11/11: gnu: plink-ng: Enable tests.

[guix-commits]

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+)))