Date: Fri, 20 Apr 2018 00:07:28 +0000 (UTC) From: "Jason W. Bacon" <jwb@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r467806 - in head/biology: . freebayes freebayes/files Message-ID: <201804200007.w3K07SCC024580@repo.freebsd.org>
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Author: jwb Date: Fri Apr 20 00:07:27 2018 New Revision: 467806 URL: https://svnweb.freebsd.org/changeset/ports/467806 Log: biology/freebayes: Bayesian haplotype-based polymorphism discovery and genotyping Approved by: jrm (mentor) Differential Revision: https://reviews.freebsd.org/D15116 Added: head/biology/freebayes/ head/biology/freebayes/Makefile (contents, props changed) head/biology/freebayes/distinfo (contents, props changed) head/biology/freebayes/files/ head/biology/freebayes/files/patch-Makefile (contents, props changed) head/biology/freebayes/files/patch-SeqLib_bwa_Makefile (contents, props changed) head/biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c (contents, props changed) head/biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h (contents, props changed) head/biology/freebayes/files/patch-SeqLib_bwa_kthread.c (contents, props changed) head/biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile (contents, props changed) head/biology/freebayes/files/patch-SeqLib_htslib_Makefile (contents, props changed) head/biology/freebayes/files/patch-src_LargeFileSupport.h (contents, props changed) head/biology/freebayes/files/patch-src_Makefile (contents, props changed) head/biology/freebayes/files/patch-vcflib_Makefile (contents, props changed) head/biology/freebayes/pkg-descr (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu Apr 19 20:52:41 2018 (r467805) +++ head/biology/Makefile Fri Apr 20 00:07:27 2018 (r467806) @@ -33,6 +33,7 @@ SUBDIR += fasttree SUBDIR += fastx-toolkit SUBDIR += fluctuate + SUBDIR += freebayes SUBDIR += garlic SUBDIR += gff2ps SUBDIR += gmap Added: head/biology/freebayes/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/Makefile Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,50 @@ +# $FreeBSD$ + +PORTNAME= freebayes +DISTVERSIONPREFIX= v +DISTVERSION= 1.2.0 +CATEGORIES= biology + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Bayesian haplotype-based polymorphism discovery and genotyping + +LICENSE= MIT + +# Submodules use older versions than the ports, so we cannot safely unbundle +# No shared libs are built by the submodules so there will be no conflicts +USES= gmake tar:xz +USE_GITHUB= yes +GH_ACCOUNT= ekg +GH_TUPLE= walaj:SeqLib:5941c68:SeqLib/SeqLib-temp \ + jwalabroad:bwa:c02766e:bwa/SeqLib/bwa \ + jwalabroad:fermi-lite:5bc90f8:fermi/SeqLib/fermi-lite \ + samtools:htslib:49fdfbd:htslib/SeqLib/htslib \ + ekg:bamtools:e77a43f:bamtools/bamtools \ + ekg:intervaltree:dbb4c51:interval1/intervaltree \ + vcflib:vcflib:5e3ce04:vcflib/vcflib-temp \ + ekg:fastahack:c68cebb:fastahack/vcflib/fastahack \ + ekg:filevercmp:1a9b779:filevercmp/vcflib/filevercmp \ + ekg:fsom:a6ef318:fsom/vcflib/fsom \ + google:googletest:d225acc:google/vcflib/googletest \ + ekg:intervaltree:b704f19:interval2/vcflib/intervaltree \ + ekg:multichoose:73d35da:multichoose/vcflib/multichoose \ + ekg:smithwaterman:84c08d7:smithwaterman/vcflib/smithwaterman \ + ekg:tabixpp:80012f8:tabixpp/vcflib/tabixpp \ + samtools:htslib:0f298ce:hts2/vcflib/tabixpp/htslib + +# GCC disables sse2 by default on i386, but it's required for vcflib +CXXFLAGS+= --std=c++11 +CFLAGS_i386= -msse2 +MAKE_JOBS_UNSAFE= yes +PLIST_FILES= bin/bamleftalign bin/freebayes + +# GH_TUPLEs cannot seem to share a top-level subdirectory, so we work around +# by dumping the parent in a temp directory and then moving the contents +post-extract: + ${MV} -n ${WRKSRC}/SeqLib-temp/* ${WRKSRC}/SeqLib + ${MV} -n ${WRKSRC}/vcflib-temp/* ${WRKSRC}/vcflib + +do-install: + ${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin + +.include <bsd.port.mk> Added: head/biology/freebayes/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/distinfo Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,35 @@ +TIMESTAMP = 1523932688 +SHA256 (ekg-freebayes-v1.2.0_GH0.tar.gz) = a5626636112966cac87095365986722d1c871759f03c5a143646da65c416ba8a +SIZE (ekg-freebayes-v1.2.0_GH0.tar.gz) = 2639725 +SHA256 (walaj-SeqLib-5941c68_GH0.tar.gz) = 0ac2b63f5fd7b1cec20a18ebb6799bf1f9b88d6c7cd95f7dd7410b1b82c8703f +SIZE (walaj-SeqLib-5941c68_GH0.tar.gz) = 314968 +SHA256 (jwalabroad-bwa-c02766e_GH0.tar.gz) = cce547db0efef8572d63b47d2065f07e36f770fc8a6f15f5cd03d6fa9ab9b1f7 +SIZE (jwalabroad-bwa-c02766e_GH0.tar.gz) = 205546 +SHA256 (jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz) = 2b3b9b637f48dc3239618efd6b55183eef6b6232013c217eb1c319f1dd3da224 +SIZE (jwalabroad-fermi-lite-5bc90f8_GH0.tar.gz) = 248454 +SHA256 (samtools-htslib-49fdfbd_GH0.tar.gz) = 0bc9c7d48e2a439badf5990113ae3e4de9acd05e4c090938236ee40588d115b9 +SIZE (samtools-htslib-49fdfbd_GH0.tar.gz) = 1145082 +SHA256 (ekg-bamtools-e77a43f_GH0.tar.gz) = d3a143636ccedcc54417a2d6d88dd726c7d2c046318620b88c7ba2fb30b01419 +SIZE (ekg-bamtools-e77a43f_GH0.tar.gz) = 540118 +SHA256 (ekg-intervaltree-dbb4c51_GH0.tar.gz) = 1f3ba92a83cb782cf22dfb383b8c93c11c1c88e0b2e5fa434e24668260ecd1f8 +SIZE (ekg-intervaltree-dbb4c51_GH0.tar.gz) = 3780 +SHA256 (vcflib-vcflib-5e3ce04_GH0.tar.gz) = d084c1df7bb0004df18e013da3cbf896b642d853c855aea58ae029abe1d2097a +SIZE (vcflib-vcflib-5e3ce04_GH0.tar.gz) = 20119782 +SHA256 (ekg-fastahack-c68cebb_GH0.tar.gz) = c6f7186bbe733ff78c25b2afd7e7ba79daa3ecd14a5876ea0b033a43744c876d +SIZE (ekg-fastahack-c68cebb_GH0.tar.gz) = 17312 +SHA256 (ekg-filevercmp-1a9b779_GH0.tar.gz) = 34c21d1b58295bca72b92c1cd832a4171b07ec97c19ffc0d4d8ec67e266c6070 +SIZE (ekg-filevercmp-1a9b779_GH0.tar.gz) = 3053 +SHA256 (ekg-fsom-a6ef318_GH0.tar.gz) = 68351c16d5c4b96142409e38c6828b6199eae44eaa7579bde165734d4832565b +SIZE (ekg-fsom-a6ef318_GH0.tar.gz) = 9686 +SHA256 (google-googletest-d225acc_GH0.tar.gz) = 6880e0d51fa80a508ad5674ce483c1c468315faddac10d580b5505e8e7ef6bfa +SIZE (google-googletest-d225acc_GH0.tar.gz) = 1279815 +SHA256 (ekg-intervaltree-b704f19_GH0.tar.gz) = 7e38b5f5873790afbcfdf6adbb621cdf4a1d9f22e28934a8edfe62cd65918f0d +SIZE (ekg-intervaltree-b704f19_GH0.tar.gz) = 3768 +SHA256 (ekg-multichoose-73d35da_GH0.tar.gz) = af52475d7568863ad8173aebfb6b8b87690118bad8945876b629a2b3c05577cf +SIZE (ekg-multichoose-73d35da_GH0.tar.gz) = 4697 +SHA256 (ekg-smithwaterman-84c08d7_GH0.tar.gz) = 299c9e28e50977642d1538f8940852976b6db3241619eb1f40b78484b1cde58e +SIZE (ekg-smithwaterman-84c08d7_GH0.tar.gz) = 38382 +SHA256 (ekg-tabixpp-80012f8_GH0.tar.gz) = 6aecc865673776bec4e2ddb14e629a4798ad36bf8f7639968812a6262675fb3f +SIZE (ekg-tabixpp-80012f8_GH0.tar.gz) = 3530 +SHA256 (samtools-htslib-0f298ce_GH0.tar.gz) = 829bb54383745fb923ed5d8dabbb6aa8b5d9501601c7a4163276d86aca1196ee +SIZE (samtools-htslib-0f298ce_GH0.tar.gz) = 1065854 Added: head/biology/freebayes/files/patch-Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-Makefile Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,20 @@ +--- Makefile.orig 2018-03-23 14:01:01 UTC ++++ Makefile +@@ -5,7 +5,7 @@ wbamtools: vcflib/Makefile log + cd src && $(MAKE) -f Makefile.bamtools + + log: src/version_git.h +- wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\ | sed s/\"//g) & ++ # wget -q http://hypervolu.me/freebayes/build/$(shell cat src/version_git.h | grep v | cut -f 3 -d\ | sed s/\"//g) & + + src/version_git.h: + cd src && $(MAKE) autoversion +@@ -27,7 +27,7 @@ uninstall: + rm /usr/local/bin/freebayes /usr/local/bin/bamleftalign + + test: +- cd test && make test ++ cd test && ${MAKE} test + + clean: + cd src && $(MAKE) clean Added: head/biology/freebayes/files/patch-SeqLib_bwa_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-SeqLib_bwa_Makefile Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,14 @@ +--- SeqLib/bwa/Makefile.orig 2018-03-23 18:47:04 UTC ++++ SeqLib/bwa/Makefile +@@ -1,8 +1,8 @@ +-CC= gcc ++CC ?= gcc + #CC= clang --analyze +-CFLAGS= -g -Wall -Wno-unused-function -O2 ++CFLAGS ?= -g -Wall -Wno-unused-function -O2 + WRAP_MALLOC=-DUSE_MALLOC_WRAPPERS +-AR= ar ++AR ?= ar + DFLAGS= -DHAVE_PTHREAD $(WRAP_MALLOC) + ## moved is.o bwtiindex.o rope.o to LOBJS + LOBJS= utils.o kthread.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o \ Added: head/biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-SeqLib_bwa_bwt__lite.c Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,10 @@ +--- SeqLib/bwa/bwt_lite.c.orig 2018-03-23 18:49:48 UTC ++++ SeqLib/bwa/bwt_lite.c +@@ -1,6 +1,7 @@ + #include <stdlib.h> + #include <string.h> + #include <stdio.h> ++#include <sys/types.h> + #include "bwt_lite.h" + + #ifdef USE_MALLOC_WRAPPERS Added: head/biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-SeqLib_bwa_bwtgap.h Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,10 @@ +--- SeqLib/bwa/bwtgap.h.orig 2018-03-23 18:49:18 UTC ++++ SeqLib/bwa/bwtgap.h +@@ -3,6 +3,7 @@ + + #include "bwt.h" + #include "bwtaln.h" ++#include <sys/types.h> + + typedef struct { // recursion stack + u_int32_t info; // score<<21 | i Added: head/biology/freebayes/files/patch-SeqLib_bwa_kthread.