Date: Fri, 5 Jun 2020 01:55:49 +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: r537982 - in head/biology: . subread subread/files Message-ID: <202006050155.0551tnSD075259@repo.freebsd.org>
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Author: jwb Date: Fri Jun 5 01:55:49 2020 New Revision: 537982 URL: https://svnweb.freebsd.org/changeset/ports/537982 Log: biology/subread: Read alignment, quantification and mutation discovery The Subread package comprises a suite of software programs for processing next-gen sequencing read data including: Subread: a general-purpose read aligner Subjunc: a read aligner developed for aligning RNA-seq reads featureCounts: a software program developed for counting reads to genomic features such as genes, exons, promoters and genomic bins. Sublong: a long-read aligner that is designed based on seed-and-vote. exactSNP: discovers SNPs by testing signals against local background noise. Added: head/biology/subread/ head/biology/subread/Makefile (contents, props changed) head/biology/subread/distinfo (contents, props changed) head/biology/subread/files/ head/biology/subread/files/Makefile.pkg (contents, props changed) head/biology/subread/files/patch-HelperFunctions.c (contents, props changed) head/biology/subread/files/patch-core-junction.c (contents, props changed) head/biology/subread/files/patch-gene-algorithms.c (contents, props changed) head/biology/subread/files/patch-input-files.c (contents, props changed) head/biology/subread/files/patch-long-hashtable.c (contents, props changed) head/biology/subread/files/patch-longread-one_LRMsorted-hashtable.c (contents, props changed) head/biology/subread/files/patch-longread-one_Makefile (contents, props changed) head/biology/subread/files/patch-longread-one_longread-mapping.c (contents, props changed) head/biology/subread/files/patch-read-repair.c (contents, props changed) head/biology/subread/files/patch-sambam-file.c (contents, props changed) head/biology/subread/files/patch-sorted-hashtable.c (contents, props changed) head/biology/subread/files/patch-subread.h (contents, props changed) head/biology/subread/pkg-descr (contents, props changed) head/biology/subread/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Thu Jun 4 23:51:51 2020 (r537981) +++ head/biology/Makefile Fri Jun 5 01:55:49 2020 (r537982) @@ -160,6 +160,7 @@ SUBDIR += stacks SUBDIR += star SUBDIR += stringtie + SUBDIR += subread SUBDIR += tRNAscan-SE SUBDIR += tabixpp SUBDIR += tophat Added: head/biology/subread/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/Makefile Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,23 @@ +# $FreeBSD$ + +PORTNAME= subread +DISTVERSION= 2.0.1 +DISTVERSIONSUFFIX= -source +CATEGORIES= biology +MASTER_SITES= SF/${PORTNAME}/${PORTNAME}-${PORTVERSION} + +MAINTAINER= jwb@FreeBSD.org +COMMENT= High-performance read alignment, quantification and mutation discovery + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKDIR}/${DISTNAME}/LICENSE + +LIB_DEPENDS= libsysinfo.so:devel/libsysinfo + +USES= gmake localbase:ldflags + +MAKEFILE= ${FILESDIR}/Makefile.pkg +WRKSRC_SUBDIR= src +INSTALL_TARGET= install-strip + +.include <bsd.port.mk> Added: head/biology/subread/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/distinfo Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,3 @@ +TIMESTAMP = 