biology/bowtie2: Upgrade to 2.3.5
- Add bowtie2-test script
- Separate Makefile patches into a static patch for upstream and reinplace
for ports-specifics
- Allow aarch64 per upstream Makefile (untested)
This commit is contained in:
Jason W. Bacon
parent
c5d3ac8294
commit
b4553c66ec
Notes:
svn2git
2021-03-31 03:12:20 +00:00
svn path=/head/; revision=496155
@ -1,10 +1,9 @@
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# $FreeBSD$
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PORTNAME= bowtie2
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PORTVERSION= 2.3.3.1
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PORTNAME= bowtie2
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DISTVERSIONPREFIX= v
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PORTREVISION= 2
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CATEGORIES= biology
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DISTVERSION= 2.3.5
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CATEGORIES= biology perl5 python
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MAINTAINER= jwb@FreeBSD.org
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COMMENT= Ultrafast, memory-efficient short read aligner
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@ -13,20 +12,28 @@ LICENSE= GPLv3+
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LICENSE_FILE= ${WRKSRC}/LICENSE
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# May also work on other 64-bit platforms, but untested
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ONLY_FOR_ARCHS= amd64
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ONLY_FOR_ARCHS= aarch64 amd64
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LIB_DEPENDS= libtbb.so:devel/tbb
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USES= gmake perl5 python shebangfix
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USES= gmake localbase:ldflags perl5 python shebangfix
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USE_PERL5= run
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SHEBANG_FILES= bowtie2-build bowtie2-inspect scripts/*.pl
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USE_GITHUB= yes
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SHEBANG_FILES= bowtie2 bowtie2-build bowtie2-inspect scripts/*.pl
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GH_ACCOUNT= BenLangmead
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OPTIONS_DEFINE= DOCS EXAMPLES
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SUB_FILES= bowtie2-test
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pre-configure:
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@${REINPLACE_CMD} \
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-e 's|^RELEASE_FLAGS|# RELEASE_FLAGS|' \
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-e 's|tbbmalloc_proxy|tbbmalloc|' \
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${WRKSRC}/Makefile
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post-install:
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${MKDIR} ${STAGEDIR}${DATADIR}/scripts
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@${MKDIR} ${STAGEDIR}${DATADIR}/scripts
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${INSTALL_PROGRAM} \
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${WRKSRC}/bowtie2*-s \
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${WRKSRC}/bowtie2*-l \
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@ -35,6 +42,7 @@ post-install:
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${WRKSRC}/scripts/*.sh \
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${WRKSRC}/scripts/*.pl \
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${STAGEDIR}${DATADIR}/scripts
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${INSTALL_SCRIPT} ${WRKDIR}/bowtie2-test ${STAGEDIR}${PREFIX}/bin
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post-install-DOCS-on:
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(cd ${WRKSRC}/doc && ${COPYTREE_SHARE} . ${STAGEDIR}${DOCSDIR})
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@ -1,3 +1,3 @@
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TIMESTAMP = 1511991430
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SHA256 (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 8b9c0b9c595ebcddcac5feaf6acb44b2294d6deb91de107596ecad242a1a58e9
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SIZE (BenLangmead-bowtie2-v2.3.3.1_GH0.tar.gz) = 5796279
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TIMESTAMP = 1552832567
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SHA256 (BenLangmead-bowtie2-v2.3.5_GH0.tar.gz) = c5daeb0249e98dfe8f70dac7d660b100365a00a22df4cad94d3e383f489911ae
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SIZE (BenLangmead-bowtie2-v2.3.5_GH0.tar.gz) = 10584383
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69
biology/bowtie2/files/bowtie2-test.in
Normal file
69
biology/bowtie2/files/bowtie2-test.in
Normal file
@ -0,0 +1,69 @@
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#!/bin/sh -e
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##########################################################################
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# Script description:
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# Test bowtie2 on examples provided
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# http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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#
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# History:
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# Date Name Modification
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# 2019-03-17 Jason Bacon Begin
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##########################################################################
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usage()
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{
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printf "Usage: $0 \n"
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exit 1
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}
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##########################################################################
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# Main
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##########################################################################
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if [ $# != 0 ]; then
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usage
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fi
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##########################################################################
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# Function description:
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# Pause until user presses return
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##########################################################################
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pause()
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{
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local junk
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printf "Press return to continue..."
