diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 39 |
1 files changed, 12 insertions, 27 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 82506c1c3a..c6531d669f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -2388,7 +2388,7 @@ distribution, coverage uniformity, strand specificity, etc.") (define-public samtools (package (name "samtools") - (version "1.2") + (version "1.3") (source (origin (method url-fetch) @@ -2397,38 +2397,23 @@ distribution, coverage uniformity, strand specificity, etc.") version "/samtools-" version ".tar.bz2")) (sha256 (base32 - "1akdqb685pk9xk1nb6sa9aq8xssjjhvvc06kp4cpdqvz2157l3j2")))) + "03mnf0mhbfwhqlqfslrhfnw68s3g0fs1as354i9a584mqw1l1smy")))) (build-system gnu-build-system) (arguments - `(;; There are 87 test failures when building on non-64-bit architectures - ;; due to invalid test data. This has since been fixed upstream (see - ;; <https://github.com/samtools/samtools/pull/307>), but as there has - ;; not been a new release we disable the tests for all non-64-bit - ;; systems. - #:tests? ,(string=? (or (%current-system) (%current-target-system)) - "x86_64-linux") - #:modules ((ice-9 ftw) + `(#:modules ((ice-9 ftw) (ice-9 regex) (guix build gnu-build-system) (guix build utils)) - #:make-flags (list "LIBCURSES=-lncurses" - (string-append "prefix=" (assoc-ref %outputs "out"))) + #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out"))) + #:configure-flags (list "--with-ncurses") #:phases (alist-cons-after - 'unpack - 'patch-tests - (lambda* (#:key inputs #:allow-other-keys) - (let ((bash (assoc-ref inputs "bash"))) - (substitute* "test/test.pl" - ;; The test script calls out to /bin/bash - (("/bin/bash") - (string-append bash "/bin/bash")) - ;; There are two failing tests upstream relating to the "stats" - ;; subcommand in test_usage_subcommand ("did not have Usage" - ;; and "usage