git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqbias@99905 bc3139a8-67e5-0310-9ffc-ced21a209358
Nathaniel Hayden authored on 27/02/2015 01:47:48
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Package: seqbias |
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-Version: 1.15.0 |
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+Version: 1.15.1 |
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Date: 25-12-2010 |
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Title: Estimation of per-position bias in high-throughput sequencing |
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data |
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@@ -11,7 +11,7 @@ Author: Daniel Jones <dcjones@cs.washington.edu> |
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Maintainer: Daniel Jones <dcjones@cs.washington.edu> |
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Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>= |
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2.15.0), methods |
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-LinkingTo: Rsamtools |
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+LinkingTo: Rsamtools (>= 1.19.36) |
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Imports: zlibbioc |
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Suggests: Rsamtools, ggplot2 |
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LazyLoad: yes |
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include Makevars.common |
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+SAMTOOLS_PATH=\ |
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+ `echo 'cat(system.file("usrlib", package="Rsamtools", mustWork=TRUE))' |\
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+ "${R_HOME}/bin/R" --vanilla --slave`
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+SAMTOOLS_LIBS="$(SAMTOOLS_PATH)/libbam.a" "$(SAMTOOLS_PATH)/libbcf.a"\ |
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+ "$(SAMTOOLS_PATH)/libtabix.a" -lz -pthread |
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+SAMTOOLS_CPPFLAGS=-D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 \ |
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+ -D_LARGEFILE64_SOURCE |
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+ |
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+PKG_LIBS=$(SAMTOOLS_LIBS) |
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+PKG_CPPFLAGS=$(SAMTOOLS_CPPFLAGS) |
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+ |
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OBJECTS = $(SEQBIAS_OBJ) \ |
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$(YAML_CPP_OBJ:%=yaml-cpp/%) |
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-SAMVARS=$(shell\ |
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- echo 'cat(system.file(\ |
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- "usretc", .Platform[["r_arch"]], "Rsamtools.mk",\ |
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- package="Rsamtools", mustWork=TRUE))' |\ |
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- "${R_HOME}/bin/R" --vanilla --slave)
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-include $(SAMVARS) |
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- |
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YAML_CPP_OBJ = aliasmanager.o conversion.o directives.o \ |
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emitfromevents.o emitter.o emitterstate.o \ |
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emitterutils.o exp.o iterator.o nodebuilder.o \ |
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include Makevars.common |
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+SAMVARS=$(shell echo 'cat(system.file("usretc", .Platform[["r_arch"]],\
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+ "Rsamtools.mk", package="Rsamtools", mustWork=TRUE))' |\ |
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+ "${R_HOME}/bin/R" --vanilla --slave)
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+include $(SAMVARS) |
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+ |
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+PKG_LIBS=$(SAMTOOLS_LIBS) |
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+PKG_CPPFLAGS=$(SAMTOOLS_CPPFLAGS) |
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+ |
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OBJECTS = $(SEQBIAS_OBJ) \ |
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$(YAML_CPP_OBJ:%=yaml-cpp/%) |
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