diff options
author | bacon <bacon@pkgsrc.org> | 2018-12-22 21:52:06 +0000 |
---|---|---|
committer | bacon <bacon@pkgsrc.org> | 2018-12-22 21:52:06 +0000 |
commit | a04716fded51f0c8a15aeb89562bfc26033f2688 (patch) | |
tree | 822826a3d70950febb58708471e83e8d2b64bee1 /biology/stacks | |
parent | 2bb907ebbc8e0bc3450b925cbcecd918874fe0af (diff) | |
download | pkgsrc-a04716fded51f0c8a15aeb89562bfc26033f2688.tar.gz |
biology/stacks: import stacks-2.2
Stacks is a software pipeline for building loci from short-read sequences, such
as those generated on the Illumina platform. Stacks was developed to work with
restriction enzyme-based data, such as RAD-seq, for the purpose of building
genetic maps and conducting population genomics and phylogeography.
Diffstat (limited to 'biology/stacks')
-rw-r--r-- | biology/stacks/DESCR | 4 | ||||
-rw-r--r-- | biology/stacks/Makefile | 26 | ||||
-rw-r--r-- | biology/stacks/PLIST | 66 | ||||
-rw-r--r-- | biology/stacks/distinfo | 6 |
4 files changed, 102 insertions, 0 deletions
diff --git a/biology/stacks/DESCR b/biology/stacks/DESCR new file mode 100644 index 00000000000..91c14fbc8df --- /dev/null +++ b/biology/stacks/DESCR @@ -0,0 +1,4 @@ +Stacks is a software pipeline for building loci from short-read sequences, such +as those generated on the Illumina platform. Stacks was developed to work with +restriction enzyme-based data, such as RAD-seq, for the purpose of building +genetic maps and conducting population genomics and phylogeography. diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile new file mode 100644 index 00000000000..ed32c60154f --- /dev/null +++ b/biology/stacks/Makefile @@ -0,0 +1,26 @@ +# $NetBSD: Makefile,v 1.1 2018/12/22 21:52:06 bacon Exp $ + +DISTNAME= stacks-2.2 +CATEGORIES= biology +MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ + +MAINTAINER= bacon@NetBSD.org +HOMEPAGE= http://catchenlab.life.illinois.edu/stacks/ +COMMENT= Software pipeline for building loci from short-read sequences +LICENSE= gnu-gpl-v2 + +USE_LANGUAGES= c c++14 +GCC_REQD+= 4.9 +USE_TOOLS+= bash perl:run +GNU_CONFIGURE= yes + +REPLACE_BASH= scripts/stacks-integrate-alignments scripts/stacks-gdb +REPLACE_BASH+= scripts/stacks-dist-extract +REPLACE_PERL= scripts/*.pl +REPLACE_PYTHON= scripts/*.py + +CFLAGS+= -fopenmp + +.include "../../lang/python/application.mk" +.include "../../devel/zlib/buildlink3.mk" +.include "../../mk/bsd.pkg.mk" diff --git a/biology/stacks/PLIST b/biology/stacks/PLIST new file mode 100644 index 00000000000..357dc2052af --- /dev/null +++ b/biology/stacks/PLIST @@ -0,0 +1,66 @@ +@comment $NetBSD: PLIST,v 1.1 2018/12/22 21:52:06 bacon Exp $ +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-dist-extract +bin/stacks-gdb +bin/stacks-integrate-alignments +bin/tsv2bam +bin/ustacks +share/stacks/php/CatalogClass.php +share/stacks/php/Locus.php +share/stacks/php/ajax.js +share/stacks/php/annotate.js +share/stacks/php/annotate_marker.php +share/stacks/php/catalog.php +share/stacks/php/catalog_genotypes.php +share/stacks/php/constants.php.dist +share/stacks/php/correct_genotype.php +share/stacks/php/correct_genotypes.php +share/stacks/php/db_functions.php +share/stacks/php/export.js +share/stacks/php/export_batch.php +share/stacks/php/fst_view.php +share/stacks/php/hapstat_view.php +share/stacks/php/header.php +share/stacks/php/images/caret-d.png +share/stacks/php/images/caret-u.png +share/stacks/php/images/excel_icon.png +share/stacks/php/images/l-arrow-disabled.png +share/stacks/php/images/l-arrow.png +share/stacks/php/images/r-arrow-disabled.png +share/stacks/php/images/r-arrow.png +share/stacks/php/images/stacks_bg.png +share/stacks/php/images/stacks_logo_rev_small.png +share/stacks/php/index.php +share/stacks/php/last_modified.php +share/stacks/php/phist_view.php +share/stacks/php/pop_view.php +share/stacks/php/population_view.js +share/stacks/php/samples.php +share/stacks/php/sequence_blast.php +share/stacks/php/stack_view.php +share/stacks/php/stacks.css +share/stacks/php/stacks.js +share/stacks/php/stacks_functions.php +share/stacks/php/sumstat_view.php +share/stacks/php/tag.php +share/stacks/php/tags.php +share/stacks/php/version.php +share/stacks/php/view_sequence.php +share/stacks/sql/catalog_index.sql +share/stacks/sql/chr_index.sql +share/stacks/sql/mysql.cnf.dist +share/stacks/sql/stacks.sql +share/stacks/sql/tag_index.sql +@pkgdir share/stacks/php/export diff --git a/biology/stacks/distinfo b/biology/stacks/distinfo new file mode 100644 index 00000000000..65fce4d9111 --- /dev/null +++ b/biology/stacks/distinfo @@ -0,0 +1,6 @@ +$NetBSD: distinfo,v 1.1 2018/12/22 21:52:06 bacon Exp $ + +SHA1 (stacks-2.2.tar.gz) = ee99798378b906f356c23da0073d0361440263bf +RMD160 (stacks-2.2.tar.gz) = 2f5097c668d9662dbbec705fe3bf00216c11d388 +SHA512 (stacks-2.2.tar.gz) = f1cffd12313fed1c171af46f9fb501373b43d57cd3004edae1034074f43169d43398743cf625ffa21be412c808ba1168513a33c63377ee13dd056406fa222095 +Size (stacks-2.2.tar.gz) = 10822973 bytes |