1591305316 +SHA256 (subread-2.0.1-source.tar.gz) = d808eb5b1823c572cb45a97c95a3c5acb3d8e29aa47ec74e3ca1eb345787c17b +SIZE (subread-2.0.1-source.tar.gz) = 23260381 Added: head/biology/subread/files/Makefile.pkg ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/Makefile.pkg Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,104 @@ + + +include makefile.version + +CCFLAGS = -DMAKE_FOR_EXON -DMAKE_STANDALONE \ + -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" -D_FILE_OFFSET_BITS=64 +LDFLAGS += -DMAKE_FOR_EXON -DMAKE_STANDALONE -pthread -lsysinfo -lz -lm +CC ?= gcc +CC += ${CCFLAGS} + +BINS = detectionCall sublong repair txUnique featureCounts removeDup \ + exactSNP subread-buildindex subindel subread-align subjunc \ + qualityScores subread-fullscan propmapped flattenGTF \ + +MKDIR ?= mkdir -p +INSTALL ?= install +DESTDIR ?= . +PREFIX ?= local +STRIP ?= strip + +ALL_LIBS= core core-junction core-indel sambam-file sublog gene-algorithms hashtable input-files sorted-hashtable gene-value-index exon-algorithms HelperFunctions interval_merge long-hashtable core-bigtable seek-zlib input-blc +ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS}) +ALL_H=$(addsuffix .h, ${ALL_LIBS}) +ALL_C=$(addsuffix .c, ${ALL_LIBS}) + +all: genRandomReads detectionCall sublong repair txUnique featureCounts removeDup exactSNP subread-buildindex subindel subread-align subjunc qualityScores subread-fullscan propmapped flattenGTF # samMappedBases mergeVCF testZlib + mkdir -p ../bin/utilities + mv longread-one/LRM longread-one/sublong + mv longread-one/sublong subread-align subjunc featureCounts subindel exactSNP subread-buildindex ../bin/ + mv detectionCall genRandomReads repair propmapped qualityScores removeDup subread-fullscan txUnique flattenGTF ../bin/utilities + +sublong: longread-one/longread-mapping.c ${ALL_OBJECTS} + echo " " > longread-one/make.version + rm -f longread-one/*.o + cd longread-one && $(MAKE) + +genRandomReads: gen_rand_reads.c ${ALL_OBJECTS} + ${CC} -o genRandomReads gen_rand_reads.c ${ALL_OBJECTS} ${LDFLAGS} + +flattenGTF: flattenAnnotations.c ${ALL_OBJECTS} + ${CC} -o flattenGTF flattenAnnotations.c ${ALL_OBJECTS} ${LDFLAGS} + +detectionCall: detection-calls.c ${ALL_OBJECTS} + ${CC} -o detectionCall detection-calls.c ${ALL_OBJECTS} ${LDFLAGS} + +repair: read-repair.c ${ALL_OBJECTS} + ${CC} -o repair read-repair.c ${ALL_OBJECTS} ${LDFLAGS} + +txUnique: tx-unique.c tx-unique.h ${ALL_OBJECTS} + ${CC} -o txUnique tx-unique.c ${ALL_OBJECTS} ${LDFLAGS} + +globalReassembly: global-reassembly.c ${ALL_OBJECTS} + ${CC} -o globalReassembly global-reassembly.c ${ALL_OBJECTS} ${LDFLAGS} + +propmapped: propmapped.c ${ALL_OBJECTS} + ${CC} -o propmapped propmapped.c ${ALL_OBJECTS} ${LDFLAGS} + +exactSNP: SNPCalling.c SNPCalling.h ${ALL_OBJECTS} + ${CC} -o exactSNP SNPCalling.c ${ALL_OBJECTS} ${LDFLAGS} + +subread-buildindex: index-builder.c subread.h ${ALL_OBJECTS} + ${CC} -o subread-buildindex index-builder.c ${ALL_OBJECTS} ${LDFLAGS} + +removeDup: removeDupReads.c removeDupReads.h subread.h ${ALL_OBJECTS} + ${CC} -o removeDup removeDupReads.c ${ALL_OBJECTS} ${LDFLAGS} + +subindel: SUBindel.c core.h subread.h ${ALL_OBJECTS} + ${CC} -o subindel SUBindel.c ${ALL_OBJECTS} ${LDFLAGS} + +featureCounts: readSummary.c subread.h ${ALL_OBJECTS} + ${CC} -o featureCounts readSummary.c ${ALL_OBJECTS} ${LDFLAGS} + +subread-align: