Date: Fri, 11 Jan 2019 16:02:05 +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: r489981 - in head/biology: . hisat2 hisat2/files Message-ID: <201901111602.x0BG25TQ054209@repo.freebsd.org>
next in thread | raw e-mail | index | archive | help
Author: jwb Date: Fri Jan 11 16:02:05 2019 New Revision: 489981 URL: https://svnweb.freebsd.org/changeset/ports/489981 Log: New port: biology/hisat2: Program for mapping next-generation sequencing reads Approved by: jrm (mentor, implicit) Added: head/biology/hisat2/ head/biology/hisat2/Makefile (contents, props changed) head/biology/hisat2/distinfo (contents, props changed) head/biology/hisat2/files/ head/biology/hisat2/files/Makefile.pkg (contents, props changed) head/biology/hisat2/files/patch-hisat2 (contents, props changed) head/biology/hisat2/pkg-descr (contents, props changed) head/biology/hisat2/pkg-plist (contents, props changed) Modified: head/biology/Makefile Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Fri Jan 11 15:09:34 2019 (r489980) +++ head/biology/Makefile Fri Jan 11 16:02:05 2019 (r489981) @@ -45,6 +45,7 @@ SUBDIR += grappa SUBDIR += groopm SUBDIR += hmmer + SUBDIR += hisat2 SUBDIR += htslib SUBDIR += hyphy SUBDIR += igv Added: head/biology/hisat2/Makefile ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hisat2/Makefile Fri Jan 11 16:02:05 2019 (r489981) @@ -0,0 +1,30 @@ +# $FreeBSD$ + +PORTNAME= hisat2 +DISTVERSION= 2.1.0-23 +DISTVERSIONSUFFIX= -g20f333e +CATEGORIES= biology perl5 python + +MAINTAINER= jwb@FreeBSD.org +COMMENT= Alignment program for mapping next-generation sequencing reads + +LICENSE= GPLv3 +LICENSE_FILE= ${WRKSRC}/LICENSE + +# May work on other 64-bit archs, untested +ONLY_FOR_ARCHS= amd64 +ONLY_FOR_ARCHS_REASON= 64-bit code, some assembly language + +USES= gmake perl5 python shebangfix +USE_GITHUB= yes + +SHEBANG_FILES= hisat2 hisat2-build hisat2-inspect *.py \ + scripts/*.sh scripts/*.pl \ + hisatgenotype_modules/*.py \ + hisatgenotype_scripts/*.py \ + hisatgenotype_scripts/*.sh +GH_ACCOUNT= infphilo + +MAKEFILE= ${FILESDIR}/Makefile.pkg + +.include <bsd.port.mk> Added: head/biology/hisat2/distinfo ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hisat2/distinfo Fri Jan 11 16:02:05 2019 (r489981) @@ -0,0 +1,3 @@ +TIMESTAMP = 1547001889 +SHA256 (infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz) = 7327fa50f51cd1a0fefe1a379cfeb2f06eefdbbe8f49b04b0d79332080f6be57 +SIZE (infphilo-hisat2-2.1.0-23-g20f333e_GH0.tar.gz) = 3972398 Added: head/biology/hisat2/files/Makefile.pkg ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hisat2/files/Makefile.pkg Fri Jan 11 16:02:05 2019 (r489981) @@ -0,0 +1,446 @@ +# +# Generic Makefile for package managers +# J Bacon <bacon4000@gmail.com> +# +# This Makefile respects standard make variables provided by package +# managers, such as CXX, CXXFLAGS, etc. It is intended to work on +# any POSIX platform. Default behaviour should be similar to the +# original Makefile. +# +# This file is part of HISAT2. +# +# HISAT 2 is free software: you can redistribute it and/or modify +# it under the terms of the GNU General Public License as published by +# the Free Software Foundation, either version 3 of the License, or +# (at your option) any later version. +# +# HISAT 2 is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with HISAT. If not, see <http://www.gnu.org/licenses/>. +# + +INC = +GCC_PREFIX = $(shell dirname `which gcc`) +GCC_SUFFIX = + +CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX) +CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX) +CXX ?