From e024f97ea8886191fa49d56782dc42954bdc9880 Mon Sep 17 00:00:00 2001
From: Roel Janssen
Date: Wed, 16 Mar 2016 13:49:52 +0100
Subject: Add delly.

---
 delly-use-system-libraries.patch | 65 ++++++++++++++++++++++++++++++++++++++++
 gn/packages/bioinformatics.scm   | 56 ++++++++++++++++++++++++++++++++++
 2 files changed, 121 insertions(+)
 create mode 100644 delly-use-system-libraries.patch

diff --git a/delly-use-system-libraries.patch b/delly-use-system-libraries.patch
new file mode 100644
index 0000000..3ce817f
--- /dev/null
+++ b/delly-use-system-libraries.patch
@@ -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)
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index a0a375b..a4d14b0 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -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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