reinit the tree, so we can have metadata

6 files changed, 314 insertions, 0 deletions

diff --git a/sci-biology/primer3/Manifest b/sci-biology/primer3/Manifest
new file mode 100644
index 000000000000..756fda39e824
--- /dev/null
+++ b/sci-biology/primer3/Manifest
@@ -0,0 +1,10 @@
+AUX primer3-2.3.4-buildsystem.patch 5460 SHA256 13fa4df0026faa97b574e3de3a99183e66ab18eec883db92e9f234acafe8b3b8 SHA512 52f539f52c92e5e21c3166da62813c6fa9f90fd9e0ca87d9ab67658496e13f4b5ce5c53770802cb1cdd21044244e21f09b0de2ce3c6d3db0182b3d9cbf64a037 WHIRLPOOL f09d952479f929d5e17abc3bb3a0313eae9d5811c3da14beb4d7111d17035f4077798b13f7b047ba7decd2b841c731373fb477f71a9b82f64906bbacf0118e2a
+DIST primer3-2.3.5.tar.gz 1655871 SHA256 e0c06a36dc384f656835a8d5ecb4b5069493b7dd98775b38a233863ab591c54b SHA512 e64c27eea0258af913304963254494d6c874e7776b09a14ee9a273f1a3cdfa908acf92b78affc0102f06df17effbf011181c60d97ebd0a645044df7a28b41fec WHIRLPOOL 321069f568fad409b31f2fd4caa36f1128523383f5b294dffc68d57a67489ee2ac17d53bedd8e36df9b688c43c06c91f47bdaf81b4fda6597d916ea06643e666
+DIST primer3-2.3.7.tar.gz 1658090 SHA256 9e37a301d2ca9e5034c9a9d4afcb3e90041f6cc44c658b63598d0ccfcb176e5e SHA512 f227f80d395cb682a9d65e0ac3afdcacb8385d66e721b9163fda939a9c788a7c6907273f6223782702b48d7df66ea2331114f6303fcd29e3b3c50a2717da2fa7 WHIRLPOOL a092cb3a117f4d70178266ea9ae9205df567c8d18d4dbff3b5279860b22f9e4cce5484393771f37ce16a9f6e5ff4e5a51d66f9c0f35bf5cfce84a18225e3bfd8
+DIST primer3-src-2.3.6.tar.gz 1667573 SHA256 2ff54faf957f0d7e4c79d9536fa1027b028bc5e4c6005f142df42ef85562ecd4 SHA512 671b420f3bc9b6b9972e19a757925ada170e5f8c0e3e8a90630a48e6cde44abc0e1e09b9ea90129f94b58f835e30440f3d91c14fb4b796fd94eb478b2ca28ead WHIRLPOOL 61bbc676c38b1b96806c9ac54d130aae936a5406213759613a3be76016cdd4ebf76c5a54d1ceffc7bd2634829d9aef9d64f87cc85289793b40ab031e01a5917f
+EBUILD primer3-2.3.5.ebuild 1029 SHA256 660f5115d451de4a7cbbc2095c38edbd8c68fc9c66cfc28f59ccba595fa29be8 SHA512 a52d99dde78f30879e6d109d36d5d2d258494d5dda1548b78044731decd772ccf78c0203dc1844a4c08b96f26ac52671da4b11efdbb732a578c45cf31b68119a WHIRLPOOL 2f27877af3cea502ed71f563ffef7242a2d5161d5d7d92c825ec30ac88a67b9edd43510e954f97664232a74e66c3ff096a15d27fdd69a900fb7649ece8e0dcda
+EBUILD primer3-2.3.6.ebuild 1040 SHA256 bdb0937adce3d209e93ecdb02a0b7e1dee9e284dc5433631a4e7f183204aeeda SHA512 f0471de087faa4e41123c94a1ef6dd32635edd5482d05724e135f8b05bcc073475206256e17f4547bbd269fbcc564f89dc0b4ff8aec33888c9095abcdc7c951d WHIRLPOOL b364572731f169ec2a1864e0443bdd67a078b5143aa538ca48555e73faa80cd2a976a1e255a89f80be13b4eac40abfa9d316143f840f9bd0bec843699ec458d9
+EBUILD primer3-2.3.7.ebuild 1072 SHA256 89fd122355086924fff8271ddffecd8db020389d54d75c00c6c146717a884181 SHA512 0ba2a4ff56a4ecc8abd17888acd22275f8330418d250503def828f83b047bf84d6a17224e65de75199923b40e95926128a885419b65325a09c061cdeba30f05f WHIRLPOOL 30f075c58925b63d050ce2562186187d12dad8fda68510c5132b5937a85fa9c619d3e600b7fdb803de9be02c7554aaf3568d4f9cdf8bf1e444469f898dc228ff
+MISC ChangeLog 3451 SHA256 efd791c4864ab436b63e1e7c92147579ce770f6995784867b648fd7071b5c4df SHA512 c4379a8c99f503f520d17a89921e3f3943f87d2c336759a613de772fbc8670cef8bb120caec1f1180527f7ec0bb233cdd443177108e23831eeb016c37e11bb1d WHIRLPOOL 3b6f7a2e7ace70d4078a4df34225e2c424fda82dd8d0435961af8195325b845bbfac75e08b68f96dff64165d862fffb837d503bf080c85231f4ccba38e2a7082
