[pkgsrc/trunk]: pkgsrc/biology/peak-classifier biology/peak-classifier: impor...

[bacon <bacon%pkgsrc.org@localhost>]

details:   https://anonhg.NetBSD.org/pkgsrc/rev/d434aba2774e
branches:  trunk
changeset: 454716:d434aba2774e
user:      bacon <bacon%pkgsrc.org@localhost>
date:      Tue Jun 15 13:54:14 2021 +0000

description:
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.

diffstat:

 biology/peak-classifier/DESCR    |   5 +++++
 biology/peak-classifier/Makefile |  22 ++++++++++++++++++++++
 biology/peak-classifier/PLIST    |  10 ++++++++++
 biology/peak-classifier/distinfo |   6 ++++++
 4 files changed, 43 insertions(+), 0 deletions(-)

diffs (59 lines):

diff -r dd8e44c71d7d -r d434aba2774e biology/peak-classifier/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/peak-classifier/DESCR     Tue Jun 15 13:54:14 2021 +0000
@@ -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.
diff -r dd8e44c71d7d -r d434aba2774e biology/peak-classifier/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/peak-classifier/Makefile  Tue Jun 15 13:54:14 2021 +0000
@@ -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"
diff -r dd8e44c71d7d -r d434aba2774e biology/peak-classifier/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/peak-classifier/PLIST     Tue Jun 15 13:54:14 2021 +0000
@@ -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
diff -r dd8e44c71d7d -r d434aba2774e biology/peak-classifier/distinfo
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/peak-classifier/distinfo  Tue Jun 15 13:54:14 2021 +0000
@@ -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