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-SeqLib_bwa_kthread.c Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,10 @@ +--- SeqLib/bwa/kthread.c.orig 2018-03-23 18:48:35 UTC ++++ SeqLib/bwa/kthread.c +@@ -1,6 +1,7 @@ + #include <pthread.h> + #include <stdlib.h> + #include <limits.h> ++#include <inttypes.h> + + /************ + * kt_for() * Added: head/biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-SeqLib_fermi-lite_Makefile Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,12 @@ +--- SeqLib/fermi-lite/Makefile.orig 2018-03-23 18:50:25 UTC ++++ SeqLib/fermi-lite/Makefile +@@ -1,6 +1,6 @@ +-CC= gcc +-CFLAGS= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once +-CPPFLAGS= ++CC ?= gcc ++CFLAGS ?= -g -Wall -O2 -Wno-unused-function #-fno-inline-functions -fno-inline-functions-called-once ++CPPFLAGS ?= + INCLUDES= + OBJS= kthread.o misc.o \ + bseq.o htab.o bfc.o \ Added: head/biology/freebayes/files/patch-SeqLib_htslib_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-SeqLib_htslib_Makefile Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,38 @@ +--- SeqLib/htslib/Makefile.orig 2017-06-20 12:40:28 UTC ++++ SeqLib/htslib/Makefile +@@ -22,20 +22,20 @@ + # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER + # DEALINGS IN THE SOFTWARE. + +-CC = gcc +-AR = ar +-RANLIB = ranlib ++CC ?= gcc ++AR ?= ar ++RANLIB ?= ranlib + + # Default libraries to link if configure is not used + htslib_default_libs = -lz -lm -lbz2 -llzma + +-CPPFLAGS = ++CPPFLAGS ?= + # TODO: probably update cram code to make it compile cleanly with -Wc++-compat + # For testing strict C99 support add -std=c99 -D_XOPEN_SOURCE=600 + #CFLAGS = -g -Wall -O2 -pedantic -std=c99 -D_XOPEN_SOURCE=600 -D__FUNCTION__=__func__ +-CFLAGS = -g -Wall -O2 ++CFLAGS ?= -g -Wall -O2 + EXTRA_CFLAGS_PIC = -fpic +-LDFLAGS = ++LDFLAGS ?= + LIBS = $(htslib_default_libs) + + prefix = /usr/local +@@ -86,7 +86,7 @@ BUILT_THRASH_PROGRAMS = \ + test/thrash_threads5 \ + test/thrash_threads6 + +-all: lib-static lib-shared $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) ++all: lib-static $(BUILT_PROGRAMS) plugins $(BUILT_TEST_PROGRAMS) + + HTSPREFIX = + include htslib_vars.mk Added: head/biology/freebayes/files/patch-src_LargeFileSupport.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-src_LargeFileSupport.h Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,11 @@ +--- src/LargeFileSupport.h.orig 2018-03-23 21:15:04 UTC ++++ src/LargeFileSupport.h +@@ -8,7 +8,7 @@ typedef __int64 off_type; + #define ftell64(a) ftell(a) + #define fseek64(a,b,c) fseek(a,b,c) + typedef __int64_t off_type; +-#elif defined(__APPLE__) ++#elif defined(__APPLE__) || defined(__FreeBSD__) + #define ftell64(a) ftello(a) + #define fseek64(a,b,c) fseeko(a,b,c) + typedef off_t off_type; Added: head/biology/freebayes/files/patch-src_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-src_Makefile Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,62 @@ +--- src/Makefile.orig 2018-03-23 14:01:01 UTC ++++ src/Makefile +@@ -5,8 +5,9 @@ + ################################################################################ + + # Compiler +-CXX=g++ ${CXXFLAGS} +-C=gcc ++CXX ?= g++ ++# CXX += ${CXXFLAGS} ++CC ?