= $(CPP) +CXXFLAGS ?= -O2 -Wall +INSTALL ?= install + +HEADERS = $(wildcard *.h) +BOWTIE_MM = 1 +BOWTIE_SHARED_MEM = 0 + +MACOS = 0 +ifneq (,$(findstring Darwin,$(shell uname))) + MACOS = 1 +endif + +# EXTRA_FLAGS += -DPOPCNT_CAPABILITY +INC += -I third_party + +MM_DEF = + +ifeq (1,$(BOWTIE_MM)) + MM_DEF = -DBOWTIE_MM +endif + +SHMEM_DEF = + +ifeq (1,$(BOWTIE_SHARED_MEM)) + SHMEM_DEF = -DBOWTIE_SHARED_MEM +endif + +PTHREAD_PKG = +PTHREAD_LIB = -lpthread + +SEARCH_LIBS = +BUILD_LIBS = +INSPECT_LIBS = + +USE_SRA = 0 +SRA_DEF = +SRA_LIB = +SERACH_INC = +ifeq (1,$(USE_SRA)) + SRA_DEF = -DUSE_SRA + SRA_LIB = -lncbi-ngs-c++-static -lngs-c++-static -lncbi-vdb-static -ldl + SEARCH_INC += -I$(NCBI_NGS_DIR)/include -I$(NCBI_VDB_DIR)/include + SEARCH_LIBS += -L$(NCBI_NGS_DIR)/lib64 -L$(NCBI_VDB_DIR)/lib64 +endif + +LIBS = $(PTHREAD_LIB) + +SHARED_CPPS = ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp \ + edit.cpp gfm.cpp \ + reference.cpp ds.cpp multikey_qsort.cpp limit.cpp \ + random_source.cpp tinythread.cpp +SEARCH_CPPS = qual.cpp pat.cpp \ + read_qseq.cpp aligner_seed_policy.cpp \ + aligner_seed.cpp \ + aligner_seed2.cpp \ + aligner_sw.cpp \ + aligner_sw_driver.cpp aligner_cache.cpp \ + aligner_result.cpp ref_coord.cpp mask.cpp \ + pe.cpp aln_sink.cpp dp_framer.cpp \ + scoring.cpp presets.cpp unique.cpp \ + simple_func.cpp \ + random_util.cpp \ + aligner_bt.cpp sse_util.cpp \ + aligner_swsse.cpp outq.cpp \ + aligner_swsse_loc_i16.cpp \ + aligner_swsse_ee_i16.cpp \ + aligner_swsse_loc_u8.cpp \ + aligner_swsse_ee_u8.cpp \ + aligner_driver.cpp \ + splice_site.cpp + +SEARCH_OBJS = qual.o pat.o \ + read_qseq.o aligner_seed_policy.o \ + aligner_seed.o \ + aligner_seed2.o \ + aligner_sw.o \ + aligner_sw_driver.o aligner_cache.o \ + aligner_result.o ref_coord.o mask.o \ + pe.o aln_sink.o dp_framer.o \ + scoring.o presets.o unique.o \ + simple_func.o \ + random_util.o \ + aligner_bt.o sse_util.o \ + aligner_swsse.o outq.o \ + aligner_swsse_loc_i16.o \ + aligner_swsse_ee_i16.o \ + aligner_swsse_loc_u8.o \ + aligner_swsse_ee_u8.o \ + aligner_driver.o \ + splice_site.o + +BUILD_CPPS = diff_sample.cpp + +HISAT2_CPPS_MAIN = $(SEARCH_CPPS) hisat2_main.cpp +HISAT2_BUILD_CPPS_MAIN = $(BUILD_CPPS) hisat2_build_main.cpp + +SEARCH_FRAGMENTS = $(wildcard search_*_phase*.c) +VERSION = $(shell cat VERSION) + +DEBUG_FLAGS = $(CXXFLAGS) -O0 -g3 +DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\"" +RELEASE_FLAGS = $(CXXFLAGS) +RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\"" +NOASSERT_FLAGS = -DNDEBUG +FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE + +ifeq (1,$(USE_SRA)) + ifeq (1, $(MACOS)) + DEBUG_FLAGS += -mmacosx-version-min=10.6 + RELEASE_FLAGS += -mmacosx-version-min=10.6 + endif +endif + + +HISAT2_BIN_LIST = hisat2-build-s \ + hisat2-build-l \ + hisat2-align-s \ + hisat2-align-l \ + hisat2-inspect-s \ + hisat2-inspect-l +HISAT2_BIN_LIST_AUX = hisat2-build-s-debug \ + hisat2-build-l-debug \ + hisat2-align-s-debug \ + hisat2-align-l-debug \ + hisat2-inspect-s-debug \ + hisat2-inspect-l-debug + +GENERAL_LIST = $(wildcard scripts/*.sh) \ + $(wildcard scripts/*.pl) \ + $(wildcard *.py) \ + $(wildcard hisatgenotype_modules/*.py) \ + $(wildcard hisatgenotype_scripts/*.py) \ + doc/manual.inc.html \ + doc/README \ + doc/style.css \ + $(wildcard example/index/*.ht2) \ + $(wildcard example/reads/*.fa) \ + example/reference/22_20-21M.fa \ + example/reference/22_20-21M.snp \ + $(PTHREAD_PKG) \ + hisat2 \ + hisat2-build \ + hisat2-inspect \ + AUTHORS \ + LICENSE \ + NEWS \ + MANUAL \ + MANUAL.markdown \ + TUTORIAL \ + VERSION + +ifeq (1,$(WINDOWS)) + HISAT2_BIN_LIST := $(HISAT2_BIN_LIST) hisat2.bat hisat2-build.bat hisat2-inspect.bat +endif + +# This is helpful on Windows under MinGW/MSYS, where Make might go for +# the Windows FIND tool instead. +FIND=$(shell which find) + +SRC_PKG_LIST = $(wildcard *.h) \ + $(wildcard *.hh) \ + $(wildcard *.c) \ + $(wildcard *.cpp) \ + doc/strip_markdown.pl \ + Makefile \ + $(GENERAL_LIST) + +BIN_PKG_LIST = $(GENERAL_LIST) + +.PHONY: all allall both both-debug install + +all: $(HISAT2_BIN_LIST) + +allall: $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) + +both: hisat2-align-s hisat2-align-l hisat2-build-s hisat2-build-l + +both-debug: hisat2-align-s-debug hisat2-align-l-debug hisat2-build-s-debug hisat2-build-l-debug + +DEFS=-fno-strict-aliasing \ + -DHISAT2_VERSION="\"`cat VERSION`\"" \ + -DBUILD_HOST="\"`hostname`\"" \ + -DBUILD_TIME="\"`date`\"" \ + -DCOMPILER_VERSION="\"`$(CXX) -v 2>&1 | tail -1`\"" \ + $(FILE_FLAGS) \ + $(PREF_DEF) \ + $(MM_DEF) \ + $(SHMEM_DEF) + +# +# hisat-bp targets +# + +hisat-bp-bin: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) + $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) \ + $(INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT_CPPS_MAIN) \ + $(LIBS) $(SEARCH_LIBS) + +hisat-bp-bin-debug: hisat_bp.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) + $(CXX) $(DEBUG_FLAGS) \ + $(DEBUG_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 \ + $(INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT_CPPS_MAIN) \ + $(LIBS) $(SEARCH_LIBS) + + +# +# hisat2-build targets +# + +hisat2-build-s: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS) + $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 $(NOASSERT_FLAGS) -DMASSIVE_DATA_RLCSA \ + $(INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \ + $(LIBS) $(BUILD_LIBS) + +hisat2-build-l: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS) + $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) \ + $(INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \ + $(LIBS) $(BUILD_LIBS) + +hisat2-build-s-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS) + $(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 -DMASSIVE_DATA_RLCSA \ + $(INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \ + $(LIBS) $(BUILD_LIBS) + +hisat2-build-l-debug: hisat2_build.cpp $(SHARED_CPPS) $(HEADERS) + $(CXX) $(DEBUG_FLAGS) $(DEBUG_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX \ + $(INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT2_BUILD_CPPS_MAIN) \ + $(LIBS) $(BUILD_LIBS) + +# +# hisat2 targets +# + +hisat2-align-s: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) + $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) $(SRA_DEF) -DBOWTIE2 $(NOASSERT_FLAGS) \ + $(INC) $(SEARCH_INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \ + $(LIBS) $(SRA_LIB) $(SEARCH_LIBS) + +hisat2-align-l: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) + $(CXX) $(RELEASE_FLAGS) $(RELEASE_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX $(NOASSERT_FLAGS) \ + $(INC) $(SEARCH_INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \ + $(LIBS) $(SRA_LIB) $(SEARCH_LIBS) + +hisat2-align-s-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) + $(CXX) $(DEBUG_FLAGS) \ + $(DEBUG_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) $(SRA_DEF) -DBOWTIE2 \ + $(INC) $(SEARCH_INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \ + $(LIBS) $(SRA_LIB) $(SEARCH_LIBS) + +hisat2-align-l-debug: hisat2.cpp $(SEARCH_CPPS) $(SHARED_CPPS) $(HEADERS) $(SEARCH_FRAGMENTS) + $(CXX) $(DEBUG_FLAGS) \ + $(DEBUG_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) $(SRA_DEF) -DBOWTIE2 -DBOWTIE_64BIT_INDEX \ + $(INC) $(SEARCH_INC) \ + -o $@ $< \ + $(SHARED_CPPS) $(HISAT2_CPPS_MAIN) \ + $(LIBS) $(SRA_LIB) $(SEARCH_LIBS) + +# +# hisat2-inspect targets +# + +hisat2-inspect-s: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) + $(CXX) $(RELEASE_FLAGS) \ + $(RELEASE_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \ + $(INC) -I . \ + -o $@ $< \ + $(SHARED_CPPS) \ + $(LIBS) $(INSPECT_LIBS) + +hisat2-inspect-l: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) + $(CXX) $(RELEASE_FLAGS) \ + $(RELEASE_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \ + $(INC) -I . \ + -o $@ $< \ + $(SHARED_CPPS) \ + $(LIBS) $(INSPECT_LIBS) + +hisat2-inspect-s-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) + $(CXX) $(DEBUG_FLAGS) \ + $(DEBUG_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \ + $(INC) -I . \ + -o $@ $< \ + $(SHARED_CPPS) \ + $(LIBS) $(INSPECT_LIBS) + +hisat2-inspect-l-debug: hisat2_inspect.cpp $(HEADERS) $(SHARED_CPPS) + $(CXX) $(DEBUG_FLAGS) \ + $(DEBUG_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 -DBOWTIE_64BIT_INDEX -DHISAT2_INSPECT_MAIN \ + $(INC) -I . \ + -o $@ $< \ + $(SHARED_CPPS) \ + $(LIBS) $(INSPECT_LIBS) + +%.o: %.cpp + $(CXX) -c $(RELEASE_FLAGS) \ + $(RELEASE_DEFS) $(EXTRA_FLAGS) \ + $(DEFS) -DBOWTIE2 -DHISAT2_INSPECT_MAIN \ + $(INC) -I . $< -o $@ $< + +hisat2: ; + +hisat2.bat: + echo "@echo off" > hisat2.bat + echo "perl %~dp0/hisat2 %*" >> hisat2.bat + +hisat2-build.bat: + echo "@echo off" > hisat2-build.bat + echo "python %~dp0/hisat2-build %*" >> hisat2-build.bat + +hisat2-inspect.bat: + echo "@echo off" > hisat2-inspect.bat + echo "python %~dp0/hisat2-inspect %*" >> hisat2-inspect.bat + + +.PHONY: hisat2-src +hisat2-src: $(SRC_PKG_LIST) + chmod a+x scripts/*.sh scripts/*.pl + mkdir .src.tmp + mkdir .src.tmp/hisat2-$(VERSION) + zip tmp.zip $(SRC_PKG_LIST) + mv tmp.zip .src.tmp/hisat2-$(VERSION) + cd .src.