reinit the tree, so we can have metadata

5 files changed, 112 insertions, 0 deletions

diff --git a/sci-biology/pilercr/Manifest b/sci-biology/pilercr/Manifest
new file mode 100644
index 000000000000..62051e7c76c4
--- /dev/null
+++ b/sci-biology/pilercr/Manifest
@@ -0,0 +1,7 @@
+AUX pilercr-1.0-fix-build-system.patch 673 SHA256 4f33e868c973bbc6b787ed4618574e92562a927382908f123ecd7cde0fe546ef SHA512 b744c3fdc6e1ec152a27592ce8036de080c113b6385c5743dfca325ae8e0435d34418ca9f51830c540cf8efae710d842b89dd1b2b7b772379a4f527a72ff2c06 WHIRLPOOL a011e5302a3d46de49e2263273c50a367b7bebfec25305b11cf325963933d01e033d7e965787dd597e826bb4b94fbee1aed53e80572c4dce2734aad0bd7997d5
+AUX pilercr-1.0-gcc43.patch 854 SHA256 ee86cf9ad7ab5f18f9d06673c930d4c72f1e387c5b5fccc81044edbf613d7123 SHA512 7e83a1c29f2b6b11e101ffebf99516c9da06f7fa7645aa619a89c365dc89d6ea2659d4610eea25b6e260328b56320e6d720f3d0d67a01aae450104fc9513d58e WHIRLPOOL 721e2a8207631e96adb1b9a3c638b0306f2364fae763a68d6fc9b64bfc4971803ae7c15f300116a6146d9634ced1b5d73c82923ebdde7d30d010c37dc4f32daa
+DIST pilercr-1.0.tar.gz 1709144 SHA256 75f58d58567c478e271c4c554071a7d6d642e6daef8981ee2618daa7b53fa923 SHA512 c262ceef1d1af9e71f454809e940c2ad6d835a8404daa51ccef698b8348a504c697f5b5c268ec24df611f5adda2932e4982bcdabe4fbdf99d8c204f0f77f1be5 WHIRLPOOL 31639d51cb219efb62a70e05fe7be9d8e3c1980fdb11dfe6c32248f962881403a95553623de6f4a0f93897f6cc41e0344f355079a0ff2c386afa5e6d275f3304
+EBUILD pilercr-1.0-r1.ebuild 594 SHA256 4be488e3f5002392c3b0ee4c9cb0601b22a867054ed1155015cb43dbca8f6046 SHA512 5841ff12c7fa7d2290b2310aaba5fd0ec2688e5364e0f973314d9eeb6641fe43d0ff30374bc327f3d6152fd81476424f423841adac6d52656690d0a12090119c WHIRLPOOL 499287f2484a296ae3e993a9ab31cb8f7a4e08dce187144421d48746d33bdf950fc8e4c5f00b53fa644f5d33cab64d78c66643df2a821b6c1d71232568d5ff7f
+MISC ChangeLog 2458 SHA256 ffa5ca6853f53b10817890f92a1b7fbc083638122e8c0c9f30f1b20fb0a0a126 SHA512 9cfeb9fd545d2b78de02c543d49198cf943285d8684dcdb6b6202718d43498bcd0e03255828a61af52148ef8c25a80245dfeba55c756c55dc1729d51b9b11639 WHIRLPOOL 53e05a378ba39e35a8506e7b048af29269676987d2382432a14d0f54181b120e6fff2e544bb230166d11267fa3f5d569d1dc7735ac0137f34e0b67e9b7b229f5
+MISC ChangeLog-2015 1130 SHA256 f497b5ef24802df4a8eac553ec05249f0c9cadb928192a13cf0945818eef4514 SHA512 5d7877a119a157a9fb36e772db9a4b105ee75e84865f223012519f4679a7e2261a9566a5d8ea73a0dcf1857b1281f3cbe0fb590589eac79c5d269801dc0e0c57 WHIRLPOOL fde7155161c441ba0d3a232ee87d6727d8b15236582a7ef4c5cfb9ad89fdaa8c82595c406e3b9a2bf49bdc7b95fbaa5b1ca713094bf29beb2baa5b6ffe7d544e
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch b/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch
new file mode 100644
index 000000000000..3754f80a9346
--- /dev/null
+++ b/sci-biology/pilercr/files/pilercr-1.0-fix-build-system.patch
@@ -0,0 +1,34 @@
+Make build system honour user variables
+
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,4 @@
+-CFLAGS = -O3 -funroll-loops -Winline -DNDEBUG=1
+-#CFLAGS = -O3 -funroll-loops -Winline
+-LDLIBS = -lm -static
+-# LDLIBS = -lm
++LDLIBS = -lm
+ 
+ OBJ = .o
+ EXE =
+@@ -9,17 +6,13 @@
+ RM = rm -f
+ CP = cp
+ 
+-GPP = g++
+-LD = $(GPP) $(CFLAGS)
+-CPP = $(GPP) -c $(CFLAGS) 
+-
+ all: pilercr
+ 
+ CPPSRC = $(sort $(wildcard *.cpp))
+ CPPOBJ	= $(subst .cpp,.o,$(CPPSRC))
+ 
+-$(CPPOBJ): %.o: %.cpp
+-	$(CPP) $< -o $@
++%.o: %.cpp
++	$(CXX) $(CXXFLAGS) -DNDEBUG $(CPPFLAGS) -c $< -o $@
+ 
+ pilercr: $(CPPOBJ)
+-	$(LD) -o pilercr $(CPPOBJ) $(LDLIBS)
++	$(CXX) $(LDFLAGS) $(CXXFLAGS) -o pilercr $(CPPOBJ) $(LDLIBS)
diff --git a/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch
new file mode 100644
index 000000000000..7b49df872e27
--- /dev/null
+++ b/sci-biology/pilercr/files/pilercr-1.0-gcc43.patch
@@ -0,0 +1,33 @@
+diff -dur work/multaln.h work-orig/multaln.h
+--- work/multaln.h	2007-04-17 19:02:18.000000000 +0000
++++ work-orig/multaln.h	2009-02-18 21:25:26.166333299 +0000
+@@ -6,6 +6,7 @@
+ #define _CRT_SECURE_NO_DEPRECATE	1

