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branch master updated: gnu: plink-ng: Build sources from 2.0 directory
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guix-commits |
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branch master updated: gnu: plink-ng: Build sources from 2.0 directory |
Date: |
Mon, 15 Aug 2022 12:10:31 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new c3c2dfdb5e gnu: plink-ng: Build sources from 2.0 directory
c3c2dfdb5e is described below
commit c3c2dfdb5e8e4210382c8e822e392044ade2ee63
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Aug 15 17:52:58 2022 +0200
gnu: plink-ng: Build sources from 2.0 directory
* 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.
---
gnu/packages/bioinformatics.scm | 51 +++++++++++++++++++++--------------------
1 file 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/")
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