CVS commit: pkgsrc/biology/chip-seq

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Wed Jun 14 21:28:31 UTC 2023

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

Log Message:
biology/chip-seq: Core tools needed for ChIP-Seq analysis

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.

Presently identical to biology/atac-seq, but may diverge in the future.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/chip-seq/DESCR \
    pkgsrc/biology/chip-seq/Makefile

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

Added files:

Index: pkgsrc/biology/chip-seq/DESCR
diff -u /dev/null pkgsrc/biology/chip-seq/DESCR:1.1
--- /dev/null   Wed Jun 14 21:28:31 2023
+++ pkgsrc/biology/chip-seq/DESCR       Wed Jun 14 21:28:31 2023
@@ -0,0 +1,5 @@
+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 /dev/null pkgsrc/biology/chip-seq/Makefile:1.1
--- /dev/null   Wed Jun 14 21:28:31 2023
+++ pkgsrc/biology/chip-seq/Makefile    Wed Jun 14 21:28:31 2023
@@ -0,0 +1,28 @@
+# $NetBSD: Makefile,v 1.1 2023/06/14 21:28:31 bacon Exp $
+
+DISTNAME=      chip-seq-1.1
+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
+
+META_PACKAGE=  yes
+
+PYTHON_VERSIONS_INCOMPATIBLE=  27 # py-macs2
+
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"