reinit the tree, so we can have metadata

6 files changed, 252 insertions, 0 deletions

diff --git a/sci-biology/fasta/Manifest b/sci-biology/fasta/Manifest
new file mode 100644
index 000000000000..936de1abe1eb
--- /dev/null
+++ b/sci-biology/fasta/Manifest
@@ -0,0 +1,9 @@
+AUX 35.4.10-ldflags.patch 1036 SHA256 21b6c290ca565c50376da61cd980f21f7a96598ea5da046294321d8d6be5d5fe SHA512 8136536c7f9887920a045dbcd04fa9d01dc0a3b22ed0a1771df715e288d6c889d87b0a6d0f52c947b54185f6a5e92fe902316b502074200a13820cac9dfa6594 WHIRLPOOL 35ff6b7fba2b8f16eb51795c48fd1636708155b1ad405be62850def9934a7d7556644ce808360375b4e658098ada81d7d89d2c53eb04f020d4af2aea127c8100
+AUX fasta-36.3.5e-ldflags.patch 2781 SHA256 baaa544d74ec1367875c96945fc5046182b6502be8d5565806b6c4cb81ae819c SHA512 5424bb8385def72ff75701c2da153f697520cbec82f36cbed8de0e98f93d399de660e79da7700ab0ff688fd5388cf9f42a30ccc4359335ae02042bf8cbb3aae7 WHIRLPOOL 1cbb12763b22e4424d953562b7b681ccb6fcbb58df0772a9ad73cb7c28892dae7afd09626fc275371c762eff73f143390b478ff84ad9d1f7f524dce77ff8a4f5
+DIST fasta-35.4.10.tar.gz 618971 SHA256 60616963093784d2e41ff9c125d68d7a43bbe411cdef8dc37ce922b4c3aec758 SHA512 f04268f0eea59cd40985c86597ab68bef40ee28e6ca914a7182c0edfe943ec8fb2a860558f422f210a4c03f3c34f36c677bd3971bc240cb87695826c755f5a47 WHIRLPOOL 87eb008bc507923ceaebe93c5eb2ab367ca184c0fa2304491ba8edf09e5f6eabe16a8823a1b6a11d5157355406157d1c97da9bd1e194dc26709188b995a386ce
+DIST fasta-36.3.5e.tar.gz 943763 SHA256 92f44a0e0e13bcd6782489f2db42044d7109a9071d775fb0435df24288be90c2 SHA512 ddfcae36dadd7e2ed5c8c8c0bda2eed077e9f6cd55e4ebf507690671af156358e9da4e7cb1406d2b8713c326c54a9d829fc25e668b16dfa6df48d18e3a009812 WHIRLPOOL 803cee2c7da8487811b6aa9776bfa737ab35c4de2f76887915ab285802a738cb073059f4122379512195bd54ad63db42c61059587b6a2aa34550774e57f9f5fa
+EBUILD fasta-35.4.10.ebuild 1352 SHA256 43c59c1720195243c6b4114407f10651ac8bc86e8d695fa959ae6ad88bed6fbc SHA512 eba62f3358ef8553e61be08759202b941df00d7862901899cafe5fe4d76d1dcd8dcb25d0410720393db8263e3b9bfd5d9c627ca09b726c1a66b14a4200fc60fa WHIRLPOOL d2de9999035e0e6208f403883e002d00be7511b786a5c8e64f4b04df89253b679dc446748b2225892410fa05eeac94268fbd3fec7e4176824a501bca366055f8
+EBUILD fasta-36.3.5e.ebuild 1625 SHA256 fe3bbcfce5feadac083f70674b9c8c69b19cc4c4855d25907e3e884901600c6c SHA512 618aa434a8271332dc1042c731d6f19d99f08eb90cc156af3b855d8df9664d5efa62a40a043c031205a03e768cf8251d246e4e7b14d7ca14deb47678399e5797 WHIRLPOOL c3b2a2bc375b796493ea4a47ee74d6cb6ebe6be391272db799e7cdfceca401b1b171122a9aca4b6699ff1aa82dd21fffc7b897f7b99696242884feb4d86df298
+MISC ChangeLog 2669 SHA256 5117f39b304513d45ef77b698cbf45d6c4445a25ec7ea2546b747b0a56df7db4 SHA512 3c4786b769dfc165e1a2f158f258e753ea820d4ca7f284cc958bfddec7599a2f7ebe34a00dc4f66233781fb12d4faae1cb51e545da4e4be5fb713ad6c82ba470 WHIRLPOOL b7ee69bb74d9d8ba89c2d5925423b4e855ec2b6f2e9aa9a3b51051b247b285201acdb7f370e459f069b3ee770c2e5c0299615dd6461ffca0c4e363379cba7c48
+MISC ChangeLog-2015 1496 SHA256 0a0cbd3c826f7fd604891da3d3a5ef8afee3e7d61f843f6cc5af9b8981000b17 SHA512 20a918d0095cb7df79811d272df82439a4adedbe6af9045e742283a1e9a4885cdf1353aaa00bbeb6f6ab9c3e661890d7ba751021964a3af300634c45a3c71527 WHIRLPOOL 4769fe648579339bba258b023d63515ae40ce41f52847bff59e9201a0872c32365f6d103296a4e3cca3c92cac346a0fd83e27cb59462565762d378a77cedc04d
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/fasta/fasta-35.4.10.ebuild b/sci-biology/fasta/fasta-35.4.10.ebuild
