epacts: Efficient and Parallelizable Association Container Toolbox

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: epacts: Efficient and Parallelizable Association Container Toolbox
From: Jason Bacon <bacon4000%gmail.com@localhost>
Date: Wed, 30 Aug 2017 19:28:52 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon4000%gmail.com@localhost>
Pushed By:	outpaddling
Date:		Wed Aug 30 14:28:52 2017 -0500
Changeset:	4774614371381334fae33000d21ce71c8836cb8d

Modified Files:
	Makefile
Added Files:
	epacts/DESCR
	epacts/Makefile
	epacts/PLIST
	epacts/distinfo
	epacts/patches/patch-Makefile
	epacts/patches/patch-Makefile.am
	epacts/patches/patch-data_Makefile
	epacts/patches/patch-data_Makefile.in
	epacts/patches/patch-src_FreqTable.h

Log Message:
epacts: Efficient and Parallelizable Association Container Toolbox

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=4774614371381334fae33000d21ce71c8836cb8d

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                              |  1 +
 epacts/DESCR                          |  4 ++
 epacts/Makefile                       | 52 +++++++++++++++++++++
 epacts/PLIST                          | 87 +++++++++++++++++++++++++++++++++++
 epacts/distinfo                       | 11 +++++
 epacts/patches/patch-Makefile         | 14 ++++++
 epacts/patches/patch-Makefile.am      | 15 ++++++
 epacts/patches/patch-data_Makefile    | 14 ++++++
 epacts/patches/patch-data_Makefile.in | 14 ++++++
 epacts/patches/patch-src_FreqTable.h  | 14 ++++++
 10 files changed, 226 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 498a1a1585..20f3392813 100644
--- a/Makefile
+++ b/Makefile
@@ -695,6 +695,7 @@ SUBDIR+=	enigma2000
 SUBDIR+=	entrance
 SUBDIR+=	eor
 SUBDIR+=	eot
+SUBDIR+=	epacts
 SUBDIR+=	epeg
 SUBDIR+=	epiphany
 SUBDIR+=	epsilon
diff --git a/epacts/DESCR b/epacts/DESCR
new file mode 100644
index 0000000000..23ae8622d0
--- /dev/null
+++ b/epacts/DESCR
@@ -0,0 +1,4 @@
+EPACTS (Efficient and Parallelizable Association Container Toolbox) is a
+versatile software pipeline to perform various statistical tests for
+identifying genome-wide association from sequence data through a user-friendly
+interface, both to scientific analysts and to method developers.
diff --git a/epacts/Makefile b/epacts/Makefile
new file mode 100644
index 0000000000..78a6e9cf52
--- /dev/null
+++ b/epacts/Makefile
@@ -0,0 +1,52 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Wed Aug 30 13:54:33 CDT 2017               #
+###########################################################
+
+# Bugs: Conflicts with bgzip, tabix, epstopdf
+
+DISTNAME=	epacts-${PORTVERSION}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=statgen/}
+GITHUB_PROJECT=	EPACTS
+GITHUB_TAG=	a5209db1b3929c4dd2f15f27ea085edf3a634ee7
+
+MAINTAINER=	bacon4000%gmail.com@localhost
+HOMEPAGE=	https://genome.sph.umich.edu/wiki/EPACTS
