diff options
| author | jwb <jwb@FreeBSD.org> | 2019-03-25 05:44:17 +0800 |
|---|---|---|
| committer | jwb <jwb@FreeBSD.org> | 2019-03-25 05:44:17 +0800 |
| commit | 35b117862a6c2a25b42d653e3e4aae5405fc0e7f (patch) | |
| tree | 088f2c2d76243384327e873a6365d03815d16f69 /biology | |
| parent | 1ae3145b3965c50338194489ce74689399cdb8a4 (diff) | |
| download | freebsd-ports-gnome-35b117862a6c2a25b42d653e3e4aae5405fc0e7f.tar.gz freebsd-ports-gnome-35b117862a6c2a25b42d653e3e4aae5405fc0e7f.tar.zst freebsd-ports-gnome-35b117862a6c2a25b42d653e3e4aae5405fc0e7f.zip | |
biology/p5-TrimGalore: Upgrade to 0.6.1
Add test script
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/p5-TrimGalore/Makefile | 19 | ||||
| -rw-r--r-- | biology/p5-TrimGalore/distinfo | 6 | ||||
| -rw-r--r-- | biology/p5-TrimGalore/files/trim_galore-test.in | 13 | ||||
| -rw-r--r-- | biology/p5-TrimGalore/pkg-plist | 12 |
4 files changed, 39 insertions, 11 deletions
diff --git a/biology/p5-TrimGalore/Makefile b/biology/p5-TrimGalore/Makefile index f0d420f6888a..7b5f2c4ebf3f 100644 --- a/biology/p5-TrimGalore/Makefile +++ b/biology/p5-TrimGalore/Makefile @@ -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 -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> diff --git a/biology/p5-TrimGalore/distinfo b/biology/p5-TrimGalore/distinfo index 2b718e79b72d..da6ec9ed81ef 100644 --- a/biology/p5-TrimGalore/distinfo +++ b/biology/p5-TrimGalore/distinfo @@ -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 diff --git a/biology/p5-TrimGalore/files/trim_galore-test.in b/biology/p5-TrimGalore/files/trim_galore-test.in new file mode 100644 index 000000000000..183c14230a71 --- /dev/null +++ b/biology/p5-TrimGalore/files/trim_galore-test.in @@ -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 diff --git a/biology/p5-TrimGalore/pkg-plist b/biology/p5-TrimGalore/pkg-plist index a9fa63919c1f..e9859dc7b3b4 100644 --- a/biology/p5-TrimGalore/pkg-plist +++ b/biology/p5-TrimGalore/pkg-plist @@ -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 |