prodigal: Prokaryotic Dynamic Programming Genefinding Algorithm

[Jason Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Sat Oct 27 21:55:00 2018 -0500
Changeset:	6f0867e8bdda6efd1e6454fdc1c652790ef2378c

Modified Files:
	Makefile
Added Files:
	prodigal/DESCR
	prodigal/Makefile
	prodigal/PLIST
	prodigal/distinfo
	prodigal/patches/patch-Makefile

Log Message:
prodigal: Prokaryotic Dynamic Programming Genefinding Algorithm

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=6f0867e8bdda6efd1e6454fdc1c652790ef2378c

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

diffstat:
 Makefile                        |  1 +
 prodigal/DESCR                  |  3 +++
 prodigal/Makefile               | 25 +++++++++++++++++++++++
 prodigal/PLIST                  |  2 ++
 prodigal/distinfo               |  7 +++++++
 prodigal/patches/patch-Makefile | 45 +++++++++++++++++++++++++++++++++++++++++
 6 files changed, 83 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 6067d2fa23..eab520dc08 100644
--- a/Makefile
+++ b/Makefile
@@ -2916,6 +2916,7 @@ SUBDIR+=	printrun
 SUBDIR+=	probcons
 SUBDIR+=	probe
 SUBDIR+=	procps
+SUBDIR+=	prodigal
 SUBDIR+=	profanity
 SUBDIR+=	progreiserfs
 SUBDIR+=	proplib
diff --git a/prodigal/DESCR b/prodigal/DESCR
new file mode 100644
index 0000000000..bb647826e6
--- /dev/null
+++ b/prodigal/DESCR
@@ -0,0 +1,3 @@
+Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial
+(bacterial and archaeal) gene finding program developed at Oak Ridge National
+Laboratory and the University of Tennessee.
diff --git a/prodigal/Makefile b/prodigal/Makefile
new file mode 100644
index 0000000000..cf2774a43b
--- /dev/null
+++ b/prodigal/Makefile
@@ -0,0 +1,25 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Sat Oct 27 21:43:14 CDT 2018               #
+###########################################################
+
+DISTNAME=	Prodigal-${PV}
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=hyattpd/}
+GITHUB_PROJECT=	Prodigal
+GITHUB_TAG=	v${PV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	http://compbio.ornl.gov/prodigal/
+COMMENT=	Prokaryotic Dynamic Programming Genefinding Algorithm
+LICENSE=	gnu-gpl-v3
+
+USE_TOOLS+=	gmake
+
+PV=		2.6.3
+
+INSTALLATION_DIRS=	bin
+
+.include "../../mk/bsd.pkg.mk"
diff --git a/prodigal/PLIST b/prodigal/PLIST
new file mode 100644
index 0000000000..133cb5b376
--- /dev/null
+++ b/prodigal/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/prodigal
diff --git a/prodigal/distinfo b/prodigal/distinfo
new file mode 100644
index 0000000000..d3c32f8a4b
--- /dev/null
+++ b/prodigal/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (Prodigal-2.6.3.tar.gz) = 1259e999193cd0c095935baebfb8bcb0233e850f
+RMD160 (Prodigal-2.6.3.tar.gz) = 9c0c9a4c14c5d0f748ce4d9e8700e82d7de6eea7
+SHA512 (Prodigal-2.6.3.tar.gz) = 6d6ec310143c50c0d65dbdbd26d6d271839bb23b1da376ecef20059731a9e643d631613eccaac2eb548b295264b9fe58c21b083f1511a6554912cb7d5351d541
+Size (Prodigal-2.6.3.tar.gz) = 610934 bytes
+SHA1 (patch-Makefile) = 566be8f2b3e2f9895271e6369250e20b1c117801
diff --git a/prodigal/patches/patch-Makefile b/prodigal/patches/patch-Makefile
new file mode 100644
index 0000000000..255979c828
--- /dev/null
+++ b/prodigal/patches/patch-Makefile
@@ -0,0 +1,45 @@
+$NetBSD$
+
+# Respect env, add destdir support
+
+--- Makefile.orig	2016-02-12 00:28:35 UTC
++++ Makefile
+@@ -19,17 +19,19 @@
+ ##############################################################################
+ 
+ SHELL   = /bin/sh
+-CC      = gcc
++CC      ?= gcc
+ 
+-CFLAGS  += -pedantic -Wall -O3
+-LFLAGS = -lm $(LDFLAGS)
++CFLAGS	?= -O3
++CFLAGS  += -pedantic -Wall
++LFLAGS  += -lm
+ 
+ TARGET  = prodigal
+ SOURCES = $(shell echo *.c)
+ HEADERS = $(shell echo *.h)
+ OBJECTS = $(SOURCES:.c=.o)
+ 
+-INSTALLDIR  = /usr/local/bin
++DESTDIR	?=
++PREFIX	?= /usr/local
+ 
+ all: $(TARGET)
+ 
+@@ -40,11 +42,11 @@ $(TARGET): $(OBJECTS)
+ 	$(CC) $(CFLAGS) -c -o $@ $<
+ 
+ install: $(TARGET)
+-	install -d -m 0755 $(INSTALLDIR)
+-	install -m 0755 $(TARGET) $(INSTALLDIR)
++	install -d -m 0755 $(DESTDIR)$(PREFIX)/bin
++	install -m 0755 $(TARGET) $(DESTDIR)$(PREFIX)/bin
+  
+ uninstall:
+-	-rm $(INSTALLDIR)/$(TARGET)
++	-rm $(DESTDIR)$(PREFIX)/bin/$(TARGET)
+ 
+ clean:
+ 	-rm -f $(OBJECTS)