core-interface-aligner.c ${ALL_OBJECTS} + ${CC} -o subread-align core-interface-aligner.c ${ALL_OBJECTS} ${LDFLAGS} + +subjunc: core-interface-subjunc.c ${ALL_OBJECTS} + ${CC} -o subjunc core-interface-subjunc.c ${ALL_OBJECTS} ${LDFLAGS} + +subtools: subtools.c ${ALL_OBJECTS} + ${CC} -o subtools subtools.c ${ALL_OBJECTS} ${LDFLAGS} + +qualityScores: qualityScores.c ${ALL_OBJECTS} + ${CC} -o qualityScores qualityScores.c ${ALL_OBJECTS} ${LDFLAGS} + +subread-fullscan: fullscan.c ${ALL_OBJECTS} + ${CC} -o subread-fullscan fullscan.c ${ALL_OBJECTS} ${LDFLAGS} + +.PHONY: clean install install-strip + +install-strip: install + ${STRIP} ${DESTDIR}${PREFIX}/bin/* + +install: + ${MKDIR} ${DESTDIR}${PREFIX}/bin + ${INSTALL} -c \ + ../bin/exactSNP \ + ../bin/featureCounts \ + ../bin/sub* \ + ../bin/utilities/* \ + ${DESTDIR}${PREFIX}/bin + +clean: + rm -f core featureCounts exactSNP removeDup subread-buildindex \ + ${ALL_OBJECTS} Added: head/biology/subread/files/patch-HelperFunctions.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-HelperFunctions.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,20 @@ +--- HelperFunctions.c.orig 2020-06-04 23:58:40 UTC ++++ HelperFunctions.c +@@ -845,7 +845,7 @@ int strcmp_number(char * s1, char * s2) + + int mac_str(char * str_buff) + { +-#if defined(FREEBSD) || defined(__MINGW32__) ++#if defined(__FreeBSD__) || defined(__MINGW32__) + return 1; + #else + #ifdef MACOS +@@ -2703,7 +2703,7 @@ void main(){ + + int get_free_total_mem(size_t * total, size_t * free_mem){ + +-#ifdef FREEBSD ++#ifdef __FreeBSD__ + return -1; + #endif + Added: head/biology/subread/files/patch-core-junction.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-core-junction.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,10 @@ +--- core-junction.c.orig 2018-11-08 15:19:02 UTC ++++ core-junction.c +@@ -22,6 +22,7 @@ + #include <string.h> + #include <ctype.h> + #include <assert.h> ++#include <unistd.h> + #include "subread.h" + #include "sublog.h" + #include "gene-value-index.h" Added: head/biology/subread/files/patch-gene-algorithms.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-gene-algorithms.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,20 @@ +--- gene-algorithms.c.orig 2020-06-04 23:57:31 UTC ++++ gene-algorithms.c +@@ -28,7 +28,7 @@ + #include <sys/stat.h> + #include <sys/types.h> + +-#ifndef FREEBSD ++#ifndef __FreeBSD__ + #include <sys/timeb.h> + #endif + +@@ -1563,7 +1563,7 @@ int load_offsets(gene_offset_t* offsets , const char i + + double miltime(){ + double ret; +- #ifdef FREEBSD ++ #ifdef __FreeBSD__ + struct timeval tp; + struct timezone tz; + tz.tz_minuteswest=0; Added: head/biology/subread/files/patch-input-files.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-input-files.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,11 @@ +--- input-files.c.orig 2020-06-05 00:33:03 UTC ++++ input-files.c +@@ -48,7 +48,7 @@ FILE * f_subr_open(const char * fname, const char * mo + #ifdef __MINGW32__ + return fopen64(fname, mode); + #else +-#if defined(__LP64__) || defined(_LP64) || defined(MACOS) ++#if defined(__LP64__) || defined(_LP64) || defined(MACOS) || defined(__FreeBSD__) + return fopen(fname, mode); + #else + return fopen64(fname, mode); Added: head/biology/subread/files/patch-long-hashtable.