CVS commit: pkgsrc/biology/chip-seq

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sat Dec 23 16:35:39 UTC 2023

Modified Files:
        pkgsrc/biology/chip-seq: DESCR Makefile

Log Message:
biology/chip-seq: Update to 1.2

Update python versions to match py-macs2
Add sra-tools and a few commonly used archivers to metapkg


To generate a diff of this commit:
cvs rdiff -u -r1.1 -r1.2 pkgsrc/biology/chip-seq/DESCR
cvs rdiff -u -r1.5 -r1.6 pkgsrc/biology/chip-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/chip-seq/DESCR
diff -u pkgsrc/biology/chip-seq/DESCR:1.1 pkgsrc/biology/chip-seq/DESCR:1.2
--- pkgsrc/biology/chip-seq/DESCR:1.1   Wed Jun 14 21:28:31 2023
+++ pkgsrc/biology/chip-seq/DESCR       Sat Dec 23 16:35:38 2023
@@ -1,5 +1,6 @@
-The chip-seq meta-package provides the core tools needed for performing
-a typical ChIP-Seq differential accessibility analysis, including
-adapter trimming, quality control, alignment, peak calling, and
-identification of differentially accessible peaks.  Researchers may
-want additional tools for data manipulation, gene ontology, etc.
+The chip-seq meta-package provides the core tools needed for
+performing a typical ChIP-Seq differential accessibility analysis,
+including adapter trimming, quality control, alignment, peak calling,
+and identification of differentially accessible peaks.  Researchers
+may want additional tools for data manipulation, gene ontology,
+etc.

Index: pkgsrc/biology/chip-seq/Makefile
diff -u pkgsrc/biology/chip-seq/Makefile:1.5 pkgsrc/biology/chip-seq/Makefile:1.6
--- pkgsrc/biology/chip-seq/Makefile:1.5        Sun Nov  5 23:48:31 2023
+++ pkgsrc/biology/chip-seq/Makefile    Sat Dec 23 16:35:38 2023
@@ -1,29 +1,37 @@
-# $NetBSD: Makefile,v 1.5 2023/11/05 23:48:31 wiz Exp $
+# $NetBSD: Makefile,v 1.6 2023/12/23 16:35:38 bacon Exp $
 
-DISTNAME=      chip-seq-1.1
-PKGREVISION=   1
+# Update minor version when adding or removing dependencies
+# Update revision for all other changes
+DISTNAME=      chip-seq-1.2
 CATEGORIES=    biology meta-pkgs
 MASTER_SITES=  # empty
 
 OWNER=         bacon%NetBSD.org@localhost
 COMMENT=       Core tools needed for ChIP-Seq analysis
 
-DEPENDS+=      fastq-trim>=0:../../biology/fastq-trim
-DEPENDS+=      fastqc>=0:../../biology/fastqc
-DEPENDS+=      biolibc-tools>=0:../../biology/biolibc-tools
-DEPENDS+=      gffread>=0:../../biology/gffread
-DEPENDS+=      bwa>=0:../../biology/bwa
-DEPENDS+=      bowtie2>=0:../../biology/bowtie2
-DEPENDS+=      samtools>=0:../../biology/samtools
-DEPENDS+=      igv>=0:../../biology/igv
-DEPENDS+=      ${PYPKGPREFIX}-macs2>=0:../../biology/py-macs2
-DEPENDS+=      fasda>=0:../../biology/fasda
-DEPENDS+=      peak-classifier>=0:../../biology/peak-classifier
-DEPENDS+=      webbrowser>=0:../../www/webbrowser
+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
+DEPENDS+=      gffread>0:../../biology/gffread
+DEPENDS+=      bwa>0:../../biology/bwa
+DEPENDS+=      bowtie2>0:../../biology/bowtie2
+DEPENDS+=      samtools>0:../../biology/samtools
+DEPENDS+=      igv>0:../../biology/igv
+DEPENDS+=      ${PYPKGPREFIX}-macs2>0:../../biology/py-macs2
+DEPENDS+=      fasda>0:../../biology/fasda
+DEPENDS+=      peak-classifier>0:../../biology/peak-classifier
+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
 
-PYTHON_VERSIONS_INCOMPATIBLE=  27 38 312
+# Inherited from py-macs2 dep
+PYTHON_VERSIONS_INCOMPATIBLE=  27 38
 
 .include "../../lang/python/application.mk"
 .include "../../mk/bsd.pkg.mk"