= gcc + + export CXXFLAGS + export C +@@ -17,7 +18,7 @@ export LIBFLAGS + + # Compiler flags + +-CFLAGS=-O3 -D_FILE_OFFSET_BITS=64 -g ++CFLAGS += -D_FILE_OFFSET_BITS=64 + #CFLAGS=-O3 -static -D VERBOSE_DEBUG # enables verbose debugging via --debug2 + + SEQLIB_ROOT=../SeqLib +@@ -25,7 +26,7 @@ VCFLIB_ROOT=../vcflib + TABIX_ROOT=$(VCFLIB_ROOT)/tabixpp + HTSLIB_ROOT=$(SEQLIB_ROOT)/htslib + +-LIBS = -lz -llzma -lbz2 -lm -lpthread ++LIBS = -lz -llzma -lbz2 -lm -lpthread -lexecinfo + INCLUDE = -I../src -I../ttmath -I$(VCFLIB_ROOT)/src/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) + #INCLUDE = -I../ttmath -I$(BAMTOOLS_ROOT)/src/ -I$(VCFLIB_ROOT)/src/ -I$(TABIX_ROOT)/ -I$(VCFLIB_ROOT)/smithwaterman/ -I$(VCFLIB_ROOT)/multichoose/ -I$(VCFLIB_ROOT)/filevercmp/ -I$(VCFLIB_ROOT)/fastahack/ -I$(HTSLIB_ROOT) -I$(SEQLIB_ROOT) -I$(SEQLIB_ROOT)/htslib + +@@ -46,10 +47,10 @@ gprof: + .PHONY: all static debug profiling gprof + + $(HTSLIB_ROOT)/libhts.a: +- cd $(HTSLIB_ROOT) && make ++ cd $(HTSLIB_ROOT) && ${MAKE} + + $(SEQLIB_ROOT)/src/libseqlib.a: +- cd $(SEQLIB_ROOT) && ./configure && make ++ cd $(SEQLIB_ROOT) && ./configure && ${MAKE} + + OBJECTS=BedReader.o \ + CNV.o \ +@@ -122,7 +123,7 @@ freebayes.o: freebayes.cpp TryCatch.h $( + $(CXX) $(CXXFLAGS) $(INCLUDE) -c freebayes.cpp + + fastlz.o: fastlz.c fastlz.h +- $(C) $(CFLAGS) $(INCLUDE) -c fastlz.c ++ $(CC) $(CFLAGS) $(INCLUDE) -c fastlz.c + + Parameters.o: Parameters.cpp Parameters.h Version.h + $(CXX) $(CXXFLAGS) $(INCLUDE) -c Parameters.cpp +@@ -277,5 +278,5 @@ autoversion: + + clean: + rm -rf *.o *.cgh *~ freebayes alleles ../bin/freebayes ../bin/alleles ../vcflib/*.o ../vcflib/tabixpp/*.{o,a} tabix.hpp +- if [ -d $(BAMTOOLS_ROOT)/build ]; then make -C $(BAMTOOLS_ROOT)/build clean; fi +- make -C $(VCFLIB_ROOT)/smithwaterman clean ++ if [ -d $(BAMTOOLS_ROOT)/build ]; then ${MAKE} -C $(BAMTOOLS_ROOT)/build clean; fi ++ ${MAKE} -C $(VCFLIB_ROOT)/smithwaterman clean Added: head/biology/freebayes/files/patch-vcflib_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/files/patch-vcflib_Makefile Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,13 @@ +--- vcflib/Makefile.orig 2018-03-23 18:36:07 UTC ++++ vcflib/Makefile +@@ -136,8 +136,8 @@ all: $(OBJECTS) $(BINS) + + GIT_VERSION := $(shell git describe --abbrev=4 --dirty --always) + +-CXX = g++ +-CXXFLAGS = -O3 -D_FILE_OFFSET_BITS=64 -std=c++0x ++CXX ?= g++ ++CXXFLAGS += -D_FILE_OFFSET_BITS=64 -std=c++0x + #CXXFLAGS = -O2 + #CXXFLAGS = -pedantic -Wall -Wshadow -Wpointer-arith -Wcast-qual + Added: head/biology/freebayes/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/freebayes/pkg-descr Fri Apr 20 00:07:27 2018 (r467806) @@ -0,0 +1,7 @@ +FreeBayes is a Bayesian genetic variant detector designed to find small +polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels +(insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex +events (composite insertion and substitution events) smaller than the length of +a short-read sequencing alignment. + +WWW: https://github.com/ekg/freebayes
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