pkgsrc-WIP-changes archive
[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index][Old Index]
mothur: adding initial mothur package
Module Name: pkgsrc-wip
Committed By: Dan Siercks <dsiercks%uwm.edu@localhost>
Pushed By: dsiercks
Date: Fri Aug 17 13:44:11 2018 -0500
Changeset: 46bfcf87fffada4cfe7ac79abff8c0e1d45e4745
Modified Files:
Makefile
Added Files:
mothur/DESCR
mothur/Makefile
mothur/PLIST
mothur/distinfo
mothur/patches/patch-Makefile
Log Message:
mothur: adding initial mothur package
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=46bfcf87fffada4cfe7ac79abff8c0e1d45e4745
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
mothur/DESCR | 3 ++
mothur/Makefile | 75 +++++++++++++++++++++++++++++++++++++++++++
mothur/PLIST | 7 ++++
mothur/distinfo | 7 ++++
mothur/patches/patch-Makefile | 37 +++++++++++++++++++++
6 files changed, 130 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index c7ef81e95e..b17f58d0e9 100644
--- a/Makefile
+++ b/Makefile
@@ -2019,6 +2019,7 @@ SUBDIR+= moregroupware
SUBDIR+= morse
SUBDIR+= mosquitto
SUBDIR+= motion
+SUBDIR+= mothur
SUBDIR+= motti
SUBDIR+= mousetweaks
SUBDIR+= mozart
diff --git a/mothur/DESCR b/mothur/DESCR
new file mode 100644
index 0000000000..a8452cd46f
--- /dev/null
+++ b/mothur/DESCR
@@ -0,0 +1,3 @@
+Expandable software to fill bioinformatics needs of microbial ecology
+community. Incorporates functionality of dotur, sons, treeclimber,
+s-libshuff, unifrac, and much more.
diff --git a/mothur/Makefile b/mothur/Makefile
new file mode 100644
index 0000000000..09623a0793
--- /dev/null
+++ b/mothur/Makefile
@@ -0,0 +1,75 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Tue Jul 31 09:11:25 CDT 2018 #
+###########################################################
+
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+## $FreeBSD$
+# LIB_DEPENDS= libboost_iostreams.so:devel/boost-libs
+# RUN_DEPENDS= uchime>=0:wip/uchime
+# Unknown tool: USE_TOOLS= readline
+##MAKEFILE= makefile
+#PLIST_FILES= bin/mothur
+
+DISTNAME= mothur-${PORTVERSION}
+CATEGORIES= wip
+MASTER_SITES= ${MASTER_SITE_GITHUB:=mothur/}
+GITHUB_PROJECT= mothur
+GITHUB_TAG= v${PORTVERSION}
+
+MAINTAINER= dsiercks%uwm.edu@localhost
+HOMEPAGE= http://www.mothur.org/
+COMMENT= Bioinformatics tool for the microbial ecology community
+# Check this
+LICENSE= gnu-gpl-v3
+
+# Test and change if necessary.
+# MAKE_JOBS_SAFE= no
+
+# Just assuming C and C++: Adjust this!
+USE_LANGUAGES= c c++
+USE_TOOLS+= gmake
+BUILD_TARGET= mothur
+
+PORTVERSION= 1.40.5
+DATADIR= ${PREFIX}/share/mothur
+DOCSDIR= ${PREFIX}/share/doc/mothur
+EXAMPLESDIR= ${PREFIX}/share/examples/mothur
+
+
+SUBST_CLASSES+= thread1
+SUBST_STAGE.thread1= post-patch
+SUBST_SED.thread1= -e "s|thread[*]|std::thread*|g"
+SUBST_FILES.thread1= ${WRKSRC}/source/*.cpp
+SUBST_FILES.thread1+= ${WRKSRC}/source/*/*.cpp
+
+SUBST_CLASSES+= thread2
+SUBST_STAGE.thread2= post-patch
+SUBST_SED.thread2= -e "s|new thread(|new std::thread(|g"
+SUBST_FILES.thread2= ${WRKSRC}/source/*.cpp
+SUBST_FILES.thread2+= ${WRKSRC}/source/*/*.cpp
+
+
+# Sets OPSYS, OS_VERSION, MACHINE_ARCH, etc..
