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authorasau <asau@pkgsrc.org>2012-11-01 04:06:21 +0000
committerasau <asau@pkgsrc.org>2012-11-01 04:06:21 +0000
commitcf848f130c5a7b8bef1790089824c0c394f61767 (patch)
treea415bb8d387fc50900dd62e6210bfb01ceec98b7 /biology
parentb459a6d6cdaf7591853a348440e1b59eccb1d8eb (diff)
downloadpkgsrc-cf848f130c5a7b8bef1790089824c0c394f61767.tar.gz
Import PLINK/SEQ version 0.08 as biology/plinkseq
Packaged by Jason Bacon for pkgsrc-wip. PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package.
Diffstat (limited to 'biology')
-rw-r--r--biology/plinkseq/DESCR5
-rw-r--r--biology/plinkseq/Makefile25
-rw-r--r--biology/plinkseq/PLIST11
-rw-r--r--biology/plinkseq/distinfo5
4 files changed, 46 insertions, 0 deletions
diff --git a/biology/plinkseq/DESCR b/biology/plinkseq/DESCR
new file mode 100644
index 00000000000..d55ec958eaf
--- /dev/null
+++ b/biology/plinkseq/DESCR
@@ -0,0 +1,5 @@
+PLINK/SEQ is an open-source C/C++ library for working with human genetic
+variation data. The specific focus is to provide a platform for analytic tool
+development for variation data from large-scale resequencing and genotyping
+projects, particularly whole-exome and whole-genome studies. It is independent
+of (but designed to be complementary to) the existing PLINK package.
diff --git a/biology/plinkseq/Makefile b/biology/plinkseq/Makefile
new file mode 100644
index 00000000000..2578471abd2
--- /dev/null
+++ b/biology/plinkseq/Makefile
@@ -0,0 +1,25 @@
+# $NetBSD: Makefile,v 1.1 2012/11/01 04:06:21 asau Exp $
+
+DISTNAME= plinkseq-0.08
+CATEGORIES= biology
+MASTER_SITES= http://atgu.mgh.harvard.edu/plinkseq/dist/version-0.08/
+
+MAINTAINER= jwbacon@tds.net
+HOMEPAGE= http://atgu.mgh.harvard.edu/plinkseq/
+COMMENT= C/C++ library for working with human genetic variation data
+LICENSE= gnu-gpl-v2 # Assuming same as plink. No info on web.
+
+GNU_CONFIGURE= yes
+USE_LIBTOOL= yes
+USE_LANGUAGES= c c++
+USE_TOOLS= bash:run
+REPLACE_BASH= browser/pbrowse.in index/index.in
+
+.include "../../mk/bsd.prefs.mk"
+
+.if $(OPSYS) != "Linux"
+BUILDLINK_TRANSFORM= rm:-ldl
+.endif
+
+.include "../../devel/protobuf/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/biology/plinkseq/PLIST b/biology/plinkseq/PLIST
new file mode 100644
index 00000000000..e2efdad07eb
--- /dev/null
+++ b/biology/plinkseq/PLIST
@@ -0,0 +1,11 @@
+@comment $NetBSD: PLIST,v 1.1 2012/11/01 04:06:21 asau Exp $
+bin/behead
+bin/gcol
+bin/index
+bin/index.cgi
+bin/mongoose
+bin/pbrowse
+bin/pbrowse.cgi
+bin/pseq
+bin/tab2vcf
+lib/libplinkseq.la
diff --git a/biology/plinkseq/distinfo b/biology/plinkseq/distinfo
new file mode 100644
index 00000000000..f3abc62c19b
--- /dev/null
+++ b/biology/plinkseq/distinfo
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1 2012/11/01 04:06:21 asau Exp $
+
+SHA1 (plinkseq-0.08.tar.gz) = 8bff6b32750eee85559dda2c7c3cf9aea423a3d7
+RMD160 (plinkseq-0.08.tar.gz) = bce0966ea5f25d8c1091157561aaf533a98595ec
+Size (plinkseq-0.08.tar.gz) = 2991871 bytes