diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 51 |
1 files changed, 26 insertions, 25 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 801c9e1642..38b9fe6cf6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -6276,36 +6276,37 @@ subsequent visualization, annotation and storage of results.") (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")))))))) - (inputs - (list lapack openblas zlib)) + (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 `(,zstd "lib"))) (native-inputs (list diffutils plink python simde)) ; for tests (home-page "https://www.cog-genomics.org/plink/") |