'(#:tests? #f
#:make-flags (list (string-append "BINDIR=" %output "/bin"))
#:phases
- (alist-cons-after
- 'unpack 'unpack-tarballs
- (lambda _
- ;; FIXME: Bedops includes tarballs of minimally patched upstream
- ;; libraries jansson, zlib, and bzip2. We cannot just use stock
- ;; libraries because at least one of the libraries (zlib) is
- ;; patched to add a C++ function definition (deflateInit2cpp).
- ;; Until the Bedops developers offer a way to link against system
- ;; libraries we have to build the in-tree copies of these three
- ;; libraries.
-
- ;; See upstream discussion:
- ;; https://github.com/bedops/bedops/issues/124
-
- ;; Unpack the tarballs to benefit from shebang patching.
- (with-directory-excursion "third-party"
- (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
- (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
- (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
- ;; Disable unpacking of tarballs in Makefile.
- (substitute* "system.mk/Makefile.linux"
- (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
- (("\\./configure") "CONFIG_SHELL=bash ./configure"))
- (substitute* "third-party/zlib-1.2.7/Makefile.in"
- (("^SHELL=.*$") "SHELL=bash\n")))
- (alist-delete 'configure %standard-phases))))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'unpack-tarballs
+ (lambda _
+ ;; FIXME: Bedops includes tarballs of minimally patched upstream
+ ;; libraries jansson, zlib, and bzip2. We cannot just use stock
+ ;; libraries because at least one of the libraries (zlib) is
+ ;; patched to add a C++ function definition (deflateInit2cpp).
+ ;; Until the Bedops developers offer a way to link against system
+ ;; libraries we have to build the in-tree copies of these three
+ ;; libraries.
+
+ ;; See upstream discussion:
+ ;; https://github.com/bedops/bedops/issues/124
+
+ ;; Unpack the tarballs to benefit from shebang patching.
+ (with-directory-excursion "third-party"
+ (and (zero? (system* "tar" "xvf" "jansson-2.6.tar.bz2"))
+ (zero? (system* "tar" "xvf" "zlib-1.2.7.tar.bz2"))
+ (zero? (system* "tar" "xvf" "bzip2-1.0.6.tar.bz2"))))
+ ;; Disable unpacking of tarballs in Makefile.
+ (substitute* "system.mk/Makefile.linux"
+ (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
+ (("\\./configure") "CONFIG_SHELL=bash ./configure"))
+ (substitute* "third-party/zlib-1.2.7/Makefile.in"
+ (("^SHELL=.*$") "SHELL=bash\n"))
+ #t))
+ (delete 'configure))))
(home-page "https://github.com/bedops/bedops")
(synopsis "Tools for high-performance genomic feature operations")
(description
(arguments
'(#:tests? #f ;no "check" target
#:phases
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append
- (assoc-ref outputs "out") "/bin"))
- (doc (string-append
- (assoc-ref outputs "out") "/share/doc/bwa"))
- (man (string-append
- (assoc-ref outputs "out") "/share/man/man1")))
- (install-file "bwa" bin)
- (install-file "README.md" doc)
- (install-file "bwa.1" man)))
- ;; no "configure" script
- (alist-delete 'configure %standard-phases))))
+ (modify-phases %standard-phases
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append
+ (assoc-ref outputs "out") "/bin"))
+ (doc (string-append
+ (assoc-ref outputs "out") "/share/doc/bwa"))
+ (man (string-append
+ (assoc-ref outputs "out") "/share/man/man1")))
+ (install-file "bwa" bin)
+ (install-file "README.md" doc)
+ (install-file "bwa.1" man))
+ #t))
+ ;; no "configure" script
+ (delete 'configure))))
(inputs `(("zlib" ,zlib)))
;; Non-portable SSE instructions are used so building fails on platforms
;; other than x86_64.
