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Bacon" Date: Sat, 31 Mar 2018 13:16:05 +0000 (UTC) To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r466048 - in head/biology: . stacks stacks/files X-SVN-Group: ports-head X-SVN-Commit-Author: jwb X-SVN-Commit-Paths: in head/biology: . stacks stacks/files X-SVN-Commit-Revision: 466048 X-SVN-Commit-Repository: ports MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit X-BeenThere: svn-ports-all@freebsd.org X-Mailman-Version: 2.1.25 Precedence: list List-Id: SVN commit messages for the ports tree List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Sat, 31 Mar 2018 13:16:07 -0000 Author: jwb Date: Sat Mar 31 13:16:05 2018 New Revision: 466048 URL: https://svnweb.freebsd.org/changeset/ports/466048 Log: biology/stacks: Software pipeline for building loci from short-read sequences Reviewed by: mat Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D14885 Added: head/biology/stacks/ head/biology/stacks/Makefile (contents, props changed) head/biology/stacks/distinfo (contents, props changed) head/biology/stacks/files/ head/biology/stacks/files/patch-htslib_Makefile (contents, props changed) head/biology/stacks/pkg-descr (contents, props changed) head/biology/stacks/pkg-message (contents, props changed) head/biology/stacks/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Mar 31 13:08:42 2018 (r466047) +++ head/biology/Makefile Sat Mar 31 13:16:05 2018 (r466048) @@ -109,6 +109,7 @@ SUBDIR += sim4 SUBDIR += slclust SUBDIR += ssaha + SUBDIR += stacks SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tinker Added: head/biology/stacks/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stacks/Makefile Sat Mar 31 13:16:05 2018 (r466048) @@ -0,0 +1,20 @@ +# $FreeBSD$ + +PORTNAME= stacks +DISTVERSION= 1.48 +CATEGORIES= biology +MASTER_SITES= http://catchenlab.life.illinois.edu/stacks/source/ + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Software pipeline for building loci from short-read sequences + +LICENSE= GPLv2 +LICENSE_FILE= ${WRKSRC}/LICENSE + +USES= gmake python shebangfix +SHEBANG_FILES= scripts/*.pl scripts/*.py +GNU_CONFIGURE= yes + +LDFLAGS+= -lpthread + +.include Added: head/biology/stacks/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stacks/distinfo Sat Mar 31 13:16:05 2018 (r466048) @@ -0,0 +1,3 @@ +TIMESTAMP = 1520376299 +SHA256 (stacks-1.48.tar.gz) = e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e +SIZE (stacks-1.48.tar.gz) = 895195 Added: head/biology/stacks/files/patch-htslib_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stacks/files/patch-htslib_Makefile Sat Mar 31 13:16:05 2018 (r466048) @@ -0,0 +1,20 @@ +--- 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. + +-CC = gcc +-AR = ar +-RANLIB = ranlib ++CC ?= gcc ++AR ?= ar ++RANLIB ?= ranlib + + 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 = Added: head/biology/stacks/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stacks/pkg-descr Sat Mar 31 13:16:05 2018 (r466048) @@ -0,0 +1,6 @@ +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. + +WWW: http://catchenlab.life.illinois.edu/stacks/ Added: head/biology/stacks/pkg-message ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stacks/pkg-message Sat Mar 31 13:16:05 2018 (r466048) @@ -0,0 +1,16 @@ +=== + +If you would like to use the stacks web interface, follow the instructions at: + + http://catchenlab.life.illinois.edu/stacks/manual-v1/#install + +You will need to install databases/p5-DBD-mysql to allow the optional +wrapper scripts to interact with the database server. + +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. + +=== Added: head/biology/stacks/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/stacks/pkg-plist Sat Mar 31 13:16:05 2018 (r466048) @@ -0,0 +1,70 @@ +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