p5-trimgalore: Wrapper around Cutadapt and FastQC

[Jason Bacon <bacon4000%gmail.com@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Thu Nov 2 15:34:57 2017 -0500
Changeset:	ee9627d058ae8ef5a59cf0be738a4e615c8da90b

Modified Files:
	Makefile
Added Files:
	p5-trimgalore/DESCR
	p5-trimgalore/Makefile
	p5-trimgalore/PLIST
	p5-trimgalore/distinfo

Log Message:
p5-trimgalore: Wrapper around Cutadapt and FastQC

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=ee9627d058ae8ef5a59cf0be738a4e615c8da90b

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

diffstat:
 Makefile               |  1 +
 p5-trimgalore/DESCR    |  2 ++
 p5-trimgalore/Makefile | 48 ++++++++++++++++++++++++++++++++++++++++++++++++
 p5-trimgalore/PLIST    |  9 +++++++++
 p5-trimgalore/distinfo |  6 ++++++
 5 files changed, 66 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index e5f601ed66..933f7a1bf8 100644
--- a/Makefile
+++ b/Makefile
@@ -2503,6 +2503,7 @@ SUBDIR+=	p5-mha4mysql-node
 SUBDIR+=	p5-mozldap
 SUBDIR+=	p5-spf-policyd
 SUBDIR+=	p5-transdecoder
+SUBDIR+=	p5-trimgalore
 SUBDIR+=	p5-xmlsig-svn
 SUBDIR+=	p6-Grammar-Profiler-Simple
 SUBDIR+=	p6-Perl6-MIME-Base64
diff --git a/p5-trimgalore/DESCR b/p5-trimgalore/DESCR
new file mode 100644
index 0000000000..bffcd2c695
--- /dev/null
+++ b/p5-trimgalore/DESCR
@@ -0,0 +1,2 @@
+Wrapper around Cutadapt and FastQC to consistently apply adapter and quality
+trimming to FastQ files, with extra functionality for RRBS data.
diff --git a/p5-trimgalore/Makefile b/p5-trimgalore/Makefile
new file mode 100644
index 0000000000..e583722b71
--- /dev/null
+++ b/p5-trimgalore/Makefile
@@ -0,0 +1,48 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Thu Nov  2 15:12:06 CDT 2017               #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+#LICENSE_FILE=	${WRKSRC}/LICENSE
+# RUN_DEPENDS=	p5-IPC-Open3-Simple>=0:devel/p5-IPC-Open3-Simple \
+#		p5-File-Spec-Native>=0:devel/p5-File-Spec-Native \
+#		p5-File-BaseDir>=0:devel/p5-File-BaseDir \
+#		p5-Cwd-Guard>=0:devel/p5-Cwd-Guard \
+#		${PYPKGPREFIX}-cutadapt>0:wip/py-cutadapt \
+#		fastqc>0:wip/fastqc
+
+DISTNAME=	trimgalore-${PORTVERSION}
+PKGNAME=	p5-trimgalore-${PORTVERSION}
+CATEGORIES=	wip
+MASTER_SITES=	${MASTER_SITE_GITHUB:=FelixKrueger/}
+GITHUB_PROJECT=	trimgalore
+GITHUB_TAG=	${PORTVERSION}
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	https://github.com/FelixKrueger/TrimGalore
+COMMENT=	Wrapper around Cutadapt and FastQC for adapter and quality trimming
+LICENSE=	gnu-gpl-v3
+
+USE_TOOLS+=	perl:run pax
+REPLACE_PERL=	trim_galore
+NO_BUILD=	yes
+
+WRKSRC=		${WRKDIR}/TrimGalore-${PORTVERSION}
+
+PORTVERSION=	0.4.4
+DATADIR=	${PREFIX}/share/trimgalore
+
+INSTALLATION_DIRS=	bin share/trimgalore
+
+do-install:
+	${INSTALL_SCRIPT} ${WRKSRC}/trim_galore ${DESTDIR}${PREFIX}/bin
+	cd ${WRKSRC} && pax -rw test_files ${DESTDIR}${DATADIR}
+
+# .include "../..///buildlink3.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/p5-trimgalore/PLIST b/p5-trimgalore/PLIST
new file mode 100644
index 0000000000..41ce874246
--- /dev/null
+++ b/p5-trimgalore/PLIST
@@ -0,0 +1,9 @@
+@comment $NetBSD$
+bin/trim_galore
+share/trimgalore/test_files/4_seqs_with_Ns.fastq.gz
+share/trimgalore/test_files/colorspace_file.fastq
+share/trimgalore/test_files/empty_file.fastq
+share/trimgalore/test_files/illumina_100K.fastq.gz
+share/trimgalore/test_files/nextera_100K.fastq.gz
+share/trimgalore/test_files/smallRNA_100K.fastq.gz
+share/trimgalore/test_files/truncated.fq.gz
diff --git a/p5-trimgalore/distinfo b/p5-trimgalore/distinfo
new file mode 100644
index 0000000000..404bd00a12
--- /dev/null
+++ b/p5-trimgalore/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (trimgalore-0.4.4.tar.gz) = 4e47e0f582801f7c08fc7518232b516fa9911823
+RMD160 (trimgalore-0.4.4.tar.gz) = 35ce1adc01d191c8e3ab8cb2a8e3ed76e4bbc20f
+SHA512 (trimgalore-0.4.4.tar.gz) = eb19eadd23311aec87808de95f6a2aa41d0bb304caba1dbb2031b3a5d736ecf45710973dfe0576334ea89239eaea4e12f2ebe8448cfa0bc995fdcd6f1a0cd80b
+Size (trimgalore-0.4.4.tar.gz) = 21983719 bytes