+# .include "../../mk/bsd.prefs.mk"
+
+# Keep this if there are user-selectable options.
+# .include "options.mk"
+
+# Specify which directories to create before install.
+# You should only need this if using your own install target.
+INSTALLATION_DIRS= bin include lib ${PKGMANDIR}/man1 share/doc share/examples
+
+# Guess based on USES=
+.include "../../devel/ncurses/buildlink3.mk"
+.include "../../devel/boost-libs/buildlink3.mk"
+.include "../../devel/readline/buildlink3.mk"
+# Convert any _DEPENDS above that have a buildlink3.mk
+# .include "../..///buildlink3.mk"
+# Linux doesn't have zlib in the base, so just in case...
+.include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/mothur/PLIST b/mothur/PLIST
new file mode 100644
index 0000000000..fa93e4164e
--- /dev/null
+++ b/mothur/PLIST
@@ -0,0 +1,7 @@
+@comment $NetBSD$
+bin/mothur
+@pkgdir share/examples
+@pkgdir share/doc
+@pkgdir man/man1
+@pkgdir lib
+@pkgdir include
diff --git a/mothur/distinfo b/mothur/distinfo
new file mode 100644
index 0000000000..edd354eae5
--- /dev/null
+++ b/mothur/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+SHA1 (mothur-1.40.5.tar.gz) = 071027d188b7bd7aab2dbde918e6f5b57c642619
+RMD160 (mothur-1.40.5.tar.gz) = 07275246cdd3b5c23fde81b11942d33cbb8f6cbe
+SHA512 (mothur-1.40.5.tar.gz) = 569405703a72a1efc9c006a49aeb79b1f126d3f8078a6381056c8cf959f8326cbdd2db98cb50e1da985aa9e01480b94ca73dbbdbc96ab0b679a3662c583f34a8
+Size (mothur-1.40.5.tar.gz) = 1821436 bytes
+SHA1 (patch-Makefile) = 0858dd50719816fb960f1760daf19a7e7587503f
diff --git a/mothur/patches/patch-Makefile b/mothur/patches/patch-Makefile
new file mode 100644
index 0000000000..b839458e95
--- /dev/null
+++ b/mothur/patches/patch-Makefile
@@ -0,0 +1,37 @@
+$NetBSD$
+
+--- Makefile.orig 2018-06-19 14:16:02 UTC
++++ Makefile
+@@ -15,7 +15,11 @@
+ # BOOST_INCLUDE_DIR - location of boost include files
+ # MOTHUR_FILES - default location for mothur to look for input files at runtime. Most often used for reference files.
+
+-PREFIX := ${CURDIR}
++#PREFIX := ${CURDIR}
++DESTDIR ?= .
++PREFIX ?= /usr/local
++INSTALL ?= install
++
+
+ 64BIT_VERSION ?= yes
+ OPTIMIZE ?= yes
+@@ -89,13 +93,15 @@ endif
+ OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp))
+ OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c))
+
+-mothur : $(OBJECTS) uchime
++mothur : $(OBJECTS)
+ $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS)
++ strip mothur
+
+-uchime:
+- cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
++#uchime:
++# cd source/uchime_src && ./mk && mv uchime ../../ && cd ..
+
+-install : mothur uchime
++install : mothur
++ ${INSTALL} -c mothur ${DESTDIR}${PREFIX}/bin
+ #if [ "${CURDIR}" = "$(PREFIX)" ]; then \
+ # echo 'done'; \
+ # else \
Home |
Main Index |
Thread Index |
Old Index