+MISC ChangeLog-2015 6556 SHA256 7a6c4648e46858dc397f13486669207f9be2a1c6f90250e62421a9a4d9a48c44 SHA512 bb93c369c2b9403143e8c7e9a4776c93c6e54a9ee078e05c66793183f21c5497b72dd65578144fa716f4c1cd4c927f399aa9f1f593773a1fee4a37ffac2b541a WHIRLPOOL fef5c33af9feb026a5a9f8ebf0f2dae804b6fe8e0120d829e4434ccdc2b2b8a34f956b816dcbd3a1cd26daf98bcbefce6d92663a7b27e4391e3c02af702e8a7e
+MISC metadata.xml 808 SHA256 6cab9fc709b096b8062c49f139e68cfa4b305f9ec9e0fed8f8d17681890230c1 SHA512 9474b015028dce21ce738cb6aeaefc2ee73b292fd24b9132da303acd2b7f723444543023a46b7c00b0544ebaa03b20569a3d46657f2bbc514a8d7d5444864dc8 WHIRLPOOL 2e6e55b643d47d4d2dc68c909254f16572f133cfb2f55e31361129de081fa798d0b956b9e4b9a045ade60bda234976ef3297e79f0f978c24b34e4bb2409c5448
diff --git a/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
new file mode 100644
index 000000000000..cf47b35af502
--- /dev/null
+++ b/sci-biology/primer3/files/primer3-2.3.4-buildsystem.patch
@@ -0,0 +1,148 @@
+ src/Makefile | 61 ++++++++++++++++++++++++++++++------------------------------
+ 1 file changed, 31 insertions(+), 30 deletions(-)
+
+diff --git a/src/Makefile b/src/Makefile
+index 607ab45..a88adf4 100644
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -52,15 +52,16 @@ TESTOPTS=
+ WINMAKE=mingw32-make
+ 
+ LDLIBS     = -lm
+-AR         = ar
+-CC         = gcc
+-CPP        = g++
+-O_OPTS     = -O2
+-CC_OPTS    = -g -Wall -D__USE_FIXED_PROTOTYPES__
+-P_DEFINES  =
++AR         ?= ar
++CC         ?= gcc
++CXX        ?= g++
++O_OPTS     ?= 
++CC_OPTS    ?= -Wall -D__USE_FIXED_PROTOTYPES__
++P_DEFINES  ?=
+ 
+-CFLAGS  = $(CC_OPTS) $(O_OPTS)
+-LDFLAGS = -g
++CFLAGS    += $(CC_OPTS) $(O_OPTS)
++CXXFLAGS  += $(CC_OPTS) $(O_OPTS)
++LDFLAGS   +=
+ # Note, for profiling, use
+ # make O_OPTS='-pg -O0' LDFLAGS='-g -pg'
+ 
+@@ -92,7 +93,7 @@ LIBPRIMER3      = libprimer3.a
+ LIBPRIMER3_DYN  = libprimer3.so.1.0.0
+ LIBRARIES       = $(LIBPRIMER3) $(LIBDPAL) $(LIBTHAL) $(LIBOLIGOTM) 
+ DYNLIBS         = $(LIBPRIMER3_DYN) $(LIBDPAL_DYN) $(LIBTHAL_DYN) $(LIBOLIGOTM_DYN)
+-RANLIB          = ranlib
++RANLIB          ?= ranlib
+ 
+ PRIMER_OBJECTS1=primer3_boulder_main.o\
+                 format_output.o\
+@@ -127,85 +128,85 @@ $(LIBOLIGOTM): oligotm.o
+ 	$(RANLIB) $@
+ 
+ $(LIBOLIGOTM_LIB): oligotm.o
+-	$(CC) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
++	$(CC) $(LDFLAGS) -shared -W1,-soname,liboligotm.so.1 -o $(LIBOLIGOTM_DYN) oligotm.o
+ 
+ $(LIBDPAL): dpal_primer.o
+ 	$(AR) rv $@ dpal_primer.o
+ 	$(RANLIB) $@
+ 
+ $(LIBDPAL_DYN): dpal_primer.o
+-	$(CC) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
++	$(CC) $(LDFLAGS) -shared -W1,-soname,libdpal.so.1 -o $(LIBDPAL_DYN_LIB) dpal_primer.o
+ 
+ $(LIBTHAL): thal_primer.o
+ 	$(AR) rv $@ thal_primer.o
+ 	$(RANLIB) $@
+ 
+ $(LIBTHAL_DYN): thal_primer.o
+-	$(CC) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
++	$(CC) $(LDFLAGS) -shared -W1,-soname,libthal.so.1 -o $(LIBTHAL_DYN_LIB) thal_primer.o
+ 
+ $(LIBPRIMER3): libprimer3.o p3_seq_lib.o
+ 	$(AR) rv $@ libprimer3.o p3_seq_lib.o
+ 	$(RANLIB) $@
+ 
+ $(LIBPRIMER3_DYN): libprimer3.o p3_seq_lib.o
+-	$(CC) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
++	$(CC) $(LDFLAGS) -shared -W1,-soname,liprimer3.so.1 -o $(LIBPRIMER3_DYN) libprimer3.o p3_seq_lib.o
+ 
+ $(PRIMER_EXE): $(PRIMER_OBJECTS)
+-	$(CPP) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
++	$(CXX) $(LDFLAGS) -o $@ $(PRIMER_OBJECTS) $(LIBOPTS) $(LDLIBS)
+ 
+ libprimer3.o: libprimer3.c libprimer3.h p3_seq_lib.h dpal.h thal.h oligotm.h
+-	$(CPP) -c $(CFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
++	$(CXX) -c $(CXXFLAGS) -Wno-deprecated $(P_DEFINES) -o $@ libprimer3.c
+ 
+ $(NTDPAL_EXE): ntdpal_main.o dpal.o