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip + cd .src.tmp ; zip -r hisat2-$(VERSION)-source.zip hisat2-$(VERSION) + cp .src.tmp/hisat2-$(VERSION)-source.zip . + rm -rf .src.tmp + +.PHONY: hisat2-bin +hisat2-bin: $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) + chmod a+x scripts/*.sh scripts/*.pl + rm -rf .bin.tmp + mkdir .bin.tmp + mkdir .bin.tmp/hisat2-$(VERSION) + if [ -f hisat2.exe ] ; then \ + zip tmp.zip $(BIN_PKG_LIST) $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) ; \ + else \ + zip tmp.zip $(BIN_PKG_LIST) $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) ; \ + fi + mv tmp.zip .bin.tmp/hisat2-$(VERSION) + cd .bin.tmp/hisat2-$(VERSION) ; unzip tmp.zip ; rm -f tmp.zip + cd .bin.tmp ; zip -r hisat2-$(VERSION)-$(BITS).zip hisat2-$(VERSION) + cp .bin.tmp/hisat2-$(VERSION)-$(BITS).zip . + rm -rf .bin.tmp + +.PHONY: doc +doc: doc/manual.inc.html MANUAL + +doc/manual.inc.html: MANUAL.markdown + pandoc -T "HISAT2 Manual" -o $@ \ + --from markdown --to HTML --toc $^ + perl -i -ne \ + '$$w=0 if m|^</body>|;print if $$w;$$w=1 if m|^<body>|;' $@ + +MANUAL: MANUAL.markdown + perl doc/strip_markdown.pl < $^ > $@ + +# Install per filesystem hierarchy standard: +# https://en.wikipedia.org/wiki/Filesystem_Hierarchy_Standard + +.PHONY: install +install: + mkdir -p ${DESTDIR}${PREFIX}/bin + ${INSTALL} -c -s ${HISAT2_BIN_LIST} ${DESTDIR}${PREFIX}/bin + ${INSTALL} -c hisat2 hisat2-build hisat2-inspect \ + ${DESTDIR}${PREFIX}/bin + + mkdir -p ${DESTDIR}${PREFIX}/libexec/hisat2 + ${INSTALL} -c scripts/*.sh scripts/*.pl *.py \ + hisatgenotype_modules/hisat*.py \ + hisatgenotype_scripts/*.py hisatgenotype_scripts/*.sh \ + ${DESTDIR}${PREFIX}/libexec/hisat2 + +.PHONY: clean +clean: + rm -f $(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX) \ + $(addsuffix .exe,$(HISAT2_BIN_LIST) $(HISAT2_BIN_LIST_AUX)) \ + hisat2-src.zip hisat2-bin.zip + rm -f core.* .tmp.head + rm -rf *.dSYM + +.PHONY: push-doc +push-doc: doc/manual.inc.html + scp doc/*.*html doc/indexes.txt salz-dmz:/ccb/salz7-data/www/ccb.jhu.edu/html/software/hisat2/ Added: head/biology/hisat2/files/patch-hisat2 ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hisat2/files/patch-hisat2 Fri Jan 11 16:02:05 2019 (r489981) @@ -0,0 +1,11 @@ +--- hisat2.orig 2018-11-07 21:43:32 UTC ++++ hisat2 +@@ -45,7 +45,7 @@ while (-f $prog && -l $prog){ + + ($vol,$script_path,$prog) + = File::Spec->splitpath($prog); +-my $os_is_nix = ($^O eq "linux") || ($^O eq "darwin"); ++my $os_is_nix = ($^O ne "MSWin32") && ($^O ne "MSWin64"); + my $align_bin_s = $os_is_nix ? 'hisat2-align-s' : 'hisat2-align-s.exe'; + my $build_bin = $os_is_nix ? 'hisat2-build' : 'hisat2-build.exe'; + my $align_bin_l = $os_is_nix ? 'hisat2-align-l' : 'hisat2-align-l.exe'; Added: head/biology/hisat2/pkg-descr ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hisat2/pkg-descr Fri Jan 11 16:02:05 2019 (r489981) @@ -0,0 +1,5 @@ +HISAT2 is a fast and sensitive alignment program for mapping next-generation +sequencing reads (both DNA and RNA) to a population of human genomes (as well +as to a single reference genome). + +WWW: https://ccb.jhu.edu/software/hisat2/index.shtml Added: head/biology/hisat2/pkg-plist ============================================================================== --- /dev/null 00:00:00 1970 (empty, because file is newly added) +++ head/biology/hisat2/pkg-plist Fri Jan 11 16:02:05 2019 (r489981) @@ -0,0 +1,81 @@ +bin/hisat2 +bin/hisat2-align-l +bin/hisat2-align-s +bin/hisat2-build +bin/hisat2-build-l +bin/hisat2-build-s +bin/hisat2-inspect +bin/hisat2-inspect-l +bin/hisat2-inspect-s +libexec/hisat2/compare_HLA_Omixon.py +libexec/hisat2/convert_quals.pl +libexec/hisat2/extract_Omixon_HLA.py +libexec/hisat2/extract_exons.py +libexec/hisat2/extract_splice_sites.py +libexec/hisat2/gen_2b_occ_lookup.pl +libexec/hisat2/gen_occ_lookup.pl +libexec/hisat2/gen_solqual_lookup.pl +libexec/hisat2/hisat2_extract_exons.py +libexec/hisat2/hisat2_extract_snps_haplotypes_UCSC.py +libexec/hisat2/hisat2_extract_snps_haplotypes_VCF.py +libexec/hisat2/hisat2_extract_splice_sites.py +libexec/hisat2/hisat2_simulate_reads.py +libexec/hisat2/hisatgenotype.py +libexec/hisat2/hisatgenotype_HLA_genotyping_PGs.py +libexec/hisat2/hisatgenotype_assembly_graph.py +libexec/hisat2/hisatgenotype_build_genome.py +libexec/hisat2/hisatgenotype_convert_codis.py +libexec/hisat2/hisatgenotype_extract_codis_data.py +libexec/hisat2/hisatgenotype_extract_cyp_data.py +libexec/hisat2/hisatgenotype_extract_reads.py +libexec/hisat2/hisatgenotype_extract_vars.py +libexec/hisat2/hisatgenotype_gene_typing.py +libexec/hisat2/hisatgenotype_hla_cyp.py +libexec/hisat2/hisatgenotype_locus.py +libexec/hisat2/hisatgenotype_locus_samples.py +libexec/hisat2/hisatgenotype_typing_common.py +libexec/hisat2/infer_fraglen.pl +libexec/hisat2/make_a_thaliana_tair.sh +libexec/hisat2/make_b_taurus_UMD3.sh +libexec/hisat2/make_bdgp6.sh +libexec/hisat2/make_bdgp6_tran.sh +libexec/hisat2/make_canFam2.sh +libexec/hisat2/make_ce10.sh +libexec/hisat2/make_dm6.sh +libexec/hisat2/make_e_coli.sh +libexec/hisat2/make_grch37.sh +libexec/hisat2/make_grch37_snp.sh +libexec/hisat2/make_grch37_snp_tran.sh +libexec/hisat2/make_grch37_snp_tran_ercc.sh +libexec/hisat2/make_grch37_tran.sh +libexec/hisat2/make_grch38.sh +libexec/hisat2/make_grch38_snp.sh +libexec/hisat2/make_grch38_snp_tran.sh +libexec/hisat2/make_grch38_snp_tran_ercc.sh +libexec/hisat2/make_grch38_tran.sh +libexec/hisat2/make_grcm38.sh +libexec/hisat2/make_grcm38_snp.sh +libexec/hisat2/make_grcm38_snp_tran.sh +libexec/hisat2/make_grcm38_tran.sh +libexec/hisat2/make_hg19.sh +libexec/hisat2/make_hg38.sh +libexec/hisat2/make_hg38_allsnp.sh +libexec/hisat2/make_hg38_snp.sh +libexec/hisat2/make_hg38_snp_tran.sh +libexec/hisat2/make_mm10.sh +libexec/hisat2/make_mm9.sh +libexec/hisat2/make_r64.sh +libexec/hisat2/make_r64_tran.sh +libexec/hisat2/make_rn4.sh +libexec/hisat2/make_rn6.sh +libexec/hisat2/make_rnor6.sh +libexec/hisat2/make_rnor6_tran.sh +libexec/hisat2/make_sc3.sh +libexec/hisat2/make_wbcel235.sh +libexec/hisat2/make_wbcel235_tran.sh +libexec/hisat2/make_zm3_snp_tran_ercc.sh +libexec/hisat2/run_extract_CP.sh +libexec/hisat2/run_extract_ILMN.sh +libexec/hisat2/run_genotype_build.sh +libexec/hisat2/run_hisat2_build.sh +libexec/hisat2/run_type_CP.sh
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?201901111602.x0BG25TQ054209>