a9df23dd1d3ecf6773007f6db12d4cc4771 WHIRLPOOL 0b6d17b5f5efe31873cde93ff33cc5b01c53de8e1daf1ed473ef92d6585f34abcbb31e35e4d02537fbbc2c808131b70a0f51a3832ee332e23246cbc75edc354a
+EBUILD hmmer-2.3.2-r4.ebuild 1631 SHA256 5f9c148bb77a39f57f530f7d8ee6e968e23d657d0d3a7814e8157b5ae976866e SHA512 c237c12b1c8f0d3059055f361bd0d74aaf4997506e7ffce4ea52ba4f4ddaf96863df306f54192f42c209ca74c32d66c82ee0408c5cf44d15b774c83d2a38c188 WHIRLPOOL be4eb0afbdb674b6f5f9c5c8a2dd1cd6ab9bbba3d9d6d4f80282c0985607f6a55a0a5b2417e4a07939d20fb1a1e2a0b85751e592509abc7fa031d777d1cf650c
+EBUILD hmmer-3.1_beta2.ebuild 1039 SHA256 91fbea8012ac6a8e5ae5d756b96f5c6c6700e1ff00ccddb4e7e916e3a8b57aa8 SHA512 fdc4c77b49d32f5d767a351d09faca6c9229d0a58060514fcf9a455a50d6649b016d71269874e9de4ecd7a121a1bfa9c84f493641beb39f0da43d87155f15c6a WHIRLPOOL 91f2a297e642b06460ce950486bba9e20b06061d538d143a94465b794ea6b5c41cbc2655d7f4aa1f477ab39d24153bf02afddc3878f3089e27ee4effa6f9ea43
+MISC ChangeLog 3721 SHA256 00cdef946de218c91cb088cfc76f2b00a75b5c00e348cce7b6ad6a57c2bc7586 SHA512 b63a10d874eca6459e2f02e4b725fc0663fe8f900ce95ff46e53eb4fbd9a043c569529972497a8d374e5f9929997026d04c40046ecb1ccda8c8c5aa8811717db WHIRLPOOL 94b722a856e6edaf1ba85722a8cdcc65ae047ae2cae0f530dc7d18a806d94accbcbf1e0e65d195608c5d7201f93a1e544287a5e202d1989616f5f9d2d2c8fee5
+MISC ChangeLog-2015 5411 SHA256 6c0efb04e2ef19c016477e9f09f43844dbfa6561d0a30017788970911add7c8d SHA512 119f27f43cb815065b027d436f8e8ef81633cfb918327ff989f60728442f116ce00609e2cb8d4842b1430dd7dbea04927edb1c736217a4c59470a09a65a5c07e WHIRLPOOL c4503f79cfeef60de665e55f3138c1e261073e5751842a4fc51b0a3c70f1d9302bfd51bc97a762a6723777f1737879caddef85f582a314310932cfdf447961b7
+MISC metadata.xml 261 SHA256 15c95fe0beb2b86b616b7ac1be6f1118bd598d907b441a94d87721c0d6f36855 SHA512 537da0d3aa2741ebe4442d5dd9b53409decfc9d12ca8e5af8e737c4deb2910c884207e2d441025d19469816100889f04c11038bdffd6a1a15c6217495445090a WHIRLPOOL c00a986f98ceb4fa20ffdb0c411de9841218f8af6f7499a20a34258db4cd74cead97ef2ee18ac8cac7eae7db3c95084cbf8aa3a36f95a1ed7efbb0e088eb50c8
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-build-system-destdir.patch
new file mode 100644
index 000000000000..110c61f11821
--- /dev/null
+++ b/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".
diff --git a/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-2.3.2-fix-perl-shebangs.patch
new file mode 100644
index 000000000000..783d0530aa7a
--- /dev/null
+++ b/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.$$;
+--- a/testsuite/test1-conversion.pl
++++ b/testsuite/test1-conversion.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test hmmconvert.
+ #
diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
new file mode 100644
index 000000000000..b9ff5b92b8f9
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-header-install-path.patch
@@ -0,0 +1,89 @@
+Install headers into 'hmmer3' subdir and not into global includedir.
