reinit the tree, so we can have metadata

5 files changed, 99 insertions, 0 deletions

diff --git a/sci-biology/piler/Manifest b/sci-biology/piler/Manifest
new file mode 100644
index 000000000000..fd1a64fd3886
--- /dev/null
+++ b/sci-biology/piler/Manifest
@@ -0,0 +1,7 @@
+AUX piler-1.0-fix-build-system.patch 685 SHA256 d17834ccd3cbd1293889e7e45d00c52f9e9c443f7503e402185d6ffffd01c05d SHA512 e8a618615ce62aa6b4d7e5d0a4ec3facd13b6baf2573323a2f9c03d81171f1c32686bd7b82c4576e0b38cc3b30b201750034ab160cdb9170215ff480eb72a3a2 WHIRLPOOL f8965dbba5a91c28d41d00ab9576e1c198d1cf7eb76172e3baa14f18c70797e50f1fda29f429d255f350098bdae6945759ef7498dfdcc2dfd1d5c261b4ed607d
+AUX piler-1.0-glibc-2.10.patch 386 SHA256 46710d6d09df3eb0cd138f70df8cc522b4c7ea4cdd94ad5153800bdfb0019dfb SHA512 0773c9b6c2eb289c8dee3cc8db6ec0250cd8df3b9e5e729305b58b28db64f486571f2f54041c84d178bf984cedfb4d9941c5abd47f772ecdf29e9ec0bdb55fcc WHIRLPOOL 363f26c862cd13d44b68694ddf8fdc85ce7b846258432f59880b951c154e32b68d0e86078b67d6d9ec7b472adc66fd9a196df0e40f6293e2dcda018645880aa9
+DIST piler-1.0.tar.gz 35220 SHA256 2940530c0afd7e49ca6e9cd8a1e3fd9890d87c71f9c19a42b1e468add83ccc69 SHA512 35be1b445f1eaf26f96d0356a04d985fb528754677403df2061c0872107d31819c5fb355e7f616e953a997e67ce781846acaf3cc2a016097aca785b6a26de3d4 WHIRLPOOL 9533cbbf7f69d5022743bb4373bbd7fea65a8a7f4657b6eb2149bf861bd920b80c1a68599820007fcf302f3d651ee2eac1266d0130ecb49714835286afb3d5c3
+EBUILD piler-1.0-r1.ebuild 660 SHA256 1da2822f5328bcda50d4f3dfdb6e4dd0386bf4e762655e92cce498b5bd8ab294 SHA512 7a8b1c64559477101989e3a97eb8d0aa3b6e520df66b0f43a97f2531a2de7fa77acb6b9e6066ab0ac46668cd23bfa9357cebbeb5c610e67f3d757e53e5ce97cf WHIRLPOOL 43919a89e8872e4cc43366af233c3b79b44487aa55ac5452de7c113bc0452e5e8d5768fa766c37e61053ff14f4e991f93119d1336b4d72f2e1330a88e9483372
+MISC ChangeLog 2455 SHA256 46bba3bbc2788f8ed31047c946e5e9d2c92a5ac33862517da591c572a9a88c08 SHA512 bc83204e51c629c021a2172970a17cebb47db222d1fef1339f0119bde943d6a1b9eae425018cccde0f86b2c080ef119ecd670e518770a0b1911bac936cf9ac66 WHIRLPOOL 031a15918c4129fefb357a684363cfc91eb5fcdced21de34ff1744d3520caad8704731dd47461cf7fb24f6e963386750ccedca6b921cde24981f3c603810646a
+MISC ChangeLog-2015 995 SHA256 4855125210fca3a29776cc9f9a5b2d9d594b41fd8ff4106ea9069b8aee995668 SHA512 6fd45ade79d1988b90c20bad113867808d78ca27382c75b509d69cbffa11cc776d70f4ca5c2aba2f2de2ffef0a892e37b3ca72d75f20e08eb218af499031a00e WHIRLPOOL 59abf16de447540babf5f7cfdf94241513ce402e0d3e7488ae567828d05d09560c7687b9fa2d44d432fe8d2f8d4562c8ecc51dcead5e824dc68b6bf5f25bd257
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/piler/files/piler-1.0-fix-build-system.patch b/sci-biology/piler/files/piler-1.0-fix-build-system.patch
new file mode 100644
index 000000000000..78a72f1b4850
--- /dev/null
+++ b/sci-biology/piler/files/piler-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: piler
+ 
+ CPPSRC = $(sort $(wildcard *.cpp))
+ CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
+ 
+-$(CPPOBJ): %.o: %.cpp
+-	$(CPP) $< -o $@
++%.o: %.cpp
++	$(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@
+ 
+ piler: $(CPPOBJ)
+-	$(LD) -o piler $(CPPOBJ) $(LDLIBS)
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o piler $(CPPOBJ) $(LDLIBS)
diff --git a/sci-biology/piler/files/piler-1.0-glibc-2.10.patch b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch
new file mode 100644
index 000000000000..4c7f124c5e3d
--- /dev/null
+++ b/sci-biology/piler/files/piler-1.0-glibc-2.10.patch
@@ -0,0 +1,12 @@
+diff -ur piler.orig/gff.cpp piler/gff.cpp
+--- piler.orig/gff.cpp	2004-12-18 01:25:29.000000000 +0200
++++ piler/gff.cpp	2009-08-09 17:22:33.000000000 +0300
+@@ -70,7 +70,7 @@
+ 		const char *Attrs = Fields[8];

+ 

+ 	// Truncate attrs if comment found

+-		char *Pound = strchr(Attrs, '#');

++		char *Pound = const_cast <char*> (strchr(Attrs, '#'));

+ 		if (0 != Pound)

+ 			*Pound = 0;

+ 

diff --git a/sci-biology/piler/metadata.xml b/sci-biology/piler/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/piler/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/piler/piler-1.0-r1.ebuild b/sci-biology/piler/piler-1.0-r1.ebuild
new file mode 100644
index 000000000000..276ee9bc873e
--- /dev/null
+++ b/sci-biology/piler/piler-1.0-r1.ebuild
@@ -0,0 +1,38 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Analysis of repetitive DNA found in genome sequences"
+HOMEPAGE="http://www.drive5.com/piler/"
+SRC_URI="http://www.drive5.com/piler/piler_source.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	|| (
+		sci-biology/muscle
+		sci-libs/libmuscle
+	)
+	sci-biology/pals"
+
+S=${WORKDIR}
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.0-fix-build-system.patch
+	"${FILESDIR}"/${PN}-1.0-glibc-2.10.patch
+)
+
+src_configure() {
+	tc-export CXX
+}
+
+src_install() {
+	dobin piler
+}