[Gsrc-commit] trunk r9754: some bio updates

[Carl Hansen]

------------------------------------------------------------
revno: 9754
revision-id: carlhansen@gnu.org-20231204031753-3wjedal8bg7d83t5
parent: carlhansen@gnu.org-20231204010201-s7s4ea7sx0mnuejl
committer: carlhansen@gnu.org
branch nick: trunk
timestamp: Sun 2023-12-03 19:17:53 -0800
message:
  some bio updates
modified:
  pkg/bio/bfast/Makefile         makefile-20160617195624-kwz1a09vkg4le6fu-75
  pkg/bio/emboss/Makefile        makefile-20160617195624-kwz1a09vkg4le6fu-102
  pkg/bio/htslib/Makefile        makefile-20160617200040-lqf8h520dfq0rtk7-49
  pkg/bio/htslib/sha256sums      sha256sums-20160617200040-lqf8h520dfq0rtk7-50
  pkg/bio/samtools/Makefile      makefile-20160617195624-kwz1a09vkg4le6fu-176
  pkg/bio/samtools/sha256sums    sha256sums-20160617195624-kwz1a09vkg4le6fu-177
  pkg/bio/seqan3/Makefile        makefile-20160617200040-lqf8h520dfq0rtk7-119
  pkg/bio/seqan3/sha256sums      sha256sums-20160617200040-lqf8h520dfq0rtk7-120

=== modified file 'pkg/bio/bfast/Makefile'
--- a/pkg/bio/bfast/Makefile    2021-10-27 07:04:10 +0000
+++ b/pkg/bio/bfast/Makefile    2023-12-04 03:17:53 +0000
@@ -27,6 +27,7 @@
 LICENSE = GPLv2
 CITE = doi:10.1371/journal.pone.0007767
 
+# no longer maintained
 ######################################################################
 
 MASTER_SITES = $(MASTER_SOURCEFORGE)
@@ -39,5 +40,5 @@
 
 ######################################################################
 
-include ../../../gar/gar.lib/auto.mk
+include ../../../gar/gar.lib/autotools.mk
 include config.mk

=== modified file 'pkg/bio/emboss/Makefile'
--- a/pkg/bio/emboss/Makefile   2016-06-17 19:57:40 +0000
+++ b/pkg/bio/emboss/Makefile   2023-12-04 03:17:53 +0000
@@ -1,6 +1,7 @@
 # Copyright © 2014 Brandon Invergo <brandon@invergo.net>
+# Copyright © 2023 Carl Hansen
 #
-# This file is part of BioSRC.
+# This file is part of BioSRC, and GSRC.
 #
 # BioSRC is free software: you can redistribute it and/or modify it
 # under the terms of the GNU General Public License as published by
@@ -38,13 +39,25 @@
 BUILDDEPS =
 LIBDEPS =
 
-USE_AUTORECONF = y
+#USE_AUTORECONF = y
+CONFIGURE_SCRIPTS = myconf
+INSTALL_SCRIPTS = myinst
+WORKOBJ = $(WORKSRC)
 
 ######################################################################
 
-include ../../../gar/gar.lib/auto.mk
+include ../../../gar/gar.lib/autotools.mk
 include config.mk
 
 pre-configure:
        sed -i 
'$$s|$$(bindir)|LD_LIBRARY_PATH=$(packageDESTDIR)$(prefix)/lib:$$LD_LIBRARY_PATH
 $$(DESTDIR)$$(bindir)|' $(WORKSRC)/Makefile.am
        $(MAKECOOKIE)
+
+configure-myconf:
+       cd $(WORKSRC) &&  DESTDIR=$(packageDESTDIR)    ./configure
+       $(MAKECOOKIE)
+
+
+install-myinst:
+       cd $(WORKSRC) &&  VERBOSE=1 DESTDIR=$(packageDESTDIR) $(MAKE) -k 
install   
+

=== modified file 'pkg/bio/htslib/Makefile'
--- a/pkg/bio/htslib/Makefile   2023-04-23 21:10:43 +0000
+++ b/pkg/bio/htslib/Makefile   2023-12-04 03:17:53 +0000
@@ -22,7 +22,7 @@
 