+
+--- a/easel/Makefile.in
++++ b/easel/Makefile.in
+@@ -465,11 +465,12 @@
+ 	${INSTALL} -d ${DESTDIR}${bindir}
+ 	${INSTALL} -d ${DESTDIR}${libdir}
+ 	${INSTALL} -d ${DESTDIR}${includedir}
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	${INSTALL} -m 0644 libeasel.a ${DESTDIR}${libdir}/
+ 	for file in ${HDRS}; do\
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+-	${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/
++	${INSTALL} -m 0644 esl_config.h ${DESTDIR}${includedir}/hmmer3/
+ 	${QUIET_SUBDIR0}miniapps      ${QUIET_SUBDIR1} install
+ 
+ # "make uninstall" reverses the steps of "make install"
+--- a/Makefile.in
++++ b/Makefile.in
+@@ -143,6 +143,7 @@
+ 	${INSTALL} -d ${DESTDIR}${bindir}
+ 	${INSTALL} -d ${DESTDIR}${libdir}
+ 	${INSTALL} -d ${DESTDIR}${includedir}
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	${INSTALL} -d ${DESTDIR}${man1dir}
+ 	${INSTALL} -d ${DESTDIR}${pdfdir}
+ 	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} install
+--- a/src/impl_dummy/Makefile.in
++++ b/src/impl_dummy/Makefile.in
+@@ -152,8 +152,9 @@
+ 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+ 
+ install:
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	for file in ${HDRS}; do \
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+ 
+ uninstall:
+--- a/src/impl_sse/Makefile.in
++++ b/src/impl_sse/Makefile.in
+@@ -155,8 +155,9 @@
+ 
+ 
+ install:
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	for file in ${HDRS}; do \
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+ 
+ uninstall:
+--- a/src/impl_vmx/Makefile.in
++++ b/src/impl_vmx/Makefile.in
+@@ -152,8 +152,9 @@
+ 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+ 
+ install:
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	for file in ${HDRS}; do \
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+ 
+ uninstall:
+--- a/src/Makefile.in
++++ b/src/Makefile.in
+@@ -322,15 +322,16 @@
+ 	${CC} ${CFLAGS} ${SIMDFLAGS} ${CPPFLAGS} ${LDFLAGS} ${DEFS} ${MYLIBDIRS} ${MYINCDIRS} -D$${DFLAG} -o $@ $${DFILE} ${LIBS}
+ 
+ install:
++	${INSTALL} -d ${DESTDIR}${includedir}/hmmer3
+ 	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} install
+ 	for file in ${PROGS}; do \
+ 	   ${INSTALL} -m 0755 $$file ${DESTDIR}${bindir}/ ;\
+ 	done
+ 	${INSTALL} -m 0755 libhmmer.a ${DESTDIR}${libdir}/
+ 	for file in ${HDRS}; do \
+-	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/ ;\
++	   ${INSTALL} -m 0644 ${srcdir}/$$file ${DESTDIR}${includedir}/hmmer3/ ;\
+ 	done
+-	${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/ ;\
++	${INSTALL} -m 0644 p7_config.h ${DESTDIR}${includedir}/hmmer3/ ;\
+ 
+ uninstall:
+ 	${QUIET_SUBDIR0}${IMPLDIR} ${QUIET_SUBDIR1} uninstall
diff --git a/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch
new file mode 100644
index 000000000000..39fdbd50e457
--- /dev/null
+++ b/sci-biology/hmmer/files/hmmer-3.1_beta2-fix-perl-shebangs.patch
@@ -0,0 +1,331 @@
+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/easel/demotic/infernal_tab2gff.pl
++++ b/easel/demotic/infernal_tab2gff.pl
+@@ -1,4 +1,4 @@
+-#!/usr/bin/perl -w -I/groups/eddy/home/jonest/Demotic

++#!/usr/bin/env perl
+ 

+ # TAJ 6/23/08 last mod 7/10/08

+ # Purpose: flexibly convert "cmsearch --tabfile TAB.out" output to GFF format

+--- a/easel/demotic/test.pl
++++ b/easel/demotic/test.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ use demotic_blast;
+ 
+--- a/easel/devkit/rmanprocess.pl
++++ b/easel/devkit/rmanprocess.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # rmanprocess.pl <rman LaTeX2e output>
+ # 
+--- a/easel/miniapps/esl-afetch.itest.pl
++++ b/easel/miniapps/esl-afetch.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Testing the esl-afetch miniapp
+ #
+--- a/easel/miniapps/esl-alimanip.itest.pl
++++ b/easel/miniapps/esl-alimanip.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of the esl-alimanip miniapp.
+ #
+--- a/easel/miniapps/esl-alimap.itest.pl
++++ b/easel/miniapps/esl-alimap.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of the esl-alimap miniapp.
+ #
+--- a/easel/miniapps/esl-alimask.itest.pl
++++ b/easel/miniapps/esl-alimask.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of esl-alimask miniapp.