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-long-hashtable.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,11 @@ +--- long-hashtable.c.orig 2020-06-04 23:59:33 UTC ++++ long-hashtable.c +@@ -22,7 +22,7 @@ + #include <string.h> + + #ifndef MACOS +-#ifndef FREEBSD ++#ifndef __FreeBSD__ + #include <malloc.h> + #endif + #endif Added: head/biology/subread/files/patch-longread-one_LRMsorted-hashtable.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-longread-one_LRMsorted-hashtable.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,15 @@ +--- longread-one/LRMsorted-hashtable.c.orig 2018-11-08 14:47:43 UTC ++++ longread-one/LRMsorted-hashtable.c +@@ -22,11 +22,9 @@ + #include <string.h> + #include "LRMsorted-hashtable.h" + +-#ifndef MACOS +-#ifndef FREEBSD ++#if !defined(__APPLE__) && !defined(__FreeBSD__) + #include <malloc.h> + #endif +-#endif + + #include<math.h> + #include "LRMfile-io.h" Added: head/biology/subread/files/patch-longread-one_Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-longread-one_Makefile Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,30 @@ +--- longread-one/Makefile.orig 2019-09-04 04:22:49 UTC ++++ longread-one/Makefile +@@ -1,12 +1,12 @@ +-CC_EXEC = gcc + OPT_LEVEL = 3 + + include ../makefile.version + include make.version + +-CCFLAGS = -mtune=core2 ${MACOS} -O${OPT_LEVEL} -Wall -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} +-LDFLAGS = -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST +-CC = ${CC_EXEC} ${CCFLAGS} -fmessage-length=0 -ggdb ++CC ?= gcc ++CFLAGS += -DMAKE_FOR_EXON -D MAKE_STANDALONE -D_FILE_OFFSET_BITS=64 \ ++ -DSUBREAD_VERSION=\"${SUBREAD_VERSION}\" ${WARNING_LEVEL} ${MINGW32} ++LDFLAGS += -lpthread -lz -lm -O${OPT_LEVEL} -DMAKE_FOR_EXON -D MAKE_STANDALONE # -DREPORT_ALL_THE_BEST + + ALL_LIBS=LRMsorted-hashtable LRMbase-index LRMchro-event LRMhelper LRMseek-zlib LRMfile-io LRMhashtable + ALL_OBJECTS=$(addsuffix .o, ${ALL_LIBS}) +@@ -20,8 +20,8 @@ clean: + rm -f *.o LRM + + LRM: longread-mapping.c ${ALL_OBJECTS} +- ${CC} -o LRM longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS} ++ ${CC} -o LRM ${CFLAGS} longread-mapping.c ${ALL_OBJECTS} ${LDFLAGS} + + $(ALL_OBJECTS): $(ALL_C) $(ALL_H) +- $(CC) -o $@ -c $(subst .o,.c,$@) ++ $(CC) -o $@ -c ${CFLAGS} $(subst .o,.c,$@) + Added: head/biology/subread/files/patch-longread-one_longread-mapping.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-longread-one_longread-mapping.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,37 @@ +--- longread-one/longread-mapping.c.orig 2019-09-04 04:22:49 UTC ++++ longread-one/longread-mapping.c +@@ -30,7 +30,9 @@ + #ifndef __MINGW32__ + #include <sys/resource.h> + #endif ++#ifndef __FreeBSD__ // Deprecated on FreeBSD + #include <sys/timeb.h> ++#endif + #include <sys/stat.h> + #include <locale.h> + #include <ctype.h> +@@ -223,9 +225,24 @@ int LRMvalidate_and_init_context(LRMcontext_t ** conte + + double LRMmiltime(){ + double ret; ++ ++/* Why not use gettimeofday() on all platforms? */ ++#ifdef __FreeBSD__ ++ ++ struct timeval tp; ++ struct timezone tz; ++ tz.tz_minuteswest=0; ++ tz.tz_dsttime=0; ++ gettimeofday(&tp,&tz); ++ ret = tp.tv_sec+ 0.001*0.001* tp.tv_usec; ++ ++#else ++ + struct timeb trp; + ftime(&trp); + ret = trp.time*1.0+(trp.millitm*1.0/1000.0); ++ ++#endif + return ret; + } + Added: head/biology/subread/files/patch-read-repair.