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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 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
(define-public bedops (define-public bedops
(package (package
(name "bedops") (name "bedops")
(version "2.4.35") (version "2.4.41")
(source (origin (source (origin
(method git-fetch) (method git-fetch)
(uri (git-reference (uri (git-reference
@ -373,13 +373,18 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
(file-name (git-file-name name version)) (file-name (git-file-name name version))
(sha256 (sha256
(base32 (base32
"0mmgsgwz5r9w76hzgxkxc9s9lkdhhaf7vr6i02b09vbswvs1fyqx")))) "046037qdxsn01ln28rbrwnc7wq4a3xahmb2k74l0w75dby5ni42l"))))
(build-system gnu-build-system) (build-system gnu-build-system)
(arguments (arguments
'(#:tests? #f (list
#:make-flags (list (string-append "BINDIR=" %output "/bin")) ;; 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=" #$(cc-for-target)))
#:phases #:phases
(modify-phases %standard-phases #~(modify-phases %standard-phases
(add-after 'unpack 'unpack-tarballs (add-after 'unpack 'unpack-tarballs
(lambda _ (lambda _
;; FIXME: Bedops includes tarballs of minimally patched upstream ;; FIXME: Bedops includes tarballs of minimally patched upstream
@ -403,9 +408,14 @@ transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.")
(("^\tbzcat .*") "\t@echo \"not unpacking\"\n") (("^\tbzcat .*") "\t@echo \"not unpacking\"\n")
(("\\./configure") "CONFIG_SHELL=bash ./configure")) (("\\./configure") "CONFIG_SHELL=bash ./configure"))
(substitute* "third-party/zlib-1.2.7/Makefile.in" (substitute* "third-party/zlib-1.2.7/Makefile.in"
(("^SHELL=.*$") "SHELL=bash\n")) (("^SHELL=.*$") "SHELL=bash\n"))))
#t)) (delete 'configure)
(delete 'configure)))) (replace 'install
(lambda _
(invoke "make" "install"
(string-append "BINDIR=" #$output "/bin")))))))
(native-inputs
(list diffutils perl which))
(home-page "https://github.com/bedops/bedops") (home-page "https://github.com/bedops/bedops")
(synopsis "Tools for high-performance genomic feature operations") (synopsis "Tools for high-performance genomic feature operations")
(description (description