+ #endif

+ 

++#include <cstring>

+ #include <vector>

+ #include <limits.h>

+ #include <ctype.h>

+diff -dur work/seqvect.h work-orig/seqvect.h
+--- work/seqvect.h	2006-04-06 23:36:18.000000000 +0000
++++ work-orig/seqvect.h	2009-02-18 21:25:26.171090246 +0000
+@@ -1,6 +1,7 @@
+ #ifndef SeqVect_h

+ #define SeqVect_h

+ 

++#include <stdio.h>

+ #include <vector>

+ #include "seq.h"

+ 

+diff -dur work/tree.h work-orig/tree.h
+--- work/tree.h	2006-04-05 23:52:42.000000000 +0000
++++ work-orig/tree.h	2009-02-18 21:25:26.171090246 +0000
+@@ -1,6 +1,7 @@
+ #ifndef tree_h

+ #define tree_h

+ 

++#include <stdlib.h>

+ #include <limits.h>

+ 

+ class Clust;

diff --git a/sci-biology/pilercr/metadata.xml b/sci-biology/pilercr/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/pilercr/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/pilercr/pilercr-1.0-r1.ebuild b/sci-biology/pilercr/pilercr-1.0-r1.ebuild
new file mode 100644
index 000000000000..8b1abd5de7d7
--- /dev/null
+++ b/sci-biology/pilercr/pilercr-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="Analysis of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)"
+HOMEPAGE="http://www.drive5.com/pilercr/"
+SRC_URI="http://www.drive5.com/pilercr/pilercr1.06.tar.gz -> ${P}.tar.gz"
+
+LICENSE="public-domain"
+SLOT="0"
+KEYWORDS="amd64 x86"
+IUSE=""
+
+S=${WORKDIR}
+
+PATCHES=(
+	"${FILESDIR}"/${PN}-1.0-fix-build-system.patch
+	"${FILESDIR}"/${PN}-1.0-gcc43.patch
+)
+
+src_configure() {
+	tc-export CXX
+}
+
+src_install() {
+	dobin ${PN}
+}