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-read-repair.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,10 @@ +--- read-repair.c.orig 2018-11-08 15:20:06 UTC ++++ read-repair.c +@@ -3,6 +3,7 @@ + #include <string.h> + #include <getopt.h> + #include <zlib.h> ++#include <unistd.h> + #include "subread.h" + #include "core.h" + #include "input-files.h" Added: head/biology/subread/files/patch-sambam-file.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-sambam-file.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,10 @@ +--- sambam-file.c.orig 2018-11-08 15:20:35 UTC ++++ sambam-file.c +@@ -30,6 +30,7 @@ + #include <string.h> + #include <assert.h> + #include <ctype.h> ++#include <unistd.h> + #include "subread.h" + #include "core.h" + #include "gene-algorithms.h" Added: head/biology/subread/files/patch-sorted-hashtable.c ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-sorted-hashtable.c Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,15 @@ +--- sorted-hashtable.c.orig 2018-11-08 03:33:50 UTC ++++ sorted-hashtable.c +@@ -23,11 +23,9 @@ + #include <stdlib.h> + #include <string.h> + +-#ifndef MACOS +-#ifndef FREEBSD ++#if !defined(__FreeBSD__) && !defined(__APPLE__) + #include <malloc.h> + #endif +-#endif + + #include<math.h> + #include"core.h" Added: head/biology/subread/files/patch-subread.h ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/files/patch-subread.h Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,11 @@ +--- subread.h.orig 2018-11-08 14:46:06 UTC ++++ subread.h +@@ -102,7 +102,7 @@ + + #define USE_POSIX_MUTEX_LOCK + +-#if defined(MACOS) || defined(FREEBSD) || defined(USE_POSIX_MUTEX_LOCK) ++#if defined(__APPLE__) || defined(__FreeBSD__) || defined(USE_POSIX_MUTEX_LOCK) + typedef pthread_mutex_t subread_lock_t; + #define pthread_spinlock_t pthread_mutex_t + #define pthread_spin_lock pthread_mutex_lock Added: head/biology/subread/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/pkg-descr Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,20 @@ +The Subread package comprises a suite of software programs for processing +next-gen sequencing read data including: + + Subread: a general-purpose read aligner which can align both genomic + DNA-seq and RNA-seq reads. It can also be used to discover genomic + mutations including short indels and structural variants. + + Subjunc: a read aligner developed for aligning RNA-seq reads and for the + detection of exon-exon junctions. Gene fusion events can be detected as + well. + + featureCounts: a software program developed for counting reads to genomic + features such as genes, exons, promoters and genomic bins. + + Sublong: a long-read aligner that is designed based on seed-and-vote. + + exactSNP: a SNP caller that discovers SNPs by testing signals against local + background noises. + +WWW: http://bioinf.wehi.edu.au/subread-package/ Added: head/biology/subread/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/subread/pkg-plist Fri Jun 5 01:55:49 2020 (r537982) @@ -0,0 +1,16 @@ +bin/detectionCall +bin/exactSNP +bin/featureCounts +bin/flattenGTF +bin/genRandomReads +bin/propmapped +bin/qualityScores +bin/removeDup +bin/repair +bin/subindel +bin/subjunc +bin/sublong +bin/subread-align +bin/subread-buildindex +bin/subread-fullscan +bin/txUnique
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