+COMMENT=	Efficient and Parallelizable Association Container Toolbox
+# Check this
+LICENSE=	gnu-gpl-v3
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE=	no
+
+DEPENDS+=	gnuplot>=0:../../graphics/gnuplot
+DEPENDS+=	R>=0:../../math/R
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	autoconf automake autoreconf bash perl
+USE_LIBTOOL=	yes
+GNU_CONFIGURE=	yes
+REPLACE_BASH=	scripts/*.sh
+REPLACE_PERL=	scripts/epacts*
+
+WRKSRC=		${WRKDIR}/${GITHUB_PROJECT}-${GITHUB_TAG}
+INSTALL_TARGET=	install-strip
+
+PORTVERSION=	2017.08.15
+
+pre-configure:
+	cd ${WRKSRC} && autoreconf -if
+
+post-install:
+	${STRIP_CMD} \
+		${DESTDIR}${PREFIX}/lib/mmSKAT/libs/mmSKAT.so \
+		${DESTDIR}${PREFIX}/lib/epactsR/libs/epactsR.so
+
+# Convert any _DEPENDS above that have a buildlink3.mk
+# .include "../..///buildlink3.mk"
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/epacts/PLIST b/epacts/PLIST
new file mode 100644
index 0000000000..b02d41c173
--- /dev/null
+++ b/epacts/PLIST
@@ -0,0 +1,87 @@
+@comment $NetBSD$
+bin/anno
+bin/bgzip
+bin/chaps
+bin/epacts
+bin/epacts-anno
+bin/epacts-cat
+bin/epacts-cis-extract
+bin/epacts-download
+bin/epacts-enrich
+bin/epacts-group
+bin/epacts-make-group
+bin/epacts-make-kin
+bin/epacts-multi
+bin/epacts-pca-plot
+bin/epacts-plot
+bin/epacts-single
+bin/epacts-zoom
+bin/epacts.pm
+bin/epstopdf
+bin/pEmmax
+bin/tabix
+bin/test_run_epacts.sh
+bin/vcfast
+bin/wGetOptions.pm
+share/EPACTS/1000G_dummy_pheno.ped
+share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz
+share/EPACTS/1000G_exome_chr20_example_softFiltered.calls.vcf.gz.tbi
+share/EPACTS/GillSansItalic.pfb
+share/EPACTS/GillSansMT.pfb
+share/EPACTS/arial.pfb
+share/EPACTS/calibri.pfb
+share/EPACTS/codon.txt
+share/EPACTS/epactsGroup.R
+share/EPACTS/epactsMulti.R
+share/EPACTS/epactsR_3.3.2.tar.gz
+share/EPACTS/epactsSingle.R
+share/EPACTS/genetic_map_GRCh37_wgs.txt.gz
+share/EPACTS/genetic_map_GRCh37_wgs.txt.gz.tbi
+share/EPACTS/group.b.burden.R
+share/EPACTS/group.b.collapse.R
+share/EPACTS/group.b.madsen.R
+share/EPACTS/group.b.wcnt.R
+share/EPACTS/group.mmskat.R
+share/EPACTS/group.q.reverse.R
+share/EPACTS/group.q.wilcox.R
+share/EPACTS/group.skat.R
+share/EPACTS/hg19_gencodeV14.txt.gz
+share/EPACTS/hg19_gencodeV7.txt.gz
+share/EPACTS/hg19_refFlat.txt.gz
+share/EPACTS/hg19_refGene.txt.gz
+share/EPACTS/mmSKAT_0.95.tar.gz
+share/EPACTS/multi.q.linear.R
+share/EPACTS/priority.txt
+share/EPACTS/prologue.ps
+share/EPACTS/single.b.firth.R
+share/EPACTS/single.b.firthCov.R
+share/EPACTS/single.b.lrt.R
+share/EPACTS/single.b.score.R
+share/EPACTS/single.b.sna0.R
+share/EPACTS/single.b.sna2.R
+share/EPACTS/single.b.spa2.R
+share/EPACTS/single.b.wald.R
+share/EPACTS/single.q.emmaxR.R
+share/EPACTS/single.q.linear.R
+share/EPACTS/single.q.lm.R
+share/EPACTS/single.q.reverse.R
+share/EPACTS/single.q.wilcox.R