 NAME = HTSlib
 GARNAME = htslib
-GARVERSION = 1.17
+GARVERSION = 1.18
 HOME_URL = https://github.com/samtools/htslib
 DESCRIPTION = C library for high-throughput sequencing data formats
 define BLURB
@@ -45,8 +45,7 @@
 
 ######################################################################
 
-include ../../../gar/gar.lib/auto.mk
+include ../../../gar/gar.lib/autotools.mk
 include config.mk
 
-#INSTALL_ARGS = prefix=$(packageprefix)
 

=== modified file 'pkg/bio/htslib/sha256sums'
--- a/pkg/bio/htslib/sha256sums 2023-04-23 21:10:43 +0000
+++ b/pkg/bio/htslib/sha256sums 2023-12-04 03:17:53 +0000
@@ -1,1 +1,1 @@
-763779288c40f07646ec7ad98b96c378c739171d162ad98398868783b721839f  
download/htslib-1.17.tar.bz2
+f1ab53a593a2320a1bfadf4ef915dae784006c5b5c922c8a8174d7530a9af18f  
download/htslib-1.18.tar.bz2

=== modified file 'pkg/bio/samtools/Makefile'
--- a/pkg/bio/samtools/Makefile 2023-04-27 18:48:48 +0000
+++ b/pkg/bio/samtools/Makefile 2023-12-04 03:17:53 +0000
@@ -22,7 +22,7 @@
 
 NAME = SAMtools
 GARNAME = samtools
-GARVERSION = 1.17
+GARVERSION = 1.18
 HOME_URL = http://https://www.htslib.org/download/
 DESCRIPTION = Utilities for manipulating alignments in the SAM format
 define BLURB

=== modified file 'pkg/bio/samtools/sha256sums'
--- a/pkg/bio/samtools/sha256sums       2023-04-23 21:15:46 +0000
+++ b/pkg/bio/samtools/sha256sums       2023-12-04 03:17:53 +0000
@@ -1,1 +1,1 @@
-3adf390b628219fd6408f14602a4c4aa90e63e18b395dad722ab519438a2a729  
download/samtools-1.17.tar.bz2
+d686ffa621023ba61822a2a50b70e85d0b18e79371de5adb07828519d3fc06e1  
download/samtools-1.18.tar.bz2

=== modified file 'pkg/bio/seqan3/Makefile'
--- a/pkg/bio/seqan3/Makefile   2022-04-03 23:42:34 +0000
+++ b/pkg/bio/seqan3/Makefile   2023-12-04 03:17:53 +0000
@@ -1,5 +1,5 @@
 # Copyright © 2013, 2014, 2015 Brandon Invergo <brandon@invergo.net>
-# Copyright © 2022 Carl Hansen <carlhansen@gnu.org>
+# Copyright © 2022,2023 Carl Hansen <carlhansen@gnu.org>
 #
 # This file is part of GSRC, the GNU Source Release Collection.
 # http://www.gnu.org/software/gsrc
@@ -19,7 +19,7 @@
 
 NAME = SeqAn3
 GARNAME = seqan3
-GARVERSION = 3.1.0
+GARVERSION = 3.2.0
 HOME_URL = http://www.seqan.de
 DESCRIPTION = A C++ library for the analysis of sequences
 define BLURB

=== modified file 'pkg/bio/seqan3/sha256sums'
--- a/pkg/bio/seqan3/sha256sums 2022-04-03 23:42:34 +0000
+++ b/pkg/bio/seqan3/sha256sums 2023-12-04 03:17:53 +0000
@@ -1,2 +1,2 @@
-0b37b1c3450e19c0ebe42c052c3f87babb8074bd772f10a553949c312c285726  
download/seqan3-3.1.0-Source.tar.xz
-d54d81e140de417991c854d9242af65c59a790f3f3c2bcb60781c1f278691db5  
download/seqan3-3.1.0-Source.tar.xz.sha256
+2737a9dc20c1d728674010662c0c9452aabbb3d4a64725bda24f28335468994c  
download/seqan3-3.2.0-Source.tar.xz
+4686a3b95b6440c3132bc75c49828428aaf7e4bd848737a225b4cd657b7f9374  
download/seqan3-3.2.0-Source.tar.xz.sha256