svn commit: r496785 - in head/biology/p5-TrimGalore: . files

[Jason W. Bacon]

Author: jwb
Date: Sun Mar 24 21:44:17 2019
New Revision: 496785
URL: https://svnweb.freebsd.org/changeset/ports/496785

Log:
  biology/p5-TrimGalore: Upgrade to 0.6.1
  
  Add test script

Added:
  head/biology/p5-TrimGalore/files/
  head/biology/p5-TrimGalore/files/trim_galore-test.in   (contents, props changed)
Modified:
  head/biology/p5-TrimGalore/Makefile
  head/biology/p5-TrimGalore/distinfo   (contents, props changed)
  head/biology/p5-TrimGalore/pkg-plist   (contents, props changed)

Modified: head/biology/p5-TrimGalore/Makefile
==============================================================================
--- head/biology/p5-TrimGalore/Makefile	Sun Mar 24 21:28:02 2019	(r496784)
+++ head/biology/p5-TrimGalore/Makefile	Sun Mar 24 21:44:17 2019	(r496785)
@@ -1,8 +1,8 @@
 # $FreeBSD$
 
 PORTNAME=	TrimGalore
-DISTVERSION=	0.4.5
-CATEGORIES=	biology perl5
+DISTVERSION=	0.6.1
+CATEGORIES=	biology perl5 python
 PKGNAMEPREFIX=	p5-
 
 MAINTAINER=	jwb at FreeBSD.org
@@ -14,18 +14,21 @@ 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:3.4+,env shebangfix
-SHEBANG_FILES=	trim_galore
+# Future: Can 3.4+ be determined from cutadapt dep?
+USES=		perl5 python:env,3.4+ shebangfix
 USE_PERL5=	run
-
 USE_GITHUB=	yes
+
+SHEBANG_FILES=	trim_galore
 GH_ACCOUNT=	FelixKrueger
 
+NO_ARCH=	yes
+NO_BUILD=	yes
+SUB_FILES=	trim_galore-test
+
 do-install:
 	${INSTALL_SCRIPT} ${WRKSRC}/trim_galore ${STAGEDIR}${PREFIX}/bin
+	${INSTALL_SCRIPT} ${WRKDIR}/trim_galore-test ${STAGEDIR}${PREFIX}/bin
 	cd ${WRKSRC} && ${COPYTREE_SHARE} test_files ${STAGEDIR}${DATADIR}
 
 .include <bsd.port.mk>

Modified: head/biology/p5-TrimGalore/distinfo
==============================================================================
--- head/biology/p5-TrimGalore/distinfo	Sun Mar 24 21:28:02 2019	(r496784)
+++ head/biology/p5-TrimGalore/distinfo	Sun Mar 24 21:44:17 2019	(r496785)
@@ -1,3 +1,3 @@
-TIMESTAMP = 1512570215
-SHA256 (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = a6b97e554944ddc6ecd50e78df486521f17225d415aad84e9911163faafe1f3c
-SIZE (FelixKrueger-TrimGalore-0.4.5_GH0.tar.gz) = 21983909
+TIMESTAMP = 1553345061
+SHA256 (FelixKrueger-TrimGalore-0.6.1_GH0.tar.gz) = 658578c29d007fe66f9ab49608442be703a6fcf535db06eb82659c7edccb62b0
+SIZE (FelixKrueger-TrimGalore-0.6.1_GH0.tar.gz) = 26825390

Added: head/biology/p5-TrimGalore/files/trim_galore-test.in
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/p5-TrimGalore/files/trim_galore-test.in	Sun Mar 24 21:44:17 2019	(r496785)
@@ -0,0 +1,13 @@
+#!/bin/sh
+
+test_dir=%%DATADIR%%/test_files
+for file in $test_dir/*.fastq.gz $test_dir/*.fq.gz; do
+    cat << EOM
+
+===============================================================================
+Trimming $file...
+===============================================================================
+
+EOM
+    trim_galore $file
+done

Modified: head/biology/p5-TrimGalore/pkg-plist
==============================================================================
--- head/biology/p5-TrimGalore/pkg-plist	Sun Mar 24 21:28:02 2019	(r496784)
+++ head/biology/p5-TrimGalore/pkg-plist	Sun Mar 24 21:44:17 2019	(r496785)
@@ -1,8 +1,20 @@
 bin/trim_galore
+bin/trim_galore-test
 %%DATADIR%%/test_files/4_seqs_with_Ns.fastq.gz
+%%DATADIR%%/test_files/clock_10K_R1.fastq.gz
+%%DATADIR%%/test_files/clock_10K_R2.fastq.gz
 %%DATADIR%%/test_files/colorspace_file.fastq
 %%DATADIR%%/test_files/empty_file.fastq
 %%DATADIR%%/test_files/illumina_100K.fastq.gz
+%%DATADIR%%/test_files/illumina_100K.fastq.gz_trimming_report.txt
+%%DATADIR%%/test_files/illumina_10K.fastq.gz
+%%DATADIR%%/test_files/illumina_10K.fastq.gz_trimming_report.txt
+%%DATADIR%%/test_files/illumina_10K_trimmed.fq.gz
 %%DATADIR%%/test_files/nextera_100K.fastq.gz
+%%DATADIR%%/test_files/nextera_100K.fastq.gz_trimming_report.txt
 %%DATADIR%%/test_files/smallRNA_100K.fastq.gz
+%%DATADIR%%/test_files/smallRNA_100K.fastq.gz_trimming_report.txt
+%%DATADIR%%/test_files/smallRNA_100K_R1.fastq.gz_trimming_report.txt
+%%DATADIR%%/test_files/smallRNA_100K_R2.fastq.gz
+%%DATADIR%%/test_files/smallRNA_100K_R2.fastq.gz_trimming_report.txt
 %%DATADIR%%/test_files/truncated.fq.gz