From 7b14021ad62cdc988be61d5404504f6ef9339f19 Mon Sep 17 00:00:00 2001
From: "Jason W. Bacon" <jwb@FreeBSD.org>
Date: Sat, 9 Dec 2017 13:23:32 +0000
Subject: [PATCH] [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and
 FastQC for adapter and quality trimming Approved by: jrm (mentor)
 Differential Revision:	D13400

---
 biology/Makefile                |  1 +
 biology/p5-TrimGalore/Makefile  | 31 +++++++++++++++++++++++++++++++
 biology/p5-TrimGalore/distinfo  |  3 +++
 biology/p5-TrimGalore/pkg-descr |  4 ++++
 biology/p5-TrimGalore/pkg-plist |  8 ++++++++
 5 files changed, 47 insertions(+)
 create mode 100644 biology/p5-TrimGalore/Makefile
 create mode 100644 biology/p5-TrimGalore/distinfo
 create mode 100644 biology/p5-TrimGalore/pkg-descr
 create mode 100644 biology/p5-TrimGalore/pkg-plist

diff --git a/biology/Makefile b/biology/Makefile
index e72db4dfe68b..3f03d6c4c0de 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -73,6 +73,7 @@
     SUBDIR += p5-Bio-SCF
     SUBDIR += p5-BioPerl
     SUBDIR += p5-BioPerl-Run
+    SUBDIR += p5-TrimGalore
     SUBDIR += p5-transdecoder
     SUBDIR += paml
     SUBDIR += phrap
diff --git a/biology/p5-TrimGalore/Makefile b/biology/p5-TrimGalore/Makefile
new file mode 100644
index 000000000000..2121137a66a4
--- /dev/null
+++ b/biology/p5-TrimGalore/Makefile
@@ -0,0 +1,31 @@
+# $FreeBSD$
+
+PORTNAME=	TrimGalore
+DISTVERSION=	0.4.5
+CATEGORIES=	biology perl5
+PKGNAMEPREFIX=	p5-
+
+MAINTAINER=	jwb@FreeBSD.org
+COMMENT=	Wrapper around Cutadapt and FastQC for adapter and quality trimming
+
+LICENSE=	GPLv3
+LICENSE_FILE=	${WRKSRC}/LICENSE
+
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}cutadapt>0:biology/py-cutadapt@${PY_FLAVOR} \
+		fastqc>0:biology/fastqc
+
+NO_ARCH=	yes
+NO_BUILD=	yes
+
+USES=		perl5 python:env shebangfix
+SHEBANG_FILES=	trim_galore
+USE_PERL5=	run
+
+USE_GITHUB=	yes
+GH_ACCOUNT=	FelixKrueger
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/trim_galore ${STAGEDIR}${PREFIX}/bin
+	cd ${WRKSRC} && ${COPYTREE_SHARE} test_files ${STAGEDIR}${DATADIR}
+
+.include <bsd.port.mk>
diff --git a/biology/p5-TrimGalore/distinfo b/biology/p5-TrimGalore/distinfo
new file mode 100644
index 000000000000..2b718e79b72d
--- /dev/null
+++ b/biology/p5-TrimGalore/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1512570215
+SHA256 (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = a6b97e554944ddc6ecd50e78df486521f17225d415aad84e9911163faafe1f3c
+SIZE (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = 21983909
diff --git a/biology/p5-TrimGalore/pkg-descr b/biology/p5-TrimGalore/pkg-descr
new file mode 100644
index 000000000000..849448684845
--- /dev/null
+++ b/biology/p5-TrimGalore/pkg-descr
@@ -0,0 +1,4 @@
+Wrapper around Cutadapt and FastQC to consistently apply adapter and quality
+trimming to FastQ files, with extra functionality for RRBS data.
+
+WWW: https://github.com/FelixKrueger/TrimGalore
diff --git a/biology/p5-TrimGalore/pkg-plist b/biology/p5-TrimGalore/pkg-plist
new file mode 100644
index 000000000000..a9fa63919c1f
--- /dev/null
+++ b/biology/p5-TrimGalore/pkg-plist
@@ -0,0 +1,8 @@
+bin/trim_galore
+%%DATADIR%%/test_files/4_seqs_with_Ns.fastq.gz
+%%DATADIR%%/test_files/colorspace_file.fastq
+%%DATADIR%%/test_files/empty_file.fastq
+%%DATADIR%%/test_files/illumina_100K.fastq.gz
+%%DATADIR%%/test_files/nextera_100K.fastq.gz
+%%DATADIR%%/test_files/smallRNA_100K.fastq.gz
+%%DATADIR%%/test_files/truncated.fq.gz