+share/EPACTS/wgEncodeBroadHmmGm12878HMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmGm12878HMM.bed.gz.tbi
+share/EPACTS/wgEncodeBroadHmmH1hescHMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmH1hescHMM.bed.gz.tbi
+share/EPACTS/wgEncodeBroadHmmHepg2HMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmHepg2HMM.bed.gz.tbi
+share/EPACTS/wgEncodeBroadHmmHmecHMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmHmecHMM.bed.gz.tbi
+share/EPACTS/wgEncodeBroadHmmHsmmHMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmHsmmHMM.bed.gz.tbi
+share/EPACTS/wgEncodeBroadHmmHuvecHMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmHuvecHMM.bed.gz.tbi
+share/EPACTS/wgEncodeBroadHmmK562HMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmK562HMM.bed.gz.tbi
+share/EPACTS/wgEncodeBroadHmmNhekHMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmNhekHMM.bed.gz.tbi
+share/EPACTS/wgEncodeBroadHmmNhlfHMM.bed.gz
+share/EPACTS/wgEncodeBroadHmmNhlfHMM.bed.gz.tbi
+@pkgdir lib
diff --git a/epacts/distinfo b/epacts/distinfo
new file mode 100644
index 0000000000..f30eba1141
--- /dev/null
+++ b/epacts/distinfo
@@ -0,0 +1,11 @@
+$NetBSD$
+
+SHA1 (epacts-2017.08.15-a5209db1b3929c4dd2f15f27ea085edf3a634ee7.tar.gz) = ebd14ed6d45929f897e015514fb9898bf2c71a0a
+RMD160 (epacts-2017.08.15-a5209db1b3929c4dd2f15f27ea085edf3a634ee7.tar.gz) = 1d845f9f19a6e5c09fbe82c23e67dcace26d3915
+SHA512 (epacts-2017.08.15-a5209db1b3929c4dd2f15f27ea085edf3a634ee7.tar.gz) = 53ac5492fa18a29de05c875254c7a433b093479a5d654d1311268186d8e0fa5dc4f2023b5a635cc3bcc448ca5f43ec7a599ba1798420c44f1d31a0937d97b726
+Size (epacts-2017.08.15-a5209db1b3929c4dd2f15f27ea085edf3a634ee7.tar.gz) = 174244056 bytes
+SHA1 (patch-Makefile) = 3d4a68e7e4d6822e6c141ca084a303a358ed03b9
+SHA1 (patch-Makefile.am) = b6ff5b5e58a3c77150f8380a61ee49f7442661af
+SHA1 (patch-data_Makefile) = f89fd01c40cbd7ccc94df61ba659106b8eac5e48
+SHA1 (patch-data_Makefile.in) = c16052d736ead5c4b656e1ffb976460f2eee8b0a
+SHA1 (patch-src_FreqTable.h) = ead74052f923342f799adbadb983c574dec4c9ba
diff --git a/epacts/patches/patch-Makefile b/epacts/patches/patch-Makefile
new file mode 100644
index 0000000000..378ea5dbf8
--- /dev/null
+++ b/epacts/patches/patch-Makefile
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Non-portable mkdir flag
+--- Makefile.orig	2017-02-22 08:30:03 UTC
++++ Makefile
+@@ -820,7 +820,7 @@ uninstall-am:
+ 
+ 
+ install-exec-hook:
+-	mkdir --p $(libdir)
++	mkdir -p $(libdir)
+ 	R CMD INSTALL -l $(libdir) $(datadir)/${PACKAGE}/epactsR_3.3.2.tar.gz
+ 	R CMD INSTALL -l $(libdir) $(datadir)/${PACKAGE}/mmSKAT_0.95.tar.gz
+ 
diff --git a/epacts/patches/patch-Makefile.am b/epacts/patches/patch-Makefile.am
new file mode 100644
index 0000000000..350bcb99f1
--- /dev/null
+++ b/epacts/patches/patch-Makefile.am
@@ -0,0 +1,15 @@
+$NetBSD$
+
+# Add destdir support
+--- Makefile.am.orig	2017-02-22 08:30:03.000000000 +0000
++++ Makefile.am
