reinit the tree, so we can have metadata

4 files changed, 161 insertions, 0 deletions

diff --git a/sci-biology/phrap/Manifest b/sci-biology/phrap/Manifest
new file mode 100644
index 000000000000..d09e0882b062
--- /dev/null
+++ b/sci-biology/phrap/Manifest
@@ -0,0 +1,6 @@
+AUX phrap-1.080812-fix-build-system.patch 3600 SHA256 ce995ffdad2e8d5d63e3a095e9c7616fdc94f6a7d4401c554f3359e673ac7f3c SHA512 536ad862b9b8ce0fbc7ab67bc48db597e7d4b8c66018a5abefe5a59f4fbc30a4a76c94f4c13f5af7d42a422a22f5181d8f015b797d37f175238c3d4170adf21c WHIRLPOOL 4a4dd715bc8c71705789997a3039c07f6148f17463c9afe0456c5a9d09de4483f12923897f89cf230819476344386a40d7e926ddaf4d432ffee2d9212c413c00
+DIST phrap-1.080812-distrib.tar.gz 317350 SHA256 7025f3cb30e5a3305a13d150f39a85580ade0bbf8169b25db65cbe396e201052 SHA512 6b125b9a99b6180eb5de16bccfe068abefdb59237fd3295924c418749f2f2d6e39cdbcecc6786e42738846975334c4d8a645eae8fd0fcbda6b0e99241deb15ca WHIRLPOOL e516561804620ba8c96ed0e5c5d791f3fe1e7984e08f646e6fd7c30042f2550f5d1c9b2f800e8a853e42b049b92418ed9d0121e77bf4e9aa895974bce5e73717
+EBUILD phrap-1.080812-r2.ebuild 950 SHA256 b98d56ca4718e86872195133dc4abcbc8308faad70cb958f87c08d0228907239 SHA512 4857f1fe337f24ee33618e3dac40a5edb7210d1353c058b57a1263a4ccdd8213270827c2c2f902d454226fc65368a1588d497dcdcf2eb9c15af406d1d5cac3fe WHIRLPOOL 45f46d85e8030d8e3b1ab805b97b25b731dde1956ec39c143e7507325294c43ddd780583ab7edd074bfd9161ce6c6a8e46ccc1abb726b69c85922645dd7ff613
+MISC ChangeLog 2829 SHA256 00f1db92cfbee3d80b26fe8193ef549bd70b5900d7819b9b9cdec54f76449170 SHA512 c98163ea771352ee0930a181ebbdb521a5c9057216afee402ea5edfb784c2ec316ce6c79076a8d1be2999d9d6a01355ebf5ce203322946b16035105b9fb05f6d WHIRLPOOL 94cda4fe5d3c0abd581484bf7ef7bf8292d5d727e2eaeb2d40fa8584f54273d5b34f60e7969ab7a6583bb931e18f981445c00a651796b431572e5691e81a1da2
+MISC ChangeLog-2015 948 SHA256 e18d1784109b55db14e7b9a4fb61e5d4b66813e114669c28420953cb014b6be5 SHA512 f23fd3cf92ef5071d962702da3bd3253b949a1982ea4a67d9ea09308c6bec3811753916b37a3853c02b199bcb56245549c8d84dc7bbb84eb2cf3dcd6ad158f6e WHIRLPOOL f44d52aa4612ccf877d37ad97102a4a8d565e406b68805e366e573f179beda0d2076268298d1905202c2958d23f69bcee8e5a018ad6874cb7308a858d9151176
+MISC metadata.xml 267 SHA256 b3535fccca0fc8511c1245214c1a7c105447b35f21093bda132991874ce82d48 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403 WHIRLPOOL d841a2f928c50434f2e8c65f583ea3aa2d04e5cebd664b1531ab5373260f735219131991000bbb2b21aa3add05dcdce29548b78eac8d8c0eced6dc5505b64e13
diff --git a/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch
new file mode 100644
index 000000000000..6d30c2ce326a
--- /dev/null
+++ b/sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch
@@ -0,0 +1,100 @@
+* Fix perl shebang to be portable
+* Make build system honour LDFLAGS
+
+--- a/makefile
++++ b/makefile
+@@ -25,9 +25,8 @@
+ # Makefile for swat, phrap, cross_match, phrapview; also swprobs (currently inactivated)
+ #CC= icc
+ #CFLAGS= -O2 -wd266,880
+-CC= cc
+-CFLAGS= -O2
+-LFLAGS= -lm
++CC ?= cc
++LIBS = -lm
+ 
+ SWATOBJS= swat.o weibull.o
+ 
+@@ -96,46 +95,46 @@
+ 	chmod a+x phrapview
+ 
+ swat: makefile $(SWATOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(SWATOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r swat
+ 
+ alpha_swat: makefile $(ALPHOBJS) $(SWOBJS) 
+-	$(CC) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LFLAGS) 
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ALPHOBJS) $(SWOBJS) $(LIBS) 
+ 	chmod o-r alpha_swat
+ 
+ swat_counts: makefile $(COUNOBJS) $(SWOBJS) 
+-	$(CC) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LFLAGS) 
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(COUNOBJS) $(SWOBJS) $(LIBS) 
