centrifuge: Novel microbial classification engine

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: centrifuge: Novel microbial classification engine
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Mon, 29 Oct 2018 13:39:18 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Mon Oct 29 08:39:18 2018 -0500
Changeset:	192475a7e53ca95d0bec40b5de416be69ae2f9bf

Added Files:
	centrifuge/DESCR
	centrifuge/Makefile
	centrifuge/PLIST
	centrifuge/distinfo
	centrifuge/patches/patch-Makefile

Log Message:
centrifuge: Novel microbial classification engine

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=192475a7e53ca95d0bec40b5de416be69ae2f9bf

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

diffstat:
 centrifuge/DESCR                  |  5 +++
 centrifuge/Makefile               | 32 +++++++++++++++++
 centrifuge/PLIST                  | 27 +++++++++++++++
 centrifuge/distinfo               |  7 ++++
 centrifuge/patches/patch-Makefile | 72 +++++++++++++++++++++++++++++++++++++++
 5 files changed, 143 insertions(+)

diffs:
diff --git a/centrifuge/DESCR b/centrifuge/DESCR
new file mode 100644
index 0000000000..271b40a864
--- /dev/null
+++ b/centrifuge/DESCR
@@ -0,0 +1,5 @@
+[Centrifuge] is a novel microbial classification engine that enables rapid,
+accurate and sensitive labeling of reads and quantification of species on
+desktop computers. The system uses a novel indexing scheme based on the
+Burrows-Wheeler transform (BWT) and the Ferragina-Manzini (FM) index, optimized
+specifically for the metagenomic classification problem.
diff --git a/centrifuge/Makefile b/centrifuge/Makefile
new file mode 100644
index 0000000000..12fe414251
--- /dev/null
+++ b/centrifuge/Makefile
@@ -0,0 +1,32 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Mon Oct 29 07:50:44 CDT 2018               #
+###########################################################
+
+DISTNAME=	centrifuge-${PV}-beta
+PKGNAME=	centrifuge-${PV}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=infphilo/}
+GITHUB_PROJECT=	centrifuge
+GITHUB_TAG=	v${PV}-beta
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://www.ccb.jhu.edu/software/centrifuge/
+COMMENT=	Novel microbial classification engine
+LICENSE=	gnu-gpl-v3
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	bash gmake
+REPLACE_PERL=	centrifuge centrifuge-kreport *.pl
+REPLACE_PYTHON=	centrifuge-build centrifuge-inspect centrifuge-download
+
+# FIXME: Fix asm blocks
+MAKE_ENV+=	POPCNT_CAPABILITY=0 DOCSDIR=${DOCSDIR}
+
+PV=		1.0.4
+DOCSDIR=	${PREFIX}/share/doc/centrifuge
+
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/centrifuge/PLIST b/centrifuge/PLIST
new file mode 100644
index 0000000000..2a5d0e2f4a
--- /dev/null
+++ b/centrifuge/PLIST
@@ -0,0 +1,27 @@
+@comment $NetBSD$
+bin/centrifuge
+bin/centrifuge-BuildSharedSequence.pl
+bin/centrifuge-RemoveEmptySequence.pl
+bin/centrifuge-RemoveN.pl
+bin/centrifuge-build
+bin/centrifuge-build-bin
+bin/centrifuge-class
+bin/centrifuge-compress.pl
+bin/centrifuge-download
+bin/centrifuge-inspect
+bin/centrifuge-inspect-bin
+bin/centrifuge-kreport
+bin/centrifuge-sort-nt.pl
+share/centrifuge/indices/Makefile
+share/doc/centrifuge/README
+share/doc/centrifuge/add.css
+share/doc/centrifuge/faq.shtml
+share/doc/centrifuge/footer.inc.html
+share/doc/centrifuge/index.shtml
+share/doc/centrifuge/manual.html
+share/doc/centrifuge/manual.inc.html
+share/doc/centrifuge/manual.inc.html.old
+share/doc/centrifuge/manual.shtml
+share/doc/centrifuge/sidebar.inc.shtml
