CVS commit: pkgsrc/biology/seqtk

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Tue May 23 23:19:31 UTC 2023

Added Files:
        pkgsrc/biology/seqtk: DESCR Makefile PLIST distinfo
        pkgsrc/biology/seqtk/patches: patch-Makefile

Log Message:
biology/seqtk: Process FASTA/FASTQ sequences

Seqtk is a fast and lightweight tool for processing sequences in the
FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files
which can also be optionally compressed by gzip.  It performs basic
file conversions and edits much like standard Unix tools do with text
files.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/seqtk/DESCR \
    pkgsrc/biology/seqtk/Makefile pkgsrc/biology/seqtk/PLIST \
    pkgsrc/biology/seqtk/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/seqtk/patches/patch-Makefile

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/seqtk/DESCR
diff -u /dev/null pkgsrc/biology/seqtk/DESCR:1.1
--- /dev/null   Tue May 23 23:19:31 2023
+++ pkgsrc/biology/seqtk/DESCR  Tue May 23 23:19:31 2023
@@ -0,0 +1,4 @@
+Seqtk is a fast and lightweight tool for processing sequences in the FASTA or
+FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be
+optionally compressed by gzip.  It performs basic file conversions and edits
+much like standard Unix tools do with text files.
Index: pkgsrc/biology/seqtk/Makefile
diff -u /dev/null pkgsrc/biology/seqtk/Makefile:1.1
--- /dev/null   Tue May 23 23:19:31 2023
+++ pkgsrc/biology/seqtk/Makefile       Tue May 23 23:19:31 2023
@@ -0,0 +1,15 @@
+# $NetBSD: Makefile,v 1.1 2023/05/23 23:19:31 bacon Exp $
+
+DISTNAME=      seqtk-1.4
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=lh3/}
+GITHUB_TAG=    v${PKGVERSION_NOREV}
+
+OWNER=         bacon%NetBSD.org@localhost
+HOMEPAGE=      https://github.com/lh3/seqtk
+COMMENT=       Tool for processing sequences in FASTA/FASTQ format
+LICENSE=       gnu-gpl-v2
+
+INSTALLATION_DIRS=     bin
+
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/seqtk/PLIST
diff -u /dev/null pkgsrc/biology/seqtk/PLIST:1.1
--- /dev/null   Tue May 23 23:19:31 2023
+++ pkgsrc/biology/seqtk/PLIST  Tue May 23 23:19:31 2023
@@ -0,0 +1,2 @@
+@comment $NetBSD: PLIST,v 1.1 2023/05/23 23:19:31 bacon Exp $
+bin/seqtk
Index: pkgsrc/biology/seqtk/distinfo
diff -u /dev/null pkgsrc/biology/seqtk/distinfo:1.1
--- /dev/null   Tue May 23 23:19:31 2023
+++ pkgsrc/biology/seqtk/distinfo       Tue May 23 23:19:31 2023
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2023/05/23 23:19:31 bacon Exp $
+
+BLAKE2s (seqtk-1.4.tar.gz) = e5003661166ace64fdaf3856e23d13163ebe2d5aa3f7a684ff44f76abca5768b
+SHA512 (seqtk-1.4.tar.gz) = d94ff75e23c9c63c948fd5ba23b52ca29df709c2fef76ee201342b4f32c53cf79366b55f05a689071d1b35770e01344787a87ce590b86c542ddc7c4ae393c8a1
+Size (seqtk-1.4.tar.gz) = 23748 bytes
+SHA1 (patch-Makefile) = 73432a36f982aede58914b6e0b1e0fc8e6a77b23

Index: pkgsrc/biology/seqtk/patches/patch-Makefile
diff -u /dev/null pkgsrc/biology/seqtk/patches/patch-Makefile:1.1
--- /dev/null   Tue May 23 23:19:31 2023
+++ pkgsrc/biology/seqtk/patches/patch-Makefile Tue May 23 23:19:31 2023
@@ -0,0 +1,39 @@
+$NetBSD: patch-Makefile,v 1.1 2023/05/23 23:19:31 bacon Exp $
+
+# Respect env
+
+--- Makefile.orig      2018-06-18 00:15:09 UTC
++++ Makefile
+@@ -1,14 +1,23 @@
+-CC=gcc
+-CFLAGS=-g -Wall -O2 -Wno-unused-function
+-BINDIR=/usr/local/bin
+ 
+-all:seqtk
++# Respect user's build environment by using ?= to set defaults for variables
++# not set in the env or make arguments.  Use += to add essential args.
+ 
+-seqtk:seqtk.c khash.h kseq.h
+-              $(CC) $(CFLAGS) seqtk.c -o $@ -lz -lm
++CC    ?= gcc
++CFLAGS        ?= -g -Wall -O2 -Wno-unused-function
++LDFLAGS       += -lz -lm
++PREFIX        ?= /usr/local
++MKDIR ?= mkdir
++INSTALL       ?= install
++# DESTDIR is empty by default to install straight to PREFIX
+ 
+-install:all
+-              install seqtk $(BINDIR)
++all: seqtk
+ 
++seqtk: seqtk.c khash.h kseq.h
++      $(CC) $(CFLAGS) seqtk.c -o $@ $(LDFLAGS)
++
++install: all
++      $(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
++      $(INSTALL) -c -m 0755 seqtk $(DESTDIR)$(PREFIX)/bin
++
+ clean:
+-              rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*
++      rm -fr gmon.out *.o ext/*.o a.out seqtk trimadap *~ *.a *.dSYM session*