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

7 files changed, 136 insertions, 0 deletions

diff --git a/biology/Makefile b/biology/Makefile
index 53733c94937b..0189fabea514 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -109,6 +109,7 @@
     SUBDIR += sim4
     SUBDIR += slclust
     SUBDIR += ssaha
+    SUBDIR += stacks
     SUBDIR += tRNAscan-SE
     SUBDIR += t_coffee
     SUBDIR += tinker
diff --git a/biology/stacks/Makefile b/biology/stacks/Makefile
new file mode 100644
index 000000000000..a7582268a71d
--- /dev/null
+++ b/biology/stacks/Makefile
@@ -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 <bsd.port.mk>
diff --git a/biology/stacks/distinfo b/biology/stacks/distinfo
new file mode 100644
index 000000000000..e32def18090a
--- /dev/null
+++ b/biology/stacks/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1520376299
+SHA256 (stacks-1.48.tar.gz) = e9f6251f5f609f9dd0bb1de17a51f69ce1a9af531548c4d2456a89783b1dcd1e
+SIZE (stacks-1.48.tar.gz) = 895195
diff --git a/biology/stacks/files/patch-htslib_Makefile b/biology/stacks/files/patch-htslib_Makefile
new file mode 100644
index 000000000000..7a1235d9f2a2
--- /dev/null
+++ b/biology/stacks/files/patch-htslib_Makefile
@@ -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     =
diff --git a/biology/stacks/pkg-descr b/biology/stacks/pkg-descr
new file mode 100644
index 000000000000..f7c91c33e98f
--- /dev/null
+++ b/biology/stacks/pkg-descr
@@ -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/
diff --git a/biology/stacks/pkg-message b/biology/stacks/pkg-message
new file mode 100644
index 000000000000..6f077b3c391c
--- /dev/null
+++ b/biology/stacks/pkg-message
@@ -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.
+
+===
diff --git a/biology/stacks/pkg-plist b/biology/stacks/pkg-plist
new file mode 100644
index 000000000000..4f85229d528c
--- /dev/null
+++ b/biology/stacks/pkg-plist
@@ -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