[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
11/11: gnu: plink-ng: Enable tests.
From: |
guix-commits |
Subject: |
11/11: gnu: plink-ng: Enable tests. |
Date: |
Sat, 4 Dec 2021 10:02:36 -0500 (EST) |
rekado pushed a commit to branch core-updates-frozen
in repository guix.
commit cc491eab7ebd2de29fbb6fc31df75521afebc41b
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Sat Dec 4 16:00:08 2021 +0100
gnu: plink-ng: Enable tests.
* gnu/packages/bioinformatics.scm (plink-ng)[arguments]: Replace 'check
phase
to run tests; do not disable tests via arguments.
[native-inputs]: Add diffutils, plink, and python.
---
gnu/packages/bioinformatics.scm | 24 ++++++++++++++++++++----
1 file changed, 20 insertions(+), 4 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e24982c..227edda 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -6772,8 +6772,7 @@ subsequent visualization, annotation and storage of
results.")
(base32 "1p88lz9agzjlspjhciz61qjc36cfniv4nkxszyy0njqyc5rzc0cd"))))
(build-system gnu-build-system)
(arguments
- `(#:tests? #f ;no "check" target
- #:make-flags
+ `(#:make-flags
,#~(list "BLASFLAGS=-llapack -lopenblas"
"CFLAGS=-Wall -O2 -DDYNAMIC_ZLIB=1"
"ZLIB=-lz"
@@ -6784,12 +6783,29 @@ subsequent visualization, annotation and storage of
results.")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
- (lambda _ (chdir "1.9") #t))
- (delete 'configure)))) ; no "configure" script
+ (lambda _ (chdir "1.9")))
+ (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
`(("lapack" ,lapack)
("openblas" ,openblas)
("zlib" ,zlib)))
+ (native-inputs
+ `(("diffutils" ,diffutils)
+ ("plink" ,plink)
+ ("python" ,python))) ; for tests
(home-page "https://www.cog-genomics.org/plink/")
(license license:gpl3+)))
- 08/11: gnu: plink: Remove trailing #T., (continued)
- 08/11: gnu: plink: Remove trailing #T., guix-commits, 2021/12/04
- 09/11: gnu: plink: Remove reference to %build-inputs., guix-commits, 2021/12/04
- 03/11: gnu: prodigal: Remove reference to %outputs., guix-commits, 2021/12/04
- 01/11: gnu: prank: Remove trailing #T., guix-commits, 2021/12/04
- 07/11: gnu: rsem: Update to 1.3.3., guix-commits, 2021/12/04
- 06/11: gnu: rsem: Remove trailing #T., guix-commits, 2021/12/04
- 10/11: gnu: plink-ng: Replace reference to %outputs., guix-commits, 2021/12/04
- 02/11: gnu: prank: Bind INPUTS in 'install phase., guix-commits, 2021/12/04
- 04/11: gnu: rsem: Remove trailing #T from snippet., guix-commits, 2021/12/04
- 05/11: gnu: rsem: Remove references to %build-inputs., guix-commits, 2021/12/04
- 11/11: gnu: plink-ng: Enable tests.,
guix-commits <=