CVS commit: pkgsrc/biology/peak-classifier

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

Module Name:    pkgsrc
Committed By:   bacon
Date:           Tue Jun 15 13:54:14 UTC 2021

Added Files:
        pkgsrc/biology/peak-classifier: DESCR Makefile PLIST distinfo

Log Message:
biology/peak-classifier: import peak-classifier-0.1.1

Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
Peaks are provided in a BED file sorted by chromosome and position. The GFF
must be sorted by chromosome and position, with gene-level features separated
by ### tags and each gene organized into subfeatures such as transcripts and
exons.  This is the default for common data sources.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/peak-classifier/DESCR \
    pkgsrc/biology/peak-classifier/Makefile \
    pkgsrc/biology/peak-classifier/PLIST \
    pkgsrc/biology/peak-classifier/distinfo

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

Added files:

Index: pkgsrc/biology/peak-classifier/DESCR
diff -u /dev/null pkgsrc/biology/peak-classifier/DESCR:1.1
--- /dev/null   Tue Jun 15 13:54:14 2021
+++ pkgsrc/biology/peak-classifier/DESCR        Tue Jun 15 13:54:14 2021
@@ -0,0 +1,5 @@
+Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
+Peaks are provided in a BED file sorted by chromosome and position. The GFF
+must be sorted by chromosome and position, with gene-level features separated
+by ### tags and each gene organized into subfeatures such as transcripts and
+exons.  This is the default for common data sources.
Index: pkgsrc/biology/peak-classifier/Makefile
diff -u /dev/null pkgsrc/biology/peak-classifier/Makefile:1.1
--- /dev/null   Tue Jun 15 13:54:14 2021
+++ pkgsrc/biology/peak-classifier/Makefile     Tue Jun 15 13:54:14 2021
@@ -0,0 +1,22 @@
+# $NetBSD: Makefile,v 1.1 2021/06/15 13:54:14 bacon Exp $
+
+DISTNAME=      peak-classifier-0.1.1
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_GITHUB:=auerlab/}
+
+MAINTAINER=    bacon%NetBSD.org@localhost
+HOMEPAGE=      https://github.com/auerlab/peak-classifier
+COMMENT=       Classify ChIP/ATAC-Seq peaks based on features provided in a GFF
+LICENSE=       2-clause-bsd
+
+DEPENDS+=      bedtools>=0:../../biology/bedtools
+
+REPLACE_PYTHON=        feature-view.py
+
+pre-build:
+       cd ${WRKSRC} && make depend PREFIX=${PREFIX}
+
+.include "../../biology/biolibc/buildlink3.mk"
+.include "../../devel/libxtend/buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/peak-classifier/PLIST
diff -u /dev/null pkgsrc/biology/peak-classifier/PLIST:1.1
--- /dev/null   Tue Jun 15 13:54:14 2021
+++ pkgsrc/biology/peak-classifier/PLIST        Tue Jun 15 13:54:14 2021
@@ -0,0 +1,10 @@
+@comment $NetBSD: PLIST,v 1.1 2021/06/15 13:54:14 bacon Exp $
+bin/extract-genes
+bin/feature-view
+bin/filter-overlaps
+bin/peak-classifier
+libexec/extract-genes.awk
+man/man1/extract-genes.1
+man/man1/feature-view.1
+man/man1/filter-overlaps.1
+man/man1/peak-classifier.1
Index: pkgsrc/biology/peak-classifier/distinfo
diff -u /dev/null pkgsrc/biology/peak-classifier/distinfo:1.1
--- /dev/null   Tue Jun 15 13:54:14 2021
+++ pkgsrc/biology/peak-classifier/distinfo     Tue Jun 15 13:54:14 2021
@@ -0,0 +1,6 @@
+$NetBSD: distinfo,v 1.1 2021/06/15 13:54:14 bacon Exp $
+
+SHA1 (peak-classifier-0.1.1.tar.gz) = b5716fe3575cb9631682c8cdb4d09fd84d34ab12
+RMD160 (peak-classifier-0.1.1.tar.gz) = 2a5a8ee1c1c0a3db034395c9d71b3a7353f1a09a
+SHA512 (peak-classifier-0.1.1.tar.gz) = 5a3a5acbc815b47cfa4ba5c15eaf57be4a82b68197f031a311e41a46e33c394355687b0c709826cc214f1b36e168036b798f287c6f0391cdc39ef638d2617741
+Size (peak-classifier-0.1.1.tar.gz) = 86012 bytes