reinit the tree, so we can have metadata

4 files changed, 78 insertions, 0 deletions

diff --git a/sci-biology/pals/Manifest b/sci-biology/pals/Manifest
new file mode 100644
index 000000000000..d99fecd865d5
--- /dev/null
+++ b/sci-biology/pals/Manifest
@@ -0,0 +1,6 @@
+AUX pals-1.0-fix-build-system.patch 681 SHA256 5c76d6c96a86b41dd2233664e2c46b4f1b2dbd3eb568bc6f1f43d1d9f6341e0f SHA512 bd95517d72cf567a4608878d556919396c9dd1cd77a4e49f2f8604f058c76a1f26c31760ad6ef6048ec12b76de46a6f4c56b5cb27b4aa1f91339c8f14bd963ac WHIRLPOOL d4c573a048bff7128f83a8a9816bc357cd18822cd4207877bc0a45dcedc834518c6f7cfd7895f1dd5f8f5e909366df197778776721e2e09dd0c4cb46ccba2176
+DIST pals-1.0.tar.gz 24895 SHA256 2768adfdd93f56f859744ff9bbbabcc4571b38fa8ea247d505599beee3a962c2 SHA512 655e3311c63709dab1f8a13b193ed30a5ee97c04757a1e8408a74f6110ff3bdd96ba9eb07f4987ed5b83790ffa8cec67f722fee783c4ab4120483a683ebb9b8f WHIRLPOOL 2cfc45858796a5a0a01287cd3b5a7235e90371e092dfe1a90b9c394e8334e16fb01766c6824ca606a86de48740a8036c695517d6797fd6682a7c8fd6bd6ebb02
+EBUILD pals-1.0-r1.ebuild 537 SHA256 cac9bef59956ece082e1736ad589ced57c78ae683b7a8341c6ee2da813bd95ec SHA512 666542e4faefb47a94ab6f7cc3be531f39e2ca3f68324a80bafbccc6c0de162d2a20dbda507709cfd2f207b61734aa21211a93bd597b02599d9648ca557d4b4e WHIRLPOOL 628aa8e53256b17a7e3c8572800198cc59ae6c88edb4dda4f4e103e8c8014ba568024826e9a3ee98e45b2febe4ee8cafd11c5888fb26fe434de70cd5a26f7d28
+MISC ChangeLog 2417 SHA256 74412c43e82063d034da51de2dc2ee4715aaafcee6f221e87adeb5d757f47739 SHA512 091097d1e4fce97c70ac60981a49cda99d6aa0c810f3deeace079a53863ee26444abf1ff665b3da0490bce22bf0fbaaf6f870b4720e29a9dd71c66e80949e666 WHIRLPOOL a1009bcb63ac422303e4262562e98de741c55a488afd078db8078b2c356f9907aaa6a938e63ddb5f4caa3309a7bd48d6cdd3c59d804616b63c52e2297e4516b2
+MISC ChangeLog-2015 833 SHA256 e01db609eed792eac309ba986e590a1761cb355d386f828bf3be89fa4bad361c SHA512 301f9a20d970b2842c26ad1d22774af0739acc39740767919751554a13bd7756fe002f461d12a78f0d38f3f701176a9e63289bc34435b3f1bf9596e21b648f5b WHIRLPOOL 859f587395944c4507c7c9dc72873337b2e5fc69b62be3cd4e7b086df545933992e31cdf85c33f0a92e304d02540579e3d5c39c8d28dd0afdf975d39802e772d
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/pals/files/pals-1.0-fix-build-system.patch b/sci-biology/pals/files/pals-1.0-fix-build-system.patch
new file mode 100644
index 000000000000..a020a697f85b
--- /dev/null
+++ b/sci-biology/pals/files/pals-1.0-fix-build-system.patch
@@ -0,0 +1,34 @@
+Make build system honour user variables
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,4 @@
+-CFLAGS = -O3 -march=pentiumpro -mcpu=pentiumpro -funroll-loops -Winline -DNDEBUG=1
+-LDLIBS = -lm -static
+-# LDLIBS = -lm
++LDLIBS = -lm
+ 
+ OBJ = .o
+ EXE =
+@@ -8,18 +6,13 @@
+ RM = rm -f
+ CP = cp
+ 
+-GPP = g++
+-LD = $(GPP) $(CFLAGS)
+-CPP = $(GPP) -c $(CFLAGS) 
+-CC = gcc -c $(CFLAGS) 
+-
+ all: pals
+ 
+ CPPSRC = $(sort $(wildcard *.cpp))
+ CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
+ 
+-$(CPPOBJ): %.o: %.cpp
+-	$(CPP) $< -o $@
++%.o: %.cpp
++	$(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@
+ 
+ pals: $(CPPOBJ)
+-	$(LD) -o pals $(CPPOBJ) $(LDLIBS)
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o pals $(CPPOBJ) $(LDLIBS)
diff --git a/sci-biology/pals/metadata.xml b/sci-biology/pals/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/pals/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>
diff --git a/sci-biology/pals/pals-1.0-r1.ebuild b/sci-biology/pals/pals-1.0-r1.ebuild
new file mode 100644
index 000000000000..32579b9d0757
--- /dev/null
+++ b/sci-biology/pals/pals-1.0-r1.ebuild
@@ -0,0 +1,30 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Pairwise Aligner for Long Sequences"
+HOMEPAGE="http://www.drive5.com/pals/"
+SRC_URI="http://www.drive5.com/pals/pals_source.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+RDEPEND=""
+DEPEND="${RDEPEND}"
+
+S=${WORKDIR}
+
+PATCHES=( "${FILESDIR}"/${PN}-1.0-fix-build-system.patch )
+
+src_configure() {
+	tc-export CXX
+}
+
+src_install() {
+	dobin pals
+}