CVS commit: pkgsrc/biology/biolibc-tools

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Tue Dec 14 19:05:39 UTC 2021

Modified Files:
        pkgsrc/biology/biolibc-tools: Makefile PLIST distinfo

Log Message:
biology/biolibc-tools: Update to 0.1.1

Make all programs subcommands of "blt"
Several new commands
Updates for evolving libxtend and biolibc APIs
Add --version flag
Numerous minor fixes and enhancements

Changes: https://github.com/auerlab/biolibc-tools/releases/tag/0.1.1


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/biolibc-tools/Makefile \
    pkgsrc/biology/biolibc-tools/PLIST
cvs rdiff -u -r1.3 -r1.4 pkgsrc/biology/biolibc-tools/distinfo

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

Modified files:

Index: pkgsrc/biology/biolibc-tools/Makefile
diff -u pkgsrc/biology/biolibc-tools/Makefile:1.1 pkgsrc/biology/biolibc-tools/Makefile:1.2
--- pkgsrc/biology/biolibc-tools/Makefile:1.1   Tue Aug 31 15:55:16 2021
+++ pkgsrc/biology/biolibc-tools/Makefile       Tue Dec 14 19:05:39 2021
@@ -1,9 +1,8 @@
-# $NetBSD: Makefile,v 1.1 2021/08/31 15:55:16 bacon Exp $
+# $NetBSD: Makefile,v 1.2 2021/12/14 19:05:39 bacon Exp $
 
-DISTNAME=      biolibc-tools-0.1.0.36
+DISTNAME=      biolibc-tools-0.1.1
 CATEGORIES=    biology
 MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
-GITHUB_TAG=    0a781f7ec6566051382d7f4950fd673f73b7fb2f
 
 MAINTAINER=    bacon%NetBSD.org@localhost
 HOMEPAGE=      https://github.com/auerlab/biolibc-tools
@@ -11,10 +10,13 @@ COMMENT=    High-performance bioinformatics
 LICENSE=       2-clause-bsd
 
 BUILD_TARGET=  depend all
+MAKE_ENV+=     VERSION=${PKGVERSION}
 INSTALL_TARGET=        install-strip
 
+pre-build:
+       cd ${WRKSRC} && ${MAKE} PREFIX=${PREFIX} depend
+
 .include "../../devel/xxhash/buildlink3.mk"
 .include "../../devel/uthash/buildlink3.mk"
 .include "../../biology/biolibc/buildlink3.mk"
-.include "../../devel/libxtend/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/biolibc-tools/PLIST
diff -u pkgsrc/biology/biolibc-tools/PLIST:1.1 pkgsrc/biology/biolibc-tools/PLIST:1.2
--- pkgsrc/biology/biolibc-tools/PLIST:1.1      Tue Aug 31 15:55:16 2021
+++ pkgsrc/biology/biolibc-tools/PLIST  Tue Dec 14 19:05:39 2021
@@ -1,8 +1,22 @@
-@comment $NetBSD: PLIST,v 1.1 2021/08/31 15:55:16 bacon Exp $
-bin/fastq-derep.sh
-bin/fastx-derep
-bin/fastx2tsv
+@comment $NetBSD: PLIST,v 1.2 2021/12/14 19:05:39 bacon Exp $
+bin/blt
+libexec/biolibc-tools/chrom-lens
+libexec/biolibc-tools/extract-seq
+libexec/biolibc-tools/fasta2seq
+libexec/biolibc-tools/fastq-derep.sh
+libexec/biolibc-tools/fastx-derep
+libexec/biolibc-tools/fastx2tsv
+libexec/biolibc-tools/find-orfs
+libexec/biolibc-tools/gff2bed
 libexec/biolibc-tools/uniq-seqs.awk
-man/man1/fastq-derep.sh.1
-man/man1/fastx-derep.1
-man/man1/fastx2tsv.1
+libexec/biolibc-tools/vcf-search
+man/man1/blt-chrom-lens.1
+man/man1/blt-extract-seq.1
+man/man1/blt-fasta2seq.1
+man/man1/blt-fastq-derep.sh.1
+man/man1/blt-fastx-derep.1
+man/man1/blt-fastx2tsv.1
+man/man1/blt-find-orfs.1
+man/man1/blt-gff2bed.1
+man/man1/blt-vcf-search.1
+man/man1/blt.1

Index: pkgsrc/biology/biolibc-tools/distinfo
diff -u pkgsrc/biology/biolibc-tools/distinfo:1.3 pkgsrc/biology/biolibc-tools/distinfo:1.4
--- pkgsrc/biology/biolibc-tools/distinfo:1.3   Tue Oct 26 10:03:37 2021
+++ pkgsrc/biology/biolibc-tools/distinfo       Tue Dec 14 19:05:39 2021
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.3 2021/10/26 10:03:37 nia Exp $
+$NetBSD: distinfo,v 1.4 2021/12/14 19:05:39 bacon Exp $
 
-BLAKE2s (biolibc-tools-0.1.0.36-0a781f7ec6566051382d7f4950fd673f73b7fb2f.tar.gz) = 1a919142ac6a2fdec136ae63ca85f83885771ba7732586cdd8b4dd09b871bef7
-SHA512 (biolibc-tools-0.1.0.36-0a781f7ec6566051382d7f4950fd673f73b7fb2f.tar.gz) = 
475fd700923e9e2aa660df80cd7cdb82f0b3386b6d9ebcd3518697616240af021bb5010ff53e885d2d1d582db291a614a7ecf2c5ac4c4e4883700f282fbfadc4
-Size (biolibc-tools-0.1.0.36-0a781f7ec6566051382d7f4950fd673f73b7fb2f.tar.gz) = 11611 bytes
+BLAKE2s (biolibc-tools-0.1.1.tar.gz) = 9b8d4999c641b0b5aaaef88102d59b4972b5f1a6b6782546e274128c57f19c98
+SHA512 (biolibc-tools-0.1.1.tar.gz) = cfd2e7bacef0093a87c28dd4fbab8ee7007e874ee638816c75f6df92dd436d13a1fb6d5faa8e97491711bece19b8bf7d3f5ed0301c732d6c86f4255872884ff6
+Size (biolibc-tools-0.1.1.tar.gz) = 21700 bytes