+ #
+--- a/easel/miniapps/esl-alimerge.itest.pl
++++ b/easel/miniapps/esl-alimerge.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of esl-alimerge miniapp.
+ #
+--- a/easel/miniapps/esl-alistat.itest.pl
++++ b/easel/miniapps/esl-alistat.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of the esl-alistat miniapp.
+ #
+--- a/easel/miniapps/esl-compalign.itest.pl
++++ b/easel/miniapps/esl-compalign.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of the esl-compalign miniapp.
+ #
+--- a/easel/miniapps/esl-construct.itest.pl
++++ b/easel/miniapps/esl-construct.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of the esl-construct miniapp.
+ #
+--- a/easel/miniapps/esl-mask.itest.pl
++++ b/easel/miniapps/esl-mask.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of esl-mask miniapp.
+ #
+--- a/easel/miniapps/esl-seqrange.itest.pl
++++ b/easel/miniapps/esl-seqrange.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of the esl-seqrange miniapp.
+ #
+--- a/easel/miniapps/esl-shuffle.itest.pl
++++ b/easel/miniapps/esl-shuffle.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of esl-shuffle miniapp
+ #
+--- a/easel/miniapps/esl-ssdraw.itest.pl
++++ b/easel/miniapps/esl-ssdraw.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of the esl-ssdraw miniapp.
+ #
+--- a/easel/testsuite/coverage_report.pl
++++ b/easel/testsuite/coverage_report.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Measures testsuite coverage (as percentage of source lines),
+ # using gcov.
+--- a/easel/testsuite/driver_report.pl
++++ b/easel/testsuite/driver_report.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Make sure that all drivers compile.
+ # (Eventually, we should also make sure they run! But that 
+--- a/easel/testsuite/i1-degen-residues.pl
++++ b/easel/testsuite/i1-degen-residues.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integration tests of reading all valid protein sequence residue characters.
+ #
+--- a/easel/testsuite/i2-ncbi-indices.pl
++++ b/easel/testsuite/i2-ncbi-indices.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Testing that we can read FASTA files, even if they have NCBI
+ # formatted BLAST databases in the same directory.
+--- a/easel/testsuite/i3-blank-gf.pl
++++ b/easel/testsuite/i3-blank-gf.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Bug #e5: blank text line following #=GF <tag> handled improperly.
+ #
+--- a/easel/testsuite/valgrind_report.pl
++++ b/easel/testsuite/valgrind_report.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Run the testsuite under Valgrind, to check for memory leakage.
+ #
+--- a/profmark/pmark-master.pl
++++ b/profmark/pmark-master.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl -w
++#!/usr/bin/env perl
+ 
+ # The top level script that runs a pmark benchmark.
+ #
+--- a/profmark/rocplot.pl
++++ b/profmark/rocplot.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ $nsearches = 2809;
+ 
+--- a/src/hmmpress.itest.pl
++++ b/src/hmmpress.itest.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Integrated test of hmmpress 
+ #
+--- a/testsuite/i10-duplicate-names.pl
++++ b/testsuite/i10-duplicate-names.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Check that we can deal with profiles and sequences that contain
+ # duplicate names, both as queries and targets. 
+--- a/testsuite/i11-hmmalign-mapali.pl
++++ b/testsuite/i11-hmmalign-mapali.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Another test of the hmmalign --mapali option, after Elena reports
+ # bug #h73 in bad interaction of checksum calculation and marking
+--- a/testsuite/i12-delete-corruption.pl
++++ b/testsuite/i12-delete-corruption.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Bug #h77: hmmalign corrupts column preceding an all-delete column
+ #
+--- a/testsuite/i13-msa-integrity.pl
++++ b/testsuite/i13-msa-integrity.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Look for any problems in hmmalign that corrupt the input sequences.
+ #
+--- a/testsuite/i14-hmmemit-consensus.pl
++++ b/testsuite/i14-hmmemit-consensus.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Tests hmmemit -c and hmmemit -C consensus-generating options.
+ #
+--- a/testsuite/i15-hmmconvert.pl
++++ b/testsuite/i15-hmmconvert.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Bug #h80: hmmconvert can't read H2 Nucleic files
+ #
+--- a/testsuite/i16-build-allins.pl
++++ b/testsuite/i16-build-allins.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Bug #h82: hmmbuild corrupts resave alignment on all-insert seq
+ #
+--- a/testsuite/i17-stdin.pl
++++ b/testsuite/i17-stdin.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test that programs accept and reject argument of '-' (for reading
+ # data from stdin, rather than from files) as they're supposed to.
