Roel Janssen 4 лет назад
Родитель
Сommit
e024f97ea8
2 измененных файлов: 121 добавлений и 0 удалений
  1. +65
    -0
      delly-use-system-libraries.patch
  2. +56
    -0
      gn/packages/bioinformatics.scm

+ 65
- 0
delly-use-system-libraries.patch Просмотреть файл

@@ -0,0 +1,65 @@
This patch let's Delly use the system versions of htslib and boost.

Patch by Roel Janssen <roel@gnu.org>
--- a/Makefile 2016-03-16 13:08:49.936706607 +0100
+++ b/Makefile 2016-03-16 13:09:12.351706212 +0100
@@ -9,8 +9,8 @@
# Flags
CXX=g++
-CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall -Wno-unknown-pragmas
-LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas
+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time
# Additional flags for release/debug
ifeq (${PARALLEL}, 1)
@@ -23,7 +23,7 @@
ifeq (${STATIC}, 1)
LDFLAGS += -static -static-libgcc -pthread -lhts -lz
else
- LDFLAGS += -lhts -lz -Wl,-rpath,${SEQTK_ROOT},-rpath,${BOOST_ROOT}/stage/lib
+ LDFLAGS += -lhts -lz
endif
ifeq (${DEBUG}, 1)
CXXFLAGS += -g -O0 -fno-inline -DDEBUG
@@ -41,32 +41,24 @@
DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
# Targets
-TARGETS = .htslib .boost src/delly src/extract src/cov src/iover src/stats
+TARGETS = src/delly src/extract src/cov src/iover src/stats
all: $(TARGETS)
-.htslib: $(HTSLIBSOURCES)
- cd src/htslib && make && make lib-static && cd ../../ && touch .htslib
-
-.boost: $(BOOSTSOURCES)
- cd src/modular-boost && ./bootstrap.sh --prefix=${PWD}/src/modular-boost --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time && ./b2 && ./b2 headers && cd ../../ && touch .boost
-
-src/delly: .htslib .boost $(DELLYSOURCES)
+src/delly: $(DELLYSOURCES)
$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
-src/extract: .htslib .boost $(DELLYSOURCES)
+src/extract: $(DELLYSOURCES)
$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
-src/cov: .htslib .boost $(DELLYSOURCES)
+src/cov: $(DELLYSOURCES)
$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
-src/iover: .htslib .boost $(DELLYSOURCES)
+src/iover: $(DELLYSOURCES)
$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
-src/stats: .htslib .boost $(DELLYSOURCES)
+src/stats: $(DELLYSOURCES)
$(CXX) $(CXXFLAGS) $@.cpp -o $@ $(LDFLAGS)
clean:
- cd src/htslib && make clean
- cd src/modular-boost && ./b2 --clean-all
- rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost
+ rm -f $(TARGETS) $(TARGETS:=.o)

+ 56
- 0
gn/packages/bioinformatics.scm Просмотреть файл

@@ -113,6 +113,62 @@ standard alignment formats (BAM/SAM) and outputs in variant call format
package.")
(license license:gpl3+)))

(define boost-delly
(package (inherit boost)
(name "boost-delly")
(version "1.57.0")
(source (origin
(method url-fetch)
(uri (string-append
"mirror://sourceforge/boost/boost_"
(string-map (lambda (x) (if (eq? x #\.) #\_ x)) version)
".tar.bz2"))
(sha256
(base32
"0rs94vdmg34bwwj23fllva6mhrml2i7mvmlb11zyrk1k5818q34i"))))))

(define-public delly
(package
(name "delly")
(version "0.7.2")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/tobiasrausch/delly/archive/v"
version ".tar.gz"))
(sha256
(base32 "173mmg43dbxqkyq0kiffz63xbmggr2kzd55mwxci9yfh5md1zprn"))
(patches (list (search-patch "delly-use-system-libraries.patch")))))
(build-system gnu-build-system)
(native-inputs
`(("python" ,python-2)))
(inputs
`(("boost" ,boost-delly) ; Use version 1.57.0 instead.
("htslib" ,htslib)
("zlib" ,zlib)
("bzip2" ,bzip2)))
(arguments
`(#:tests? #f ; There are no tests to run.
#:phases
(modify-phases %standard-phases
(delete 'configure) ; There is no configure phase.
(replace 'install
(lambda _
(let ((bin (string-append (assoc-ref %outputs "out") "/bin")))
(install-file "src/cov" bin)
(install-file "src/delly" bin)
(install-file "src/extract" bin)
(install-file "src/iover" bin)
(install-file "src/stats" bin)))))))
(home-page "https://github.com/tobiasrausch/delly")
(synopsis "Integrated structural variant prediction method")
(description "Delly is an integrated structural variant prediction method
that can discover and genotype deletions, tandem duplications, inversions and
translocations at single-nucleotide resolution in short-read massively parallel
sequencing data. It uses paired-ends and split-reads to sensitively and
accurately delineate genomic rearrangements throughout the genome. Structural
variants can be visualized using Delly-maze and Delly-suave.")
(license license:gpl3)))

(define-public freec
(package
(name "control-freec")


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