new file mode 100644
index 000000000000..8cad4d2a8b08
--- /dev/null
+++ b/sci-biology/fasta/fasta-35.4.10.ebuild
@@ -0,0 +1,57 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI="2"
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}3/${P}.tar.gz"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="amd64 ~ppc x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="debug cpu_flags_x86_sse2 test"
+
+DEPEND="test? ( app-shells/tcsh )"
+RDEPEND=""
+
+src_prepare() {
+	CC_ALT=
+	CFLAGS_ALT=
+	ALT=
+
+	use debug && append-flags -DDEBUG
+
+	if [[ $(tc-getCC) == *icc* ]]; then
+		CC_ALT=icc
+		ALT="${ALT}_icc"
+	else
+		CC_ALT=$(tc-getCC)
+		use x86 && ALT="32"
+		use amd64 && ALT="64"
+	fi
+
+	if use cpu_flags_x86_sse2 ; then
+		ALT="${ALT}_sse2"
+		append-flags -msse2
+		[[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
+	fi
+
+	export CC_ALT="${CC_ALT}"
+	export ALT="${ALT}"
+
+	epatch "${FILESDIR}"/${PV}-ldflags.patch
+}
+
+src_compile() {
+	cd src
+	emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all || die
+}
+
+src_install() {
+	dobin bin/* || die
+	doman doc/{prss3.1,fasta35.1,pvcomp.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1} || die
+	dodoc  FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*} || die
+}
diff --git a/sci-biology/fasta/fasta-36.3.5e.ebuild b/sci-biology/fasta/fasta-36.3.5e.ebuild
new file mode 100644
index 000000000000..96494b79aa34
--- /dev/null
+++ b/sci-biology/fasta/fasta-36.3.5e.ebuild
@@ -0,0 +1,78 @@
+# Copyright 1999-2015 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+
+inherit eutils flag-o-matic toolchain-funcs
+
+DESCRIPTION="FASTA is a DNA and Protein sequence alignment software package"
+HOMEPAGE="http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml"
+SRC_URI="http://faculty.virginia.edu/wrpearson/${PN}/${PN}36/${P}.tar.gz"
+
+LICENSE="fasta"
+SLOT="0"
+KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux ~x64-macos ~x86-macos"
+IUSE="debug cpu_flags_x86_sse2 test"
+
+DEPEND="test? ( app-shells/tcsh )"
+RDEPEND=""
+
+src_prepare() {
+	CC_ALT=
+	CFLAGS_ALT=
+	ALT=
+
+	use debug && append-flags -DDEBUG
+
+	if [[ $(tc-getCC) == *icc* ]]; then
+		CC_ALT=icc
+		ALT="${ALT}_icc"
+	else
+		CC_ALT=$(tc-getCC)
+		use x86 && ALT="32"
+		use amd64 && ALT="64"
+	fi
+
+	if use cpu_flags_x86_sse2 ; then
+		ALT="${ALT}_sse2"
+		append-flags -msse2
+		[[ $(tc-getCC) == *icc* ]] || append-flags -ffast-math
+	fi
+
+	export CC_ALT="${CC_ALT}"
+	export ALT="${ALT}"
+
+	epatch "${FILESDIR}"/${P}-ldflags.patch
+
+	sed \
+		-e 's:-ffast-math::g' \
+		-i make/Makefile* || die
+
+}
+
+src_compile() {
+	cd src || die
+	emake -f ../make/Makefile.linux${ALT} CC="${CC_ALT} ${CFLAGS}" HFLAGS="${LDFLAGS} -o" all
+}
+
+src_test() {
+	cd test || die
+	FASTLIBS="../conf" bash test.sh || die
+}
+
+src_install() {
+	local bin
+	dobin bin/*
+
+	pushd bin > /dev/null || die
+	for bin in *36; do
+		dosym ${bin} /usr/bin/${bin%36} || die
+	done
+	popd
+
+	insinto /usr/share/${PN}
+	doins -r conf/* data seq
+
+	doman doc/{prss3.1,fasta36.1,fasts3.1,fastf3.1,ps_lav.1,map_db.1}
+	dodoc  FASTA_LIST README doc/{README.versions,readme*,fasta*,changes*}
+}
diff --git a/sci-biology/fasta/files/35.4.10-ldflags.patch b/sci-biology/fasta/files/35.4.10-ldflags.patch
new file mode 100644
index 000000000000..c3b7a9b56904
--- /dev/null
+++ b/sci-biology/fasta/files/35.4.10-ldflags.patch
