head	1.6;
access;
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locks; strict;
comment	@# @;


1.6
date	2024.10.11.22.38.32;	author bacon;	state Exp;
branches;
next	1.5;
commitid	80KZIqc54ZnYpitF;

1.5
date	2023.02.25.13.52.39;	author bacon;	state Exp;
branches;
next	1.4;
commitid	S1ER2JHjc6noBUeE;

1.4
date	2022.02.26.23.11.43;	author bacon;	state Exp;
branches;
next	1.3;
commitid	vBtXjoGGAIbsobuD;

1.3
date	2021.12.17.15.10.06;	author bacon;	state Exp;
branches;
next	1.2;
commitid	ZLdbEZtaduAK01lD;

1.2
date	2021.03.20.18.17.07;	author bacon;	state Exp;
branches;
next	1.1;
commitid	xHhEvARbUkdBL4MC;

1.1
date	2020.07.26.23.30.30;	author bacon;	state Exp;
branches;
next	;
commitid	RWPoxV3qUPCp8EhC;


desc
@@


1.6
log
@biology/samtools: Update to 1.21

Numerous bug fixes and enhancements since 1.17
Changes:        https://github.com/samtools/samtools/releases

Reported by:    portscout
@
text
@$NetBSD$

# Respect pkgsrc env

--- Makefile.orig	2021-03-19 17:48:34.572594186 +0000
+++ Makefile
@@@@ -61,12 +61,11 @@@@ misc_bindir = $(bindir)
 
 MKDIR_P = mkdir -p
 INSTALL = install -p
-INSTALL_DATA    = $(INSTALL) -m 644
-INSTALL_DIR     = $(MKDIR_P) -m 755
-INSTALL_MAN     = $(INSTALL_DATA)
-INSTALL_PROGRAM = $(INSTALL)
-INSTALL_SCRIPT  = $(INSTALL_PROGRAM)
-
+INSTALL_DATA    = ${BSD_INSTALL_DATA}
+INSTALL_DIR     = $(MKDIR_P)
+INSTALL_MAN     = ${BSD_INSTALL_MAN}
+INSTALL_PROGRAM = ${BSD_INSTALL_PROGRAM}
+INSTALL_SCRIPT  = ${BSD_INSTALL_SCRIPT}
 
 PROGRAMS = samtools
 
@


1.5
log
@biology/samtools: Update to 1.17

Numerous enhancements and bug fixes

Changes: https://github.com/samtools/samtools/releases
@
text
@@


1.4
log
@biology/samtools: Update to 1.15

Several minor enhancements and bug fixes
Changes: https://github.com/samtools/samtools/tags
@
text
@@


1.3
log
@biology/samtools: Update to 1.14

Numerous fixes and enhancements since 1.12

Changes: https://github.com/samtools/samtools/tags
@
text
@@


1.2
log
@biology/htslib: Update to 1.12
biology/bcftools: Update to 1.12
biology/samtools: Update to 1.12

Numerous enhancements, performance improvements, and bug fixes since 1.10
Minimized pkgsrc patches in all three packages
Moved htslib to custom tarball since Github-generated distfiles are incomplete
@
text
@@


1.1
log
@biology/samtools: Upgrade to 1.10

Numerous performance and feature improvements and several bug fixes since 1.9
@
text
@d5 1
a5 1
--- Makefile.orig	2020-07-21 20:20:56.996788479 +0000
d7 1
a7 34
@@@@ -21,12 +21,12 @@@@
 # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
 # DEALINGS IN THE SOFTWARE.
 
-CC       = gcc
-AR       = ar
-CPPFLAGS =
+CC       ?= gcc
+AR       ?= ar
+# CPPFLAGS =
 #CFLAGS   = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600
-CFLAGS   = -g -Wall -O2
-LDFLAGS  =
+CFLAGS   ?= -g -Wall -O2
+#LDFLAGS  =
 LIBS     =
 
 LZ4DIR   = ./lz4
@@@@ -47,10 +47,10 @@@@ AOBJS=      bam_index.o bam_plcmd.o sam_
             bam_quickcheck.o bam_addrprg.o bam_markdup.o tmp_file.o
 LZ4OBJS  =  $(LZ4DIR)/lz4.o
 
-prefix      = /usr/local
-exec_prefix = $(prefix)
+PREFIX      ?= /usr/local
+exec_prefix = $(PREFIX)
 bindir      = $(exec_prefix)/bin
-datarootdir = $(prefix)/share
+datarootdir = $(PREFIX)/share
 mandir      = $(datarootdir)/man
 man1dir     = $(mandir)/man1
 
@@@@ -58,12 +58,11 @@@@ man1dir     = $(mandir)/man1
 misc_bindir = $(bindir)
d10 1
a10 1
-INSTALL = install -p
d16 1
d23 1
a24 1
 PROGRAMS = samtools
@