+-	$(CPP) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
++	$(CXX) $(LDFLAGS) -o $@ ntdpal_main.o dpal.o
+ 
+ $(NTTHAL_EXE): thal_main.o thal.o
+-	$(CPP) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
++	$(CXX) $(LDFLAGS) -o $@ thal_main.o thal.o $(LDLIBS)
+ 
+ $(OLIGOTM_EXE): oligotm_main.c oligotm.h $(LIBOLIGOTM)
+-	$(CPP) $(CFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ oligotm_main.c $(LIBOLIGOTM) $(LIBOPTS) $(LDLIBS)
+ 
+ $(LONG_SEQ_EXE): long_seq_tm_test_main.c oligotm.o
+-	$(CPP) $(CFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o $@ long_seq_tm_test_main.c oligotm.o $(LIBOPTS) $(LDLIBS)
+ 
+ read_boulder.o: read_boulder.c read_boulder.h libprimer3.h dpal.h thal.h p3_seq_lib.h 
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ read_boulder.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ read_boulder.c
+ 
+ print_boulder.o: print_boulder.c print_boulder.h libprimer3.h p3_seq_lib.h 
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ print_boulder.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ print_boulder.c
+ 
+ dpal.o: dpal.c dpal.h
+-	$(CPP) -c $(CFLAGS) -o $@ dpal.c
++	$(CXX) -c $(CXXFLAGS) -o $@ dpal.c
+ 
+ # We use '-ffloat-store' on windows to prevent undesirable
+ # precision which may lead to differences in floating point results.
+ thal.o: thal.c thal.h
+-	$(CPP) -c $(CFLAGS) -ffloat-store -o $@ thal.c
++	$(CXX) -c $(CXXFLAGS) -ffloat-store -o $@ thal.c
+ 
+ p3_seq_lib.o: p3_seq_lib.c p3_seq_lib.h libprimer3.h
+-	$(CPP) -c $(CFLAGS) -o $@ p3_seq_lib.c
++	$(CXX) -c $(CXXFLAGS) -o $@ p3_seq_lib.c
+ 
+ dpal_primer.o: dpal.c dpal.h
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ dpal.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ dpal.c
+ 
+ thal_primer.o: thal.c thal.h
+-	$(CPP) -c $(CFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
++	$(CXX) -c $(CXXFLAGS) -ffloat-store $(P_DEFINES) -o $@ thal.c
+ 
+ format_output.o: format_output.c format_output.h libprimer3.h dpal.h thal.h p3_seq_lib.h 
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) -o $@ format_output.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) -o $@ format_output.c
+ 
+ ntdpal_main.o: ntdpal_main.c dpal.h
+-	$(CPP) -c $(CC_OPTS) -o $@ ntdpal_main.c
++	$(CXX) -c $(CXXFLAGS) -o $@ ntdpal_main.c
+ 
+ thal_main.o: thal_main.c thal.h
+-	$(CPP) -c $(CFLAGS) -o $@ thal_main.c
++	$(CXX) -c $(CXXFLAGS) -o $@ thal_main.c
+ # We use CC_OPTS above rather than CFLAGS because
+ # gcc 2.7.2 crashes while compiling ntdpal_main.c with -O2
+ 
+ oligotm.o: oligotm.c oligotm.h
+ 
+ primer3_boulder_main.o: primer3_boulder_main.c libprimer3.h dpal.h thal.h oligotm.h format_output.h print_boulder.h read_boulder.h
+-	$(CPP) -c $(CFLAGS) $(P_DEFINES) primer3_boulder_main.c
++	$(CXX) -c $(CXXFLAGS) $(P_DEFINES) primer3_boulder_main.c
+ 
+ primer_test: test
+ 
diff --git a/sci-biology/primer3/metadata.xml b/sci-biology/primer3/metadata.xml
new file mode 100644
index 000000000000..664d9cf7d141
--- /dev/null
+++ b/sci-biology/primer3/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+  <longdescription>
+		Primer3 picks primers for PCR reactions, considering: oligonucleotide
+		melting temperature, size, GC content, and primer-dimer possibilities;
+		PCR product size; positional constraints within the source sequence;
+		and miscellaneous other constraints. All of these criteria are
+		user-specifiable as constraints, and some are specifiable as terms in
+		an objective function that characterizes an optimal primer pair.
