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| author |   Aisha Tammy <gentoo@aisha.cc> | 2020-09-22 07:05:21 -0400 |
|---|---|---|
| committer | Aisha Tammy <gentoo@aisha.cc> | 2020-09-22 07:05:21 -0400 |
| commit | 14015a59ac70cd4a572b88a5be07718db566b62a (patch) | |
| tree | be0fc476bb5bd730a1453358cd901fe0daebb094 /sci-biology | |
| parent | sci-biology/blat: drop package (diff) | |
| download | sci-14015a59ac70cd4a572b88a5be07718db566b62a.tar.gz sci-14015a59ac70cd4a572b88a5be07718db566b62a.tar.bz2 sci-14015a59ac70cd4a572b88a5be07718db566b62a.zip | |
sci-biology/bwa: drop package
present in ::gentoo
Package-Manager: Portage-3.0.7, Repoman-3.0.1
Signed-off-by: Aisha Tammy <gentoo@aisha.cc>
Diffstat (limited to 'sci-biology')
| -rw-r--r-- | sci-biology/bwa/Manifest | 1 | ||||
| -rw-r--r-- | sci-biology/bwa/bwa-0.7.17.ebuild | 34 | ||||
| -rw-r--r-- | sci-biology/bwa/files/bwa-0.7.15-Makefile.patch | 27 | ||||
| -rw-r--r-- | sci-biology/bwa/metadata.xml | 11 |
4 files changed, 0 insertions, 73 deletions
diff --git a/sci-biology/bwa/Manifest b/sci-biology/bwa/Manifest deleted file mode 100644 index d5ec96afa..000000000 --- a/sci-biology/bwa/Manifest +++ /dev/null @@ -1 +0,0 @@ -DIST bwa-0.7.17.tar.bz2 190908 BLAKE2B d646352719a692d35d39ffcfbdbfdbda5d431f3b89b0d8dbc6abc21b64b249512322b123c95190ad35b65fbf3185ba86e8530d060c222d4b3a1787d338779419 SHA512 67cccfef1c7aa1b5aad6b59a49390e8d96f64320c414bfffacf232aeb08c15861e98be826c1b42b6222d6ff086eeb055b1318ea2e9eebfd87b2365d06fc89802 diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild deleted file mode 100644 index 429ba43e6..000000000 --- a/sci-biology/bwa/bwa-0.7.17.ebuild +++ /dev/null @@ -1,34 +0,0 @@ -# Copyright 1999-2018 Gentoo Foundation -# Distributed under the terms of the GNU General Public License v2 - -EAPI=6 - -inherit toolchain-funcs - -DESCRIPTION="Burrows-Wheeler Alignment Tool, a fast short genomic sequence aligner" -HOMEPAGE="http://bio-bwa.sourceforge.net/" -SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2" - -LICENSE="GPL-3" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86 ~x64-macos" - -RDEPEND="dev-lang/perl" - -PATCHES=( "${FILESDIR}"/${PN}-0.7.15-Makefile.patch ) -DOCS=( NEWS.md README-alt.md README.md ) - -src_configure() { - tc-export CC AR -} - -src_install() { - dobin bwa - - exeinto /usr/libexec/${PN} - doexe qualfa2fq.pl xa2multi.pl - - einstalldocs - doman bwa.1 -} diff --git a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch b/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch deleted file mode 100644 index 39b437a02..000000000 --- a/sci-biology/bwa/files/bwa-0.7.15-Makefile.patch +++ /dev/null @@ -1,27 +0,0 @@ ---- bwa-0.7.13/Makefile -+++ bwa-0.7.13/Makefile -@@ -1,8 +1,8 @@ --CC= gcc -+CC?= gcc - #CC= clang --analyze --CFLAGS= -g -Wall -Wno-unused-function -O2 -+CFLAGS?= -g -Wall -Wno-unused-function -O2 - WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS --AR= ar -+AR?= ar - DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) - LOBJS= utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o - AOBJS= QSufSort.o bwt_gen.o bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o \ -@@ -26,10 +26,10 @@ - all:$(PROG) - - bwa:libbwa.a $(AOBJS) main.o -- $(CC) $(CFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) $(AOBJS) main.o -o $@ -L. -lbwa $(LIBS) - - bwamem-lite:libbwa.a example.o -- $(CC) $(CFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) -+ $(CC) $(CFLAGS) $(LDFLAGS) $(DFLAGS) example.o -o $@ -L. -lbwa $(LIBS) - - libbwa.a:$(LOBJS) - $(AR) -csru $@ $(LOBJS) diff --git a/sci-biology/bwa/metadata.xml b/sci-biology/bwa/metadata.xml deleted file mode 100644 index ceb43ead2..000000000 --- a/sci-biology/bwa/metadata.xml +++ /dev/null @@ -1,11 +0,0 @@ -<?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> - <upstream> - <remote-id type="sourceforge">bio-bwa</remote-id> - </upstream> -</pkgmetadata> |