+@@ -7,6 +7,6 @@ AUTOMAKE_OPTIONS = foreign
+ SUBDIRS = src data scripts
+ 
+ install-exec-hook:
+-	mkdir --p $(libdir)
+-	R CMD INSTALL -l $(libdir) $(datadir)/${PACKAGE}/epactsR_3.3.2.tar.gz
+-	R CMD INSTALL -l $(libdir) $(datadir)/${PACKAGE}/mmSKAT_0.95.tar.gz
++	mkdir -p $(DESTDIR)$(libdir)
++	R CMD INSTALL -l $(DESTDIR)$(libdir) $(DESTDIR)$(datadir)/${PACKAGE}/epactsR_3.3.2.tar.gz
++	R CMD INSTALL -l $(DESTDIR)$(libdir) $(DESTDIR)$(datadir)/${PACKAGE}/mmSKAT_0.95.tar.gz
diff --git a/epacts/patches/patch-data_Makefile b/epacts/patches/patch-data_Makefile
new file mode 100644
index 0000000000..4021125522
--- /dev/null
+++ b/epacts/patches/patch-data_Makefile
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Upstream filename mistmatch
+--- data/Makefile.orig	2017-02-22 08:30:03 UTC
++++ data/Makefile
+@@ -284,7 +284,7 @@ dist_pkgdata_DATA = epactsSingle.R epact
+ 	group.b.collapse.R group.b.madsen.R group.q.reverse.R group.skat.R group.b.burden.R \
+ 	group.mmskat.R group.b.wcnt.R group.q.wilcox.R \
+ 	single.b.firth.R single.b.firthCov.R single.b.wald.R single.q.reverse.R \
+-	single.b.spa.R single.b.spa2.R single.b.sna0.R single.b.sna2.R \
++	single.b.spa3.R single.b.spa2.R single.b.sna0.R single.b.sna2.R \
+ 	single.b.lrt.R single.q.linear.R single.q.wilcox.R single.q.lm.R single.b.score.R \
+ 	single.q.emmaxR.R \
+ 	multi.q.linear.R \
diff --git a/epacts/patches/patch-data_Makefile.in b/epacts/patches/patch-data_Makefile.in
new file mode 100644
index 0000000000..4d720044fb
--- /dev/null
+++ b/epacts/patches/patch-data_Makefile.in
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Upstream filename mistmatch
+--- data/Makefile.in.orig	2017-02-22 08:30:03 UTC
++++ data/Makefile.in
+@@ -284,7 +284,7 @@ dist_pkgdata_DATA = epactsSingle.R epact
+ 	group.b.collapse.R group.b.madsen.R group.q.reverse.R group.skat.R group.b.burden.R \
+ 	group.mmskat.R group.b.wcnt.R group.q.wilcox.R \
+ 	single.b.firth.R single.b.firthCov.R single.b.wald.R single.q.reverse.R \
+-	single.b.spa.R single.b.spa2.R single.b.sna0.R single.b.sna2.R \
++	single.b.spa3.R single.b.spa2.R single.b.sna0.R single.b.sna2.R \
+ 	single.b.lrt.R single.q.linear.R single.q.wilcox.R single.q.lm.R single.b.score.R \
+ 	single.q.emmaxR.R \
+ 	multi.q.linear.R \
diff --git a/epacts/patches/patch-src_FreqTable.h b/epacts/patches/patch-src_FreqTable.h
new file mode 100644
index 0000000000..59a18f0e13
--- /dev/null
+++ b/epacts/patches/patch-src_FreqTable.h
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Upstream bug
+--- src/FreqTable.h.orig	2017-02-22 08:30:03 UTC
++++ src/FreqTable.h
+@@ -15,7 +15,7 @@ public:
+     };
+     void remove(const T& t) {
+         if (this->data.find(t) == this->data.end()) {
+-            return false;
++            return;
+         }
+         this->data[t] -- ;
+         this->isSorted = false;
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