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# $FreeBSD: head/biology/stacks/Makefile 475857 2018-07-29 22:18:44Z gerald $ | ||
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PORTNAME= stacks | ||
DISTVERSION= 1.48 | ||
PORTREVISION= 1 | ||
CATEGORIES= wip biology | ||
MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ | ||
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MAINTAINER= jwb@FreeBSD.org | ||
COMMENT= Software pipeline for building loci from short-read sequences | ||
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LICENSE= GPLv2 | ||
LICENSE_FILE= ${WRKSRC}/LICENSE | ||
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USES= compiler:openmp gmake python shebangfix | ||
SHEBANG_FILES= scripts/*.pl scripts/*.py | ||
GNU_CONFIGURE= yes | ||
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LDFLAGS+= -lpthread | ||
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.include <bsd.port.mk> |
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TIMESTAMP = 1520376299 | ||
SHA256 (stacks-1.48.tar.gz) = e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e | ||
SIZE (stacks-1.48.tar.gz) = 895195 |
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--- htslib/Makefile.orig 2016-09-16 15:40:03 UTC | ||
+++ htslib/Makefile | ||
@@ -22,13 +22,13 @@ | ||
# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER | ||
# DEALINGS IN THE SOFTWARE. | ||
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-CC = gcc | ||
-AR = ar | ||
-RANLIB = ranlib | ||
+CC ?= gcc | ||
+AR ?= ar | ||
+RANLIB ?= ranlib | ||
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CPPFLAGS = | ||
# TODO: probably update cram code to make it compile cleanly with -Wc++-compat | ||
-CFLAGS = -g -Wall -O2 | ||
+CFLAGS ?= -g -Wall -O2 | ||
EXTRA_CFLAGS_PIC = -fpic | ||
LDFLAGS = | ||
LIBS = |
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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. | ||
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WWW: http://catchenlab.life.illinois.edu/stacks/ |
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=== | ||
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If you would like to use the stacks web interface, follow the instructions at: | ||
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http://catchenlab.life.illinois.edu/stacks/manual-v1/#install | ||
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You will need to install databases/p5-DBD-mysql to allow the optional | ||
wrapper scripts to interact with the database server. | ||
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To set up the web server, you will need an apache server such as www/apache24, | ||
MySQL server and client packages such as databases/mysql56-client and | ||
databases/mysql56-server, and PHP interface modules such as | ||
databases/php56-mysql (php56 will be automatically installed as a dependency), | ||
and lastly textproc/p5-Spreadsheet-WriteExcel. | ||
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=== |
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bin/clone_filter | ||
bin/count_fixed_catalog_snps.py | ||
bin/cstacks | ||
bin/denovo_map.pl | ||
bin/exec_velvet.pl | ||
bin/export_sql.pl | ||
bin/genotypes | ||
bin/index_radtags.pl | ||
bin/integrate_alignments.py | ||
bin/kmer_filter | ||
bin/load_radtags.pl | ||
bin/load_sequences.pl | ||
bin/phasedstacks | ||
bin/populations | ||
bin/process_radtags | ||
bin/process_shortreads | ||
bin/pstacks | ||
bin/ref_map.pl | ||
bin/rxstacks | ||
bin/sort_read_pairs.pl | ||
bin/sstacks | ||
bin/stacks_export_notify.pl | ||
bin/ustacks | ||
%%DATADIR%%/php/CatalogClass.php | ||
%%DATADIR%%/php/Locus.php | ||
%%DATADIR%%/php/ajax.js | ||
%%DATADIR%%/php/annotate.js | ||
%%DATADIR%%/php/annotate_marker.php | ||
%%DATADIR%%/php/catalog.php | ||
%%DATADIR%%/php/catalog_genotypes.php | ||
%%DATADIR%%/php/constants.php.dist | ||
%%DATADIR%%/php/correct_genotype.php | ||
%%DATADIR%%/php/correct_genotypes.php | ||
%%DATADIR%%/php/db_functions.php | ||
%%DATADIR%%/php/export.js | ||
%%DATADIR%%/php/export_batch.php | ||
%%DATADIR%%/php/fst_view.php | ||
%%DATADIR%%/php/hapstat_view.php | ||
%%DATADIR%%/php/header.php | ||
%%DATADIR%%/php/images/caret-d.png | ||
%%DATADIR%%/php/images/caret-u.png | ||
%%DATADIR%%/php/images/excel_icon.png | ||
%%DATADIR%%/php/images/l-arrow-disabled.png | ||
%%DATADIR%%/php/images/l-arrow.png | ||
%%DATADIR%%/php/images/r-arrow-disabled.png | ||
%%DATADIR%%/php/images/r-arrow.png | ||
%%DATADIR%%/php/images/stacks_bg.png | ||
%%DATADIR%%/php/images/stacks_logo_rev_small.png | ||
%%DATADIR%%/php/index.php | ||
%%DATADIR%%/php/last_modified.php | ||
%%DATADIR%%/php/phist_view.php | ||
%%DATADIR%%/php/pop_view.php | ||
%%DATADIR%%/php/population_view.js | ||
%%DATADIR%%/php/samples.php | ||
%%DATADIR%%/php/sequence_blast.php | ||
%%DATADIR%%/php/stack_view.php | ||
%%DATADIR%%/php/stacks.css | ||
%%DATADIR%%/php/stacks.js | ||
%%DATADIR%%/php/stacks_functions.php | ||
%%DATADIR%%/php/sumstat_view.php | ||
%%DATADIR%%/php/tag.php | ||
%%DATADIR%%/php/tags.php | ||
%%DATADIR%%/php/version.php | ||
%%DATADIR%%/php/view_sequence.php | ||
%%DATADIR%%/sql/catalog_index.sql | ||
%%DATADIR%%/sql/chr_index.sql | ||
%%DATADIR%%/sql/mysql.cnf.dist | ||
%%DATADIR%%/sql/stacks.sql | ||
%%DATADIR%%/sql/tag_index.sql | ||
@dir %%DATADIR%%/php/export |