CVS commit: pkgsrc/biology/rna-seq

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Thu Apr 11 14:46:53 UTC 2024

Modified Files:
        pkgsrc/biology/rna-seq: Makefile

Log Message:
biology/rna-seq: Update to 1.3.0

Remove multiqc dep, responsible for 117 dependencies, including
gcc, llvm, and rust.
Add sra-tools, lz4, xz, and zstd


To generate a diff of this commit:
cvs rdiff -u -r1.8 -r1.9 pkgsrc/biology/rna-seq/Makefile

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

Modified files:

Index: pkgsrc/biology/rna-seq/Makefile
diff -u pkgsrc/biology/rna-seq/Makefile:1.8 pkgsrc/biology/rna-seq/Makefile:1.9
--- pkgsrc/biology/rna-seq/Makefile:1.8 Mon Aug 14 05:23:52 2023
+++ pkgsrc/biology/rna-seq/Makefile     Thu Apr 11 14:46:53 2024
@@ -1,14 +1,14 @@
-# $NetBSD: Makefile,v 1.8 2023/08/14 05:23:52 wiz Exp $
+# $NetBSD: Makefile,v 1.9 2024/04/11 14:46:53 bacon Exp $
 #
 
-DISTNAME=      rna-seq-1.2.2
-PKGREVISION=   1
+DISTNAME=      rna-seq-1.3.0
 CATEGORIES=    biology meta-pkgs
 MASTER_SITES=  # empty
 
 OWNER=         bacon%NetBSD.org@localhost
 COMMENT=       Core tools needed for RNA-Seq analysis
 
+DEPENDS+=      sra-tools>0:../../biology/sra-tools
 DEPENDS+=      fastq-trim>0:../../biology/fastq-trim
 DEPENDS+=      fastqc>0:../../biology/fastqc
 DEPENDS+=      biolibc-tools>0:../../biology/biolibc-tools
@@ -19,9 +19,11 @@ DEPENDS+=    rna-star>0:../../biology/rna-s
 DEPENDS+=      samtools>0:../../biology/samtools
 DEPENDS+=      igv>0:../../biology/igv
 DEPENDS+=      fasda>0:../../biology/fasda
-DEPENDS+=      ${PYPKGPREFIX}-multiqc-[0-9]*:../../biology/py-multiqc
 DEPENDS+=      webbrowser>0:../../www/webbrowser
 DEPENDS+=      curl>0:../../www/curl
+DEPENDS+=      lz4>0:../../archivers/lz4
+DEPENDS+=      xz>0:../../archivers/xz
+DEPENDS+=      zstd>0:../../archivers/zstd
 
 META_PACKAGE=  yes