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gnu: bedops: Update to 2.4.41.

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* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.41.
[arguments]: Remove trailing #T from build phases; do not set BINDIR in
make-flags; set CC; replace 'install phase.
[native-inputs]: Add diffutils, perl, and which.
This commit is contained in:
Ricardo Wurmus 2022-12-13 18:21:19 +01:00
parent 22acc0b029
commit 3d2b2f12e5
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GPG key ID: 197A5888235FACAC
1 changed files with 40 additions and 30 deletions
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gnu/packages/bioinformatics.scm
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@ -364,7 +364,7 @@ (define-public bcftools-1.10
(define-public bedops
(package
(name "bedops")
(version "2.4.35")
(version "2.4.41")
(source (origin
(method git-fetch)
(uri (git-reference
@ -373,39 +373,49 @@ (define-public bedops
(file-name (git-file-name name version))
(sha256
(base32
"0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx"))))
"046037qdxsn01ln28rbrwnc7wq4a3xahmb2k74l0w75dby5ni42l"))))
(build-system gnu-build-system)
(arguments
'(#:tests? #f
#:make-flags (list (string-append "BINDIR=" %output "/bin"))
#: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.
(list
;; We cannot run the tests because the build system makes strange
;; assumptions about where executables are located.
#:tests? #false
#:test-target "tests"
#:make-flags
#~(list (string-append "CC=" #$(cc-for-target)))
#:phases
#~(modify-phases %standard-phases
(add-after 'unpack 'unpack-tarballs
(lambda _
;; FIXME: Bedops includes tarballs of minimally patched upstream
;; libraries jansson, zlib, and bzip2. We cannot just use stock
;; libraries because at least one of the libraries (zlib) is
;; patched to add a C++ function definition (deflateInit2cpp).
;; Until the Bedops developers offer a way to link against system
;; libraries we have to build the in-tree copies of these three
;; libraries.
;; See upstream discussion:
;; https://github.com/bedops/bedops/issues/124
;; See upstream discussion:
;; https://github.com/bedops/bedops/issues/124
;; Unpack the tarballs to benefit from shebang patching.
(with-directory-excursion "third-party"
(invoke "tar" "xvf" "jansson-2.6.tar.bz2")
(invoke "tar" "xvf" "zlib-1.2.7.tar.bz2")
(invoke "tar" "xvf" "bzip2-1.0.6.tar.bz2"))
;; Disable unpacking of tarballs in Makefile.
(substitute* "system.mk/Makefile.linux"
(("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
(("\\./configure") "CONFIG_SHELL=bash ./configure"))
(substitute* "third-party/zlib-1.2.7/Makefile.in"
(("^SHELL=.*$") "SHELL=bash\n"))
#t))
(delete 'configure))))
;; Unpack the tarballs to benefit from shebang patching.
(with-directory-excursion "third-party"
(invoke "tar" "xvf" "jansson-2.6.tar.bz2")
(invoke "tar" "xvf" "zlib-1.2.7.tar.bz2")
(invoke "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=.*$") "SHELL=bash\n"))))
(delete 'configure)
(replace 'install
(lambda _
(invoke "make" "install"
(string-append "BINDIR=" #$output "/bin")))))))
(native-inputs
(list diffutils perl which))
(home-page "https://github.com/bedops/bedops")
(synopsis "Tools for high-performance genomic feature operations")
(description