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gnu: plink-ng: Build sources from 2.0 directory

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* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Disable tests; adjust
make flags; enter 2.0 directory in 'chdir phase; replace 'install phase.
[inputs]: Add zstd:lib.
This commit is contained in:
Ricardo Wurmus 2022-08-15 17:52:58 +02:00
parent d248d8b519
commit c3c2dfdb5e
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1 changed files with 25 additions and 24 deletions
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gnu/packages/bioinformatics.scm
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@ -6276,36 +6276,37 @@ (define-public plink-ng
(base32 "0m8wkyvbgvcr5kzc284w8fbhpxwglh2c1xq0yc3yv00a53gs7rv0"))))
(build-system gnu-build-system)
(arguments
`(#:make-flags
,#~(list "BLASFLAGS=-llapack -lopenblas"
(string-append "CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1"
" -I" (search-input-directory
%build-inputs "include/simde"))
"ZLIB=-lz"
"BIN=plink prettify"
(string-append "CC=" #$(cc-for-target))
(string-append "PREFIX=" #$output)
"DESTDIR=")
#:phases
(modify-phases %standard-phases
(list
#:tests? #false ;TEST_EXTRACT_CHR doesn't produce expected files
#:make-flags
#~(list "BLASFLAGS=-llapack -lopenblas"
"NO_SSE42=1"
"NO_AVX2=1"
"STATIC_ZSTD="
(string-append "CC=" #$(cc-for-target))
(string-append "PREFIX=" #$output)
"DESTDIR=")
#:phases
'(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _ (chdir "1.9")))
(delete 'configure) ; no "configure" script
(lambda _ (chdir "2.0/build_dynamic")))
(delete 'configure) ; no "configure" script
(replace 'check
(lambda* (#:key tests? inputs #:allow-other-keys)
(when tests?
(symlink "plink" "plink19")
(symlink (search-input-file inputs "/bin/plink") "plink107")
(setenv "PATH" (string-append (getcwd) ":" (getenv "PATH")))
(with-directory-excursion "tests"
;; The model test fails because of a 0.0001 difference.
(substitute* "tests.py"
(("diff -q test1.model test2.model")
"echo yes"))
(invoke "bash" "test_setup.sh")
(invoke "python3" "tests.py"))))))))
(with-directory-excursion "../Tests"
(substitute* "run_tests.sh"
(("^./run_tests" m)
(string-append (which "bash") " " m)))
(invoke "bash" "run_tests.sh")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(install-file "plink2"
(string-append
(assoc-ref outputs "out") "/bin")))))))
(inputs
(list lapack openblas zlib))
(list lapack openblas zlib `(,zstd "lib")))
(native-inputs
(list diffutils plink python simde)) ; for tests
(home-page "https://www.cog-genomics.org/plink/")