[gentoo-commits] proj/sci:master commit in: sci-biology/seqtk/files/, sci-biology/seqtk/

[gentoo-commits] proj/sci:master commit in: sci-biology/seqtk/files/, sci-biology/seqtk/

[Martin Mokrejs]

commit:     213fbaee602b48bf23d3de3f55691dc6ea9fea07
Author:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
AuthorDate: Tue Nov 27 13:49:25 2018 +0000
Commit:     Martin Mokrejs <mmokrejs <AT> fold <DOT> natur <DOT> cuni <DOT> cz>
CommitDate: Tue Nov 27 13:59:03 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=213fbaee

sci-biology/seqtk: new package

This package will be needed by sci-biology/tigmint

Package-Manager: Portage-2.3.51, Repoman-2.3.11
Signed-off-by: Martin Mokrejs <mmokrejs <AT> fold.natur.cuni.cz>

 sci-biology/seqtk/files/seqtk-1.3_Makefile.patch | 27 ++++++++++++++++++++++++
 sci-biology/seqtk/metadata.xml                   | 12 +++++++++++
 sci-biology/seqtk/seqtk-1.3.ebuild               | 22 +++++++++++++++++++
 3 files changed, 61 insertions(+)

diff --git a/sci-biology/seqtk/files/seqtk-1.3_Makefile.patch b/sci-biology/seqtk/files/seqtk-1.3_Makefile.patch
new file mode 100644
index 000000000..bc0af18c5
--- /dev/null
+++ b/sci-biology/seqtk/files/seqtk-1.3_Makefile.patch
@@ -0,0 +1,27 @@
+diff --git a/Makefile b/Makefile
+index 0a60ccc..1f3e429 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,6 +1,9 @@
+-CC=gcc
+-CFLAGS=-g -Wall -O2 -Wno-unused-function
+-BINDIR=/usr/local/bin
++CC ?= gcc
++CFLAGS ?= -g -Wall -O2 -Wno-unused-function
++PREFIX ?= /usr/local
++BINDIR ?= $(DESTDIR)$(PREFIX)/bin
++INSTALL ?= install
++MKDIR ?= mkdir
+ 
+ all:seqtk
+ 
+@@ -8,7 +11,8 @@ seqtk:seqtk.c khash.h kseq.h
+ 		$(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
+ 
+ install:all
+-		install seqtk $(BINDIR)
++		$(MKDIR) -p $(BINDIR)
++		$(INSTALL) seqtk $(BINDIR)
+ 
+ clean:
+ 		rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*

diff --git a/sci-biology/seqtk/metadata.xml b/sci-biology/seqtk/metadata.xml
new file mode 100644
index 000000000..138cb7705
--- /dev/null
+++ b/sci-biology/seqtk/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>mmokrejs@fold.natur.cuni.cz</email>
+		<name>Martin Mokrejs</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-biology@gentoo.org</email>
+		<name>Gentoo Biology Project</name>
+	</maintainer>
+</pkgmetadata>

diff --git a/sci-biology/seqtk/seqtk-1.3.ebuild b/sci-biology/seqtk/seqtk-1.3.ebuild
new file mode 100644
index 000000000..2024de85d
--- /dev/null
+++ b/sci-biology/seqtk/seqtk-1.3.ebuild
@@ -0,0 +1,22 @@
+# Copyright 2018 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+DESCRIPTION="Manipulate FASTA and FASTQ files"
+HOMEPAGE="https://github.com/lh3/seqtk"
+SRC_URI="https://github.com/lh3/seqtk/archive/v1.3.tar.gz -> ${P}.tar.gz"
+
+LICENSE="MIT"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+
+DEPEND=""
+RDEPEND="${DEPEND}"
+BDEPEND=""
+PATCHES="${FILESDIR}"/"${P}"_Makefile.patch
+
+src_install(){
+	emake install BINDIR="${ED}/usr/bin"
+}