diff options
Diffstat (limited to 'sci-biology/phrap')
| -rw-r--r-- | sci-biology/phrap/Manifest | 6 | ||||
| -rw-r--r-- | sci-biology/phrap/files/phrap-1.080812-fix-build-system.patch | 100 | ||||
| -rw-r--r-- | sci-biology/phrap/metadata.xml | 8 | ||||
| -rw-r--r-- | sci-biology/phrap/phrap-1.080812-r2.ebuild | 47 |
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 +} |