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biology/p5-TrimGalore: Upgrade to 0.6.1

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Add test script
This commit is contained in:
Jason W. Bacon 2019-03-24 21:44:17 +00:00
parent a079e3eb71
commit 55cf576287
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=496785
4 changed files with 40 additions and 12 deletions
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21
biology/p5-TrimGalore/Makefile
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@ -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@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
# 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
USES= perl5 python:3.4+,env shebangfix
SHEBANG_FILES= trim_galore
USE_PERL5= run
USE_GITHUB= yes
GH_ACCOUNT= FelixKrueger
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>

6
biology/p5-TrimGalore/distinfo
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@ -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

13
biology/p5-TrimGalore/files/trim_galore-test.in Normal file
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@ -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

12
biology/p5-TrimGalore/pkg-plist
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@ -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