+share/doc/centrifuge/strip_markdown.pl
+share/doc/centrifuge/style.css
diff --git a/centrifuge/distinfo b/centrifuge/distinfo
new file mode 100644
index 0000000000..8e3a5bcead
--- /dev/null
+++ b/centrifuge/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (centrifuge-1.0.4-beta.tar.gz) = d4b3cc7dda1c4340d03493fa436f05199c827039
+RMD160 (centrifuge-1.0.4-beta.tar.gz) = c41adb0ddbe11fe2d3cfb1628f7701b64ae980cd
+SHA512 (centrifuge-1.0.4-beta.tar.gz) = 859e456cc60552017bc755914f71ff890e5d1cc6e664b19ddf86d242603fe709a958f674fb47372afe4789a7773757fa7a6b87af0e552ade33edc5b119894938
+Size (centrifuge-1.0.4-beta.tar.gz) = 723189 bytes
+SHA1 (patch-Makefile) = 3d71ee94f39d5bab469f64a0e6d0bc2ff068b6ee
diff --git a/centrifuge/patches/patch-Makefile b/centrifuge/patches/patch-Makefile
new file mode 100644
index 0000000000..2266d621fd
--- /dev/null
+++ b/centrifuge/patches/patch-Makefile
@@ -0,0 +1,72 @@
+$NetBSD$
+
+# Respect env, add destdir support
+
+--- Makefile.orig	2018-06-08 21:24:17 UTC
++++ Makefile
+@@ -23,9 +23,9 @@
+ INC =
+ GCC_PREFIX = $(shell dirname `which gcc`)
+ GCC_SUFFIX =
+-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
+-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX)
+-CXX = $(CPP) #-fdiagnostics-color=always
++CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
++CXX ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
++CPP = $(CXX) #-fdiagnostics-color=always
+ HEADERS = $(wildcard *.h)
+ BOWTIE_MM = 1
+ BOWTIE_SHARED_MEM = 0
+@@ -164,7 +164,7 @@ SSE_FLAG=-msse2
+ 
+ DEBUG_FLAGS    = -O0 -g3 $(BIToS_FLAG) $(SSE_FLAG) -std=c++11
+ DEBUG_DEFS     = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
+-RELEASE_FLAGS  = -O3 $(BITS_FLAG) $(SSE_FLAG) -funroll-loops -g3 -std=c++11
++RELEASE_FLAGS  = $(CXXFLAGS) -std=c++11
+ RELEASE_DEFS   = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
+ NOASSERT_FLAGS = -DNDEBUG
+ FILE_FLAGS     = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
+@@ -409,24 +409,34 @@ doc/manual.inc.html: MANUAL.markdown
+ MANUAL: MANUAL.markdown
+ 	perl doc/strip_markdown.pl < $^ > $@
+ 
+-prefix=/usr/local
++PREFIX		?= /usr/local
++DESTDIR		?=
++STRIP_CMD	?= strip
++DOCSDIR		?= $(PREFIX)/share/centrifuge/doc
++
++.PHONY: install-strip
++install-strip: install
++	for file in $(CENTRIFUGE_BIN_LIST); do \
++		$(STRIP_CMD) $(DESTDIR)$(PREFIX)/bin/$$file; \
++	done
+ 
+ .PHONY: install
+ install: all
+-	mkdir -p $(prefix)/bin
+-	mkdir -p $(prefix)/share/centrifuge/indices
+-	install -m 0644 indices/Makefile $(prefix)/share/centrifuge/indices
+-	install -d -m 0755 $(prefix)/share/centrifuge/doc
+-	install -m 0644 doc/* $(prefix)/share/centrifuge/doc
++	mkdir -p $(DESTDIR)$(PREFIX)/bin
++	mkdir -p $(DESTDIR)$(PREFIX)/share/centrifuge/indices
++	install -m 0644 indices/Makefile \
++		$(DESTDIR)$(PREFIX)/share/centrifuge/indices
++	install -d -m 0755 $(DESTDIR)$(DOCSDIR)
++	install -m 0644 doc/* $(DESTDIR)$(DOCSDIR)
+ 	for file in $(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_SCRIPT_LIST); do \
+-		install -m 0755 $$file $(prefix)/bin ; \
++		install -m 0755 $$file $(DESTDIR)$(PREFIX)/bin ; \
+ 	done
+ 
+ .PHONY: uninstall
+ uninstall: all
+ 	for file in $(CENTRIFUGE_BIN_LIST) $(CENTRIFUGE_SCRIPT_LIST); do \
+-		rm -v $(prefix)/bin/$$file ; \
+-		rm -v $(prefix)/share/centrifuge; \
++		rm -v $(DESTDIR)$(PREFIX)/bin/$$file ; \
++		rm -v $(DESTDIR)$(PREFIX)/share/centrifuge; \
+ 	done
+ 
+
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