+ 	chmod o-r swat_counts
+ 
+ swprobs: makefile $(PROBOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(PROBOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(PROBOBJS) $(LIBS)
+ 
+ phrap: makefile phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ phrap.o call_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r phrap
+ 
+ gcphrap: makefile gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS)
+-	$(CC) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ gcphrap.o gccall_subs.o $(PHOBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS)
+ 	chmod o-r gcphrap
+ 
+ cross_match: makefile cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ cross_match.o call_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r cross_match
+ 
+ gccross_match: makefile gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS)
+-	$(CC) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ gccross_match.o gccall_subs.o $(CROBJS) $(SCANOBJS) $(SWOBJS) $(JKBSWOBJS) $(LIBS)
+ 	chmod o-r gccross_match
+ 
+ cluster: makefile $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(CLOBJS) call_subs.o $(SCANOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r cluster
+ 
+ loco: makefile $(LOCOOBJS) $(SWOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(LOCOOBJS) $(SWOBJS) $(LIBS)
+ 	chmod o-r loco
+ 
+ erf_test: $(ERFOBJS)
+-	$(CC) $(CFLAGS) -o $@ $(ERFOBJS) $(LFLAGS)
++	$(CC) $(LDFLAGS) $(CFLAGS) -o $@ $(ERFOBJS) $(LIBS)
+ 
+ loco.o: swat.h
+ 
+@@ -228,7 +227,7 @@
+ anomalies.o: swat.h 
+ 
+ fast_smith_wat.s: fast_smith_wat.c
+-	cc -S -machine_code -source_listing -O3 fast_smith_wat.c
++	$(CC) $(CFLAGS) -S -machine_code -source_listing fast_smith_wat.c
+ #N.B. fast_smith_wat.s MUST BE EDITTED BEFORE USE!!!
+ 
+ tig_node.o: swat.h
+--- a/phrapview
++++ b/phrapview
+@@ -1,4 +1,4 @@
+-#!/usr/local/bin/perl -w
++#!/usr/bin/env perl
+ 
+ 
+ #/*****************************************************************************
+@@ -25,6 +25,7 @@
+ #                                                                         
+ #*****************************************************************************/
+ 
++use warnings;
+ use strict;
+ use Tk;
+ #phrapview version 0.960731
diff --git a/sci-biology/phrap/metadata.xml b/sci-biology/phrap/metadata.xml
new file mode 100644
index 000000000000..959160fe46b1
--- /dev/null
+++ b/sci-biology/phrap/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-biology@gentoo.org</email>
+    <name>Gentoo Biology Project</name>
+  </maintainer>
+</pkgmetadata>
diff --git a/sci-biology/phrap/phrap-1.080812-r2.ebuild b/sci-biology/phrap/phrap-1.080812-r2.ebuild
new file mode 100644
index 000000000000..6cccc6c61bf0
--- /dev/null
+++ b/sci-biology/phrap/phrap-1.080812-r2.ebuild
@@ -0,0 +1,47 @@
+# Copyright 1999-2016 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="Shotgun assembly and alignment utilities"
+HOMEPAGE="http://www.phrap.org/"
+SRC_URI="phrap-${PV}-distrib.tar.gz"
+
+LICENSE="phrap"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="
+	dev-lang/perl
+	dev-perl/Tk"
+
+S="${WORKDIR}"
+
+RESTRICT="fetch"
+PATCHES=( "${FILESDIR}/${PN}-1.080812-fix-build-system.patch" )
+
+pkg_nofetch() {
+	einfo "Please visit http://www.phrap.org/phredphrapconsed.html and obtain the file"
+	einfo "\"distrib.tar.gz\", then rename it to \"phrap-${PV}-distrib.tar.gz\""
+	einfo "and put it in ${DISTDIR}"
+}
+
+src_compile() {
+	emake CC="$(tc-getCC)" \
+		CFLAGS="${CFLAGS}" \
+		LDFLAGS="${LDFLAGS}"
+}
+
+src_install() {
+	dobin cross_match loco phrap phrapview swat
+	newbin cluster cluster_phrap
+
+	local i
+	for i in {general,phrap,swat}.doc; do
+		newdoc ${i} ${i}.txt
+	done
+}