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read junk
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}
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cat << EOM
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This script follows the bowtie2 "Getting Started" section of the manual:
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http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml
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EOM
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pause
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examples_dir=%%EXAMPLESDIR%%
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bowtie2-build $examples_dir/reference/lambda_virus.fa \
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lambda_virus
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printf "Done indexing...\n"
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pause
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bowtie2 -x lambda_virus -U $examples_dir/reads/reads_1.fq -S eg1.sam
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printf "Done with alignment.\n"
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pause
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more eg1.sam
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bowtie2 -x lambda_virus -1 $examples_dir/reads/reads_1.fq -2 $examples_dir/reads/reads_2.fq -S eg2.sam
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printf "Done with paired end example.\n"
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pause
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more eg2.sam
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bowtie2 --local -x lambda_virus -U $examples_dir/reads/longreads.fq -S eg3.sam
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printf "Done with local alignment example.\n"
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pause
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more eg3.sam
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@ -1,34 +1,24 @@
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--- Makefile.orig 2017-10-05 16:45:18 UTC
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--- Makefile.orig 2019-03-16 04:14:43 UTC
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+++ Makefile
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@@ -21,10 +21,11 @@
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@@ -21,8 +21,9 @@
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# Makefile for bowtie, bowtie2-build, bowtie2-inspect
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#
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-prefix = /usr/local
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-bindir = $(prefix)/bin
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+PREFIX ?= /usr/local
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+bindir = $(PREFIX)/bin
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-prefix := /usr/local
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-bindir := $(prefix)/bin
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+# Use PREFIX (upper case) provided by many package managers
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+PREXIX ?= /usr/local
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+bindir := $(PREFIX)/bin
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INC = $(if $(RELEASE_BUILD),-I$(CURDIR)/.include)
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+INC += -I${LOCALBASE}/include
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LIBS = $(LDFLAGS) $(if $(RELEASE_BUILD),-L$(CURDIR)/.lib) -lz
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GCC_PREFIX = $(shell dirname `which gcc`)
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GCC_SUFFIX =
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@@ -98,7 +99,7 @@ endif
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#default is to use Intel TBB
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ifneq (1,$(NO_TBB))
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- LIBS += $(PTHREAD_LIB) -ltbb -ltbbmalloc$(if $(RELEASE_BUILD),,_proxy)
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+ LIBS += $(PTHREAD_LIB) -L${LOCALBASE}/lib -ltbb -ltbbmalloc
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override EXTRA_FLAGS += -DWITH_TBB
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else
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LIBS += $(PTHREAD_LIB)
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@@ -189,7 +190,7 @@ SSE_FLAG=-msse2
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DEBUG_FLAGS = -O0 -g3 -m64 $(SSE_FLAG)
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DEBUG_DEFS = -DCOMPILER_OPTIONS="\"$(DEBUG_FLAGS) $(EXTRA_FLAGS)\""
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-RELEASE_FLAGS = -O3 -m64 $(SSE_FLAG) -funroll-loops -g3
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+RELEASE_FLAGS = $(CXXFLAGS) $(SSE_FLAG) -funroll-loops
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RELEASE_DEFS = -DCOMPILER_OPTIONS="\"$(RELEASE_FLAGS) $(EXTRA_FLAGS)\""
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NOASSERT_FLAGS = -DNDEBUG
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FILE_FLAGS = -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE
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LDLIBS := -lz
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GCC_PREFIX := $(shell dirname `which gcc`)
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@@ -30,7 +31,8 @@ GCC_SUFFIX :=
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CC ?= $(GCC_PREFIX)/gcc$(GCC_SUFFIX)
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CPP ?= $(GCC_PREFIX)/g++$(GCC_SUFFIX)
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CXX ?= $(CPP)
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-CXXFLAGS += -std=c++98
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+# long long is unsupported in c++98
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+# CXXFLAGS += -std=c++98
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ifeq (aarch64,$(shell uname -m))
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CXXFLAGS += -fopenmp-simd -DWITH_AARCH64
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CPPFLAGS += -Ithird_party/simde
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@ -7,6 +7,7 @@ bin/bowtie2-build-s
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bin/bowtie2-inspect
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bin/bowtie2-inspect-l
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bin/bowtie2-inspect-s
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bin/bowtie2-test
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%%DATADIR%%/scripts/convert_quals.pl
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%%DATADIR%%/scripts/gen_2b_occ_lookup.pl
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%%DATADIR%%/scripts/gen_occ_lookup.pl
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@ -56,6 +57,8 @@ bin/bowtie2-inspect-s
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.4.bt2
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.1.bt2
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/index/lambda_virus.rev.2.bt2
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/combined_reads.bam
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/conversion_utilities.sh
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/longreads.fq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_1.fq
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%%PORTEXAMPLES%%%%EXAMPLESDIR%%/reads/reads_2.fq
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