(arguments
`(#:python ,python-2
#:phases
- (alist-cons-after
- 'unpack 'set-env
- (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1"))
- %standard-phases)))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'set-env
+ (lambda _ (setenv "CROSSMAP_USE_SYSTEM_PYSAM" "1") #t)))))
(inputs
`(("python-numpy" ,python2-numpy)
("python-pysam" ,python2-pysam)
(arguments
`(#:tests? #f ;no "check" target
#:phases
- (alist-cons-after
- 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
- (lambda* (#:key inputs #:allow-other-keys)
- (substitute* "CMakeLists.txt"
- (("set\\(Boost_USE_STATIC_LIBS ON\\)")
- "set(Boost_USE_STATIC_LIBS OFF)")
- (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
- (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
- (substitute* "src/CMakeLists.txt"
- (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
- (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
- #t)
- %standard-phases)))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'use-shared-boost-libs-and-set-bamtools-paths
+ (lambda* (#:key inputs #:allow-other-keys)
+ (substitute* "CMakeLists.txt"
+ (("set\\(Boost_USE_STATIC_LIBS ON\\)")
+ "set(Boost_USE_STATIC_LIBS OFF)")
+ (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/bamtools/include")
+ (string-append (assoc-ref inputs "bamtools") "/include/bamtools")))
+ (substitute* "src/CMakeLists.txt"
+ (("\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/\\.\\./bamtools/lib")
+ (string-append (assoc-ref inputs "bamtools") "/lib/bamtools")))
+ #t)))))
(inputs
`(("boost" ,boost)
("bamtools" ,bamtools)
(assoc-ref %outputs "out")
"/bin/"))
#:phases
- (alist-replace
- 'check
- (lambda* (#:key outputs #:allow-other-keys)
- (setenv "PATH" (string-append
- (assoc-ref outputs "out") "/bin:"
- (getenv "PATH")))
- (chdir "../flexbar_v2.5_src/test")
- (zero? (system* "bash" "flexbar_validate.sh")))
- (alist-delete 'install %standard-phases))))
+ (modify-phases %standard-phases
+ (replace 'check
+ (lambda* (#:key outputs #:allow-other-keys)
+ (setenv "PATH" (string-append
+ (assoc-ref outputs "out") "/bin:"
+ (getenv "PATH")))
+ (chdir "../flexbar_v2.5_src/test")
+ (zero? (system* "bash" "flexbar_validate.sh"))))
+ (delete 'install))))
(inputs
`(("tbb" ,tbb)
("zlib" ,zlib)))
(arguments
`(#:python ,python-2
#:phases
- (alist-cons-after
- 'unpack 'generate-from-cython-sources
- (lambda* (#:key inputs outputs #:allow-other-keys)
- ;; Delete these C files to force fresh generation from pyx sources.
- (delete-file "grit/sparsify_support_fns.c")
- (delete-file "grit/call_peaks_support_fns.c")
- (substitute* "setup.py"
- (("Cython.Setup") "Cython.Build")
- ;; Add numpy include path to fix compilation
- (("pyx\", \\]")
- (string-append "pyx\", ], include_dirs = ['"
- (assoc-ref inputs "python-numpy")
- "/lib/python2.7/site-packages/numpy/core/include/"
- "']"))) #t)
- %standard-phases)))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'generate-from-cython-sources
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ ;; Delete these C files to force fresh generation from pyx sources.
+ (delete-file "grit/sparsify_support_fns.c")
+ (delete-file "grit/call_peaks_support_fns.c")
+ (substitute* "setup.py"
+ (("Cython.Setup") "Cython.Build")
+ ;; Add numpy include path to fix compilation
+ (("pyx\", \\]")
+ (string-append "pyx\", ], include_dirs = ['"
+ (assoc-ref inputs "python-numpy")
+ "/lib/python2.7/site-packages/numpy/core/include/"
+ "']")))
+ #t)))))
(inputs
`(("python-scipy" ,python2-scipy)
("python-numpy" ,python2-numpy)
'()
'("POPCNT_CAPABILITY=0")))
#:phases
- (alist-cons-after
- 'unpack 'patch-sources
- (lambda _
- ;; XXX Cannot use snippet because zip files are not supported
- (substitute* "Makefile"
- (("^CC = .*$") "CC = gcc")
- (("^CPP = .*$") "CPP = g++")
- ;; replace BUILD_HOST and BUILD_TIME for deterministic build
- (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
- (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
- (substitute* '("hisat-build" "hisat-inspect")
- (("/usr/bin/env") (which "env"))))
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (for-each (lambda (file)
- (install-file file bin))
- (find-files
- "."
