13/28: gnu: delly: Update to 0.7.9.

[Ricardo Wurmus]

rekado pushed a commit to branch master
in repository guix.

commit 7a1e62ca67849f9ca19ded4d26c542021db71e38
Author: Ricardo Wurmus <address@hidden>
Date:   Sun Oct 21 14:00:07 2018 +0200

    gnu: delly: Update to 0.7.9.
    
    * gnu/packages/bioinformatics.scm (delly): Update to 0.7.9.
    [source]: Fetch from git.
    [arguments]: Add phase install-templates; use default install phase.
    [native-inputs]: Remove python-2.
    [home-page]: Use new home page.
    * gnu/packages/patches/delly-use-system-libraries.patch: Delete file.
    * gnu/local.mk (dist_patch_DATA): Remove patch.
---
 gnu/local.mk                                       |  1 -
 gnu/packages/bioinformatics.scm                    | 40 ++++++++--------
 .../patches/delly-use-system-libraries.patch       | 56 ----------------------
 3 files changed, 20 insertions(+), 77 deletions(-)

diff --git a/gnu/local.mk b/gnu/local.mk
index c76908f..d155b4c 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -642,7 +642,6 @@ dist_patch_DATA =                                           
\
   %D%/packages/patches/datamash-arm-tests.patch                        \
   %D%/packages/patches/dbus-helper-search-path.patch           \
   %D%/packages/patches/deja-dup-use-ref-keyword-for-iter.patch \
-  %D%/packages/patches/delly-use-system-libraries.patch                \
   %D%/packages/patches/dfu-programmer-fix-libusb.patch         \
   %D%/packages/patches/diffutils-gets-undeclared.patch         \
   %D%/packages/patches/diffutils-getopt.patch                  \
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bc21848..78debbc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2155,42 +2155,42 @@ identify enrichments with functional annotations of the 
genome.")
 (define-public delly
   (package
     (name "delly")
-    (version "0.7.7")
+    (version "0.7.9")
     (source (origin
-              (method url-fetch)
-              (uri (string-append
-                    "https://github.com/tobiasrausch/delly/archive/v";
-                    version ".tar.gz"))
-              (file-name (string-append name "-" version ".tar.gz"))
+              (method git-fetch)
+              (uri (git-reference
+                    (url "https://github.com/dellytools/delly.git";)
+                    (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
               (sha256
-               (base32 "0dkwy3pyxmi6dhh1lpsr3698ri5sslw9qz67hfys0bz8dgrqwabj"))
-              (patches (search-patches "delly-use-system-libraries.patch"))))
+               (base32 "034jqsxswy9gqdh2zkgc1js99qkv75ks4xvzgmh0284sraagv61z"))
+              (modules '((guix build utils)))
+              (snippet
+               '(begin
+                  (delete-file-recursively "src/htslib")
+                  #t))))
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ; There are no tests to run.
-       #:make-flags '("PARALLEL=1") ; Allow parallel execution at run-time.
+       #:make-flags
+       (list "PARALLEL=1"  ; Allow parallel execution at run-time.
+             (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (modify-phases %standard-phases
          (delete 'configure) ; There is no configure phase.
-         (replace 'install
-           (lambda _
-             (let ((bin (string-append (assoc-ref %outputs "out") "/bin"))
-                   (templates (string-append (assoc-ref %outputs "out")
+         (add-after 'install 'install-templates
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((templates (string-append (assoc-ref outputs "out")
                                              "/share/delly/templates")))
-               (mkdir-p bin)
                (mkdir-p templates)
                (copy-recursively "excludeTemplates" templates)
-               (install-file "src/cov" bin)
-               (install-file "src/delly" bin)
-               (install-file "src/dpe" bin)))))))
-    (native-inputs
-     `(("python" ,python-2)))
+               #t))))))
     (inputs
      `(("boost" ,boost)
        ("htslib" ,htslib)
        ("zlib" ,zlib)
        ("bzip2" ,bzip2)))
-    (home-page "https://github.com/tobiasrausch/delly";)
+    (home-page "https://github.com/dellytools/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
diff --git a/gnu/packages/patches/delly-use-system-libraries.patch 
b/gnu/packages/patches/delly-use-system-libraries.patch
deleted file mode 100644
index 3315c2a..0000000
--- a/gnu/packages/patches/delly-use-system-libraries.patch
+++ /dev/null
@@ -1,56 +0,0 @@
---- a/Makefile 2017-04-09 12:48:15.000000000 +0200
-+++ b/Makefile 2017-06-21 14:26:02.749282787 +0200
-@@ -9,8 +9,8 @@
- 
- # Flags
- CXX=g++
--CXXFLAGS += -isystem ${SEQTK_ROOT} -isystem ${BOOST_ROOT} -pedantic -W -Wall 
-Wno-unknown-pragmas -D__STDC_LIMIT_MACROS -fno-strict-aliasing
--LDFLAGS += -L${SEQTK_ROOT} -L${BOOST_ROOT}/stage/lib -lboost_iostreams 
-lboost_filesystem -lboost_system -lboost_program_options -lboost_date_time 
-+CXXFLAGS += -pedantic -W -Wall -Wno-unknown-pragmas -D__STDC_LIMIT_MACROS 
-fno-strict-aliasing
-+LDFLAGS += -lboost_iostreams -lboost_filesystem -lboost_system 
-lboost_program_options -lboost_date_time 
- 
- # Additional flags for release/debug
- ifeq (${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
-@@ -41,29 +41,17 @@
- DELLYSOURCES = $(wildcard src/*.h) $(wildcard src/*.cpp)
- 
- # Targets
--TARGETS = .htslib .bcftools .boost src/delly src/cov src/dpe
-+TARGETS = src/delly src/cov src/dpe
- 
- all:          $(TARGETS)
- 
--.htslib: $(HTSLIBSOURCES)
--      cd src/htslib && make && make lib-static && cd ../../ && touch .htslib
--
--.bcftools: $(HTSLIBSOURCES)
--      cd src/bcftools && make && cd ../../ && touch .bcftools
--
--.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 .bcftools .boost $(DELLYSOURCES)
--      $(CXX) $(CXXFLAGS) address@hidden -o $@ $(LDFLAGS)
--
--src/cov: .htslib .bcftools .boost $(DELLYSOURCES)
-+src/cov: $(DELLYSOURCES)
-       $(CXX) $(CXXFLAGS) address@hidden -o $@ $(LDFLAGS)
- 
--src/dpe: .htslib .bcftools .boost $(DELLYSOURCES)
-+src/dpe: $(DELLYSOURCES)
-       $(CXX) $(CXXFLAGS) address@hidden -o $@ $(LDFLAGS)
- 
- clean:
-       cd src/htslib && make clean
-       cd src/modular-boost && ./b2 --clean-all
--      rm -f $(TARGETS) $(TARGETS:=.o) .htslib .boost .bcftools
-+      rm -f $(TARGETS) $(TARGETS:=.o)