+	</longdescription>
+  <upstream>
+    <remote-id type="sourceforge">primer3</remote-id>
+  </upstream>
+</pkgmetadata>
diff --git a/sci-biology/primer3/primer3-2.3.5.ebuild b/sci-biology/primer3/primer3-2.3.5.ebuild
new file mode 100644
index 000000000000..513c7cb5a1a3
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.5.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Primer Design for PCR reactions"
+HOMEPAGE="http://primer3.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
+
+	if [[ ${CHOST} == *-darwin* ]]; then
+		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
+	fi
+
+	tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_test () {
+	emake -C test | tee "${T}"/test.log
+	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+}
+
+src_install () {
+	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
+	dodoc src/release_notes.txt example
+	insinto /opt/primer3_config
+	doins -r src/primer3_config/* primer3*settings.txt
+	dohtml primer3_manual.htm
+}
diff --git a/sci-biology/primer3/primer3-2.3.6.ebuild b/sci-biology/primer3/primer3-2.3.6.ebuild
new file mode 100644
index 000000000000..21a466681109
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.6.ebuild
@@ -0,0 +1,45 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Primer Design for PCR reactions"
+HOMEPAGE="http://primer3.sourceforge.net/"
+SRC_URI="mirror://sourceforge/${PN}/${PV}/${PN}-src-${PV}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+KEYWORDS="amd64 ppc ~ppc64 ~sparc x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+src_prepare() {
+	epatch "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch
+
+	if [[ ${CHOST} == *-darwin* ]]; then
+		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
+	fi
+
+	tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_test () {
+	emake -C test | tee "${T}"/test.log
+	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+}
+
+src_install () {
+	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
+	dodoc src/release_notes.txt example
+	insinto /opt/primer3_config
+	doins -r src/primer3_config/* primer3*settings.txt
+	dohtml primer3_manual.htm
+}
diff --git a/sci-biology/primer3/primer3-2.3.7.ebuild b/sci-biology/primer3/primer3-2.3.7.ebuild
new file mode 100644
index 000000000000..d0dbc7363681
--- /dev/null
+++ b/sci-biology/primer3/primer3-2.3.7.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit eutils toolchain-funcs
+
+DESCRIPTION="Primer Design for PCR reactions"
+HOMEPAGE="http://primer3.sourceforge.net/"
+SRC_URI="mirror://sourceforge/project/${PN}/${PN}/${PV}/${P}.tar.gz"
+
+SLOT="0"
+LICENSE="GPL-2"
+IUSE=""
+KEYWORDS="~amd64 ~ppc ~ppc64 ~sparc ~x86 ~amd64-linux ~x86-linux ~ppc-macos ~sparc-solaris"
+
+DEPEND="dev-lang/perl"
+RDEPEND=""
+
+PATCHES=( "${FILESDIR}"/${PN}-2.3.4-buildsystem.patch )
+
+src_prepare() {
+	default
+	if [[ ${CHOST} == *-darwin* ]]; then
+		sed -e "s:LIBOPTS ='-static':LIBOPTS =:" -i Makefile || die
+	fi
+
+	tc-export CC CXX AR RANLIB
+}
+
+src_compile() {
+	emake -C src
+}
+
+src_test () {
+	emake -C test | tee "${T}"/test.log
+	grep -q "\[FAILED\]" && die "test failed. See "${T}"/test.log"
+}
+
+src_install () {
+	dobin src/{long_seq_tm_test,ntdpal,oligotm,primer3_core}
+	dodoc src/release_notes.txt example
+	insinto /opt/primer3_config
+	doins -r src/primer3_config/* primer3*settings.txt
+	docinto html
+	dodoc primer3_manual.htm
+}