@@ -0,0 +1,26 @@
+diff --git a/make/Makefile.pcom b/make/Makefile.pcom
+index a808667..405be95 100644
+--- a/make/Makefile.pcom
++++ b/make/Makefile.pcom
+@@ -274,16 +274,16 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+ 
+ map_db : map_db.c uascii.h ncbl2_head.h
+-	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+ 
+ list_db : list_db.c
+-	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+ 
+ lav2ps : lav2plt.o lavplt_ps.o
+-	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+ 
+ lav2svg : lav2plt.o lavplt_svg.o
+-	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
+ 
+ res_stats : res_stats.o scale_se.o
+-	$(CC) -DUNIX -o $(BIN)/res_stats res_stats.o scale_se.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/res_stats res_stats.o scale_se.o -lm
diff --git a/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
new file mode 100644
index 000000000000..a6eeabfdf46c
--- /dev/null
+++ b/sci-biology/fasta/files/fasta-36.3.5e-ldflags.patch
@@ -0,0 +1,74 @@
+ make/Makefile.pcom   | 8 ++++----
+ make/Makefile.pcom_s | 8 ++++----
+ make/Makefile.pcom_t | 8 ++++----
+ 3 files changed, 12 insertions(+), 12 deletions(-)
+
+diff --git a/make/Makefile.pcom b/make/Makefile.pcom
+index 9c5f801..33fc001 100644
+--- a/make/Makefile.pcom
++++ b/make/Makefile.pcom
+@@ -209,14 +209,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+ 
+ map_db : map_db.c uascii.h ncbl2_head.h
+-	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+ 
+ list_db : list_db.c
+-	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+ 
+ 
+ lav2ps : lav2plt.o lavplt_ps.o
+-	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+ 
+ lav2svg : lav2plt.o lavplt_svg.o
+-	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
+diff --git a/make/Makefile.pcom_s b/make/Makefile.pcom_s
+index dc53001..8a45044 100644
+--- a/make/Makefile.pcom_s
++++ b/make/Makefile.pcom_s
+@@ -143,14 +143,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+ 
+ map_db : map_db.c uascii.h ncbl2_head.h
+-	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+ 
+ list_db : list_db.c
+-	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+ 
+ 
+ lav2ps : lav2plt.o lavplt_ps.o
+-	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+ 
+ lav2svg : lav2plt.o lavplt_svg.o
+-	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
+diff --git a/make/Makefile.pcom_t b/make/Makefile.pcom_t
+index 8a71438..5b08a50 100644
+--- a/make/Makefile.pcom_t
++++ b/make/Makefile.pcom_t
+@@ -164,14 +164,14 @@ print_pssm : print_pssm.c getseq.c karlin.c apam.c
+ 	$(CC) -o print_pssm $(CFLAGS) print_pssm.c getseq.c karlin.c apam.c $(LIB_M)
+ 
+ map_db : map_db.c uascii.h ncbl2_head.h
+-	$(CC) $(CFLAGS) -o $(BIN)/map_db map_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/map_db map_db.c
+ 
+ list_db : list_db.c
+-	$(CC) $(CFLAGS) -o $(BIN)/list_db list_db.c
++	$(CC) $(CFLAGS) $(HFLAGS) $(BIN)/list_db list_db.c
+ 
+ 
+ lav2ps : lav2plt.o lavplt_ps.o
+-	$(CC) -DUNIX -o $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2ps lav2plt.o lavplt_ps.o -lm
+ 
+ lav2svg : lav2plt.o lavplt_svg.o
+-	$(CC) -DUNIX -o $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
++	$(CC) -DUNIX $(HFLAGS) $(BIN)/lav2svg  lav2plt.o lavplt_svg.o -lm
diff --git a/sci-biology/fasta/metadata.xml b/sci-biology/fasta/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/fasta/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>