diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile index b4301eec2bb7..5e1b270e1b98 100644 --- a/biology/stacks/Makefile +++ b/biology/stacks/Makefile @@ -1,29 +1,21 @@ PORTNAME= stacks -DISTVERSION= 2.4 -PORTREVISION= 2 +DISTVERSION= 2.68 CATEGORIES= biology perl5 python -MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ +MASTER_SITES= https://catchenlab.life.illinois.edu/stacks/source/ MAINTAINER= jwb@FreeBSD.org COMMENT= Software pipeline for building loci from short-read sequences WWW= https://catchenlab.life.illinois.edu/stacks/ LICENSE= GPLv2 LICENSE_FILE= ${WRKSRC}/LICENSE USES= compiler:c++11-lang gmake python shebangfix -SHEBANG_FILES= scripts/*.pl scripts/*.py \ - scripts/stacks-integrate-alignments scripts/stacks-gdb +SHEBANG_FILES= scripts/* + GNU_CONFIGURE= yes LDFLAGS+= -lpthread -.include - -# Temp workaround, see PR 230888 -.if ${ARCH} == i386 -USE_GCC= yes -.endif - -.include +.include diff --git a/biology/stacks/distinfo b/biology/stacks/distinfo index 312ef425ec9d..ce462d89a52e 100644 --- a/biology/stacks/distinfo +++ b/biology/stacks/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1557519159 -SHA256 (stacks-2.4.tar.gz) = 30093d688a2dc62a19ea42a58065f024c8279419439049bcde186703e75641c1 -SIZE (stacks-2.4.tar.gz) = 10930616 +TIMESTAMP = 1733920483 +SHA256 (stacks-2.68.tar.gz) = 9dc51ea356d60eb4557b0b2d1a8854aafae492aed87f974e0249cc09aa5e7650 +SIZE (stacks-2.68.tar.gz) = 15552836 diff --git a/biology/stacks/pkg-plist b/biology/stacks/pkg-plist index 605cf4a295db..e3ca8c4a9b60 100644 --- a/biology/stacks/pkg-plist +++ b/biology/stacks/pkg-plist @@ -1,18 +1,20 @@ bin/clone_filter -bin/count_fixed_catalog_snps.py bin/cstacks bin/denovo_map.pl bin/gstacks -bin/integrate_alignments.py bin/kmer_filter bin/phasedstacks bin/populations bin/process_radtags bin/process_shortreads bin/ref_map.pl bin/sstacks +bin/stacks-count-reads-per-sample-per-locus bin/stacks-dist-extract bin/stacks-gdb +bin/stacks-hist2d-loci-samples-coverage bin/stacks-integrate-alignments +bin/stacks-private-alleles +bin/stacks-samtools-tview bin/tsv2bam bin/ustacks