+--- a/testsuite/i18-nhmmer-generic.pl
++++ b/testsuite/i18-nhmmer-generic.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test of hmmbuild/nhmmer as used to build a DNA model, then query a  
+ # a database of long (1MB).
+--- a/testsuite/i19-hmmpgmd-ga.pl
++++ b/testsuite/i19-hmmpgmd-ga.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test that hmmpgmd is correctly applying bit score thresholds;
+ # in this case, the --cut_ga threshold, using an example that
+--- a/testsuite/i20-fmindex-core.pl
++++ b/testsuite/i20-fmindex-core.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test of makenhmmerdb and the core fm-index search functionality, using extactmatch  
+ # 
+--- a/testsuite/i5-hmmbuild-naming.pl
++++ b/testsuite/i5-hmmbuild-naming.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test that HMM naming in hmmbuild works as advertised.
+ # Written to test for #h50.
+--- a/testsuite/i6-hmmalign-mapali.pl
++++ b/testsuite/i6-hmmalign-mapali.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test the hmmalign --mapali option.
+ # 
+--- a/testsuite/i7-hmmbuild-fragments.pl
++++ b/testsuite/i7-hmmbuild-fragments.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Test the ability of hmmbuild to deal with crappy alignments
+ # of lots of sequence fragments.
+--- a/testsuite/i8-nonresidues.pl
++++ b/testsuite/i8-nonresidues.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Regression test of handling a nonresidue '*' character. By design,
+ # '*' residues score 0 in insert states and N,C,J; and -inf in match
+--- a/testsuite/i9-optional-annotation.pl
++++ b/testsuite/i9-optional-annotation.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl
++#!/usr/bin/env perl
+ 
+ # Check that we can deal with HMMs with no optional annotation, in either
+ # hmmscan or hmmsearch mode.
+--- a/testsuite/test-make.pl
++++ b/testsuite/test-make.pl
+@@ -1,4 +1,4 @@
+-#! /usr/bin/perl -w
++#!/usr/bin/env perl
+ 
+ # Usage:   test-make.pl <builddir> <srcdir> <tmppfx>
+ # 
diff --git a/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
new file mode 100644
index 000000000000..cd0e1d732b8b
--- /dev/null
+++ b/sci-biology/hmmer/hmmer-2.3.2-r4.ebuild
@@ -0,0 +1,74 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+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="~amd64 ~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 ${P} binaries have been renamed, in order"
+	elog "to avoid collisions with hmmer-3. For instance"
+	elog
+	elog "    hmmalign -> hmmalign2"
+	elog
+}
diff --git a/sci-biology/hmmer/hmmer-3.1_beta2.ebuild b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
new file mode 100644
index 000000000000..f94fcca8c295
--- /dev/null
+++ b/sci-biology/hmmer/hmmer-3.1_beta2.ebuild
@@ -0,0 +1,48 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+MY_PV="${PV/_beta/b}"
+
+DESCRIPTION="Sequence analysis using profile hidden Markov models"
+HOMEPAGE="http://hmmer.org/"
+SRC_URI="http://eddylab.org/software/${PN}3/${MY_PV}/hmmer-${MY_PV}.tar.gz"
+
+LICENSE="GPL-3"
+SLOT="0"
+IUSE="altivec cpu_flags_x86_sse gsl mpi test +threads"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~ppc-macos"
+
+RDEPEND="
+	mpi? ( virtual/mpi )
+	gsl? ( sci-libs/gsl:= )"
+DEPEND="${RDEPEND}
+	test? ( dev-lang/perl )"
+
+S="${WORKDIR}/${PN}-${MY_PV}"
+PATCHES=(
+	"${FILESDIR}/${PN}-3.1_beta2-fix-perl-shebangs.patch"
+	"${FILESDIR}/${PN}-3.1_beta2-fix-header-install-path.patch"
+)
+
+src_configure() {
+	# make build verbose, bug 429308
+	export V=1
+
+	econf \
+		--disable-pic \
+		$(use_enable altivec vmx) \
+		$(use_enable cpu_flags_x86_sse sse) \
+		$(use_enable mpi) \
+		$(use_enable threads) \
+		$(use_with gsl)
+}
+
+src_install() {
+	default
+	dodoc Userguide.pdf
+
+	insinto /usr/share/${PN}
+	doins -r tutorial
+}
diff --git a/sci-biology/hmmer/metadata.xml b/sci-biology/hmmer/metadata.xml
new file mode 100644
index 000000000000..8417d1580d40
--- /dev/null
+++ b/sci-biology/hmmer/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>