- "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$"))))
- (alist-delete 'configure %standard-phases)))))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'patch-sources
+ (lambda _
+ ;; XXX Cannot use snippet because zip files are not supported
+ (substitute* "Makefile"
+ (("^CC = .*$") "CC = gcc")
+ (("^CPP = .*$") "CPP = g++")
+ ;; replace BUILD_HOST and BUILD_TIME for deterministic build
+ (("-DBUILD_HOST=.*") "-DBUILD_HOST=\"\\\"guix\\\"\"")
+ (("-DBUILD_TIME=.*") "-DBUILD_TIME=\"\\\"0\\\"\""))
+ (substitute* '("hisat-build" "hisat-inspect")
+ (("/usr/bin/env") (which "env")))
+ #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (for-each (lambda (file)
+ (install-file file bin))
+ (find-files
+ "."
+ "hisat(-(build|align|inspect)(-(s|l)(-debug)*)*)*$")))
+ #t))
+ (delete 'configure))))
(native-inputs
`(("unzip" ,unzip)))
(inputs
`(#:parallel-build? #f ; not supported
#:tests? #f ; no "check" target
#:phases
- (alist-replace
- 'configure
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((out (assoc-ref outputs "out")))
- ;; Allow 'konfigure.perl' to find 'package.prl'.
- (setenv "PERL5LIB"
- (string-append ".:" (getenv "PERL5LIB")))
-
- ;; The 'configure' script doesn't recognize things like
- ;; '--enable-fast-install'.
- (zero? (system* "./configure"
- (string-append "--build-prefix=" (getcwd) "/build")
- (string-append "--prefix=" out)))))
- (alist-cons-after
- 'unpack 'enter-dir
- (lambda _ (chdir "ngs-sdk") #t)
- %standard-phases))))
+ (modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((out (assoc-ref outputs "out")))
+ ;; Allow 'konfigure.perl' to find 'package.prl'.
+ (setenv "PERL5LIB"
+ (string-append ".:" (getenv "PERL5LIB")))
+
+ ;; The 'configure' script doesn't recognize things like
+ ;; '--enable-fast-install'.
+ (zero? (system* "./configure"
+ (string-append "--build-prefix=" (getcwd) "/build")
+ (string-append "--prefix=" out))))))
+ (add-after 'unpack 'enter-dir
+ (lambda _ (chdir "ngs-sdk") #t)))))
(native-inputs `(("perl" ,perl)))
;; According to the test
;; unless ($MARCH =~ /x86_64/i || $MARCH =~ /i?86/i)
"-f" "Makefile.Linux"
"CC=gcc ${CCFLAGS}")
#:phases
- (alist-cons-after
- 'unpack 'enter-dir
- (lambda _ (chdir "src") #t)
- (alist-replace
- 'install
- (lambda* (#:key outputs #:allow-other-keys)
- (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
- (mkdir-p bin)
- (copy-recursively "../bin" bin)))
+ (modify-phases %standard-phases
+ (add-after 'unpack 'enter-dir
+ (lambda _ (chdir "src") #t))
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin/")))
+ (mkdir-p bin)
+ (copy-recursively "../bin" bin))))
;; no "configure" script
- (alist-delete 'configure %standard-phases)))))
+ (delete 'configure))))
(inputs `(("zlib" ,zlib)))
(home-page "http://bioinf.wehi.edu.au/subread-package/")
(synopsis "Tool kit for processing next-gen sequencing data")
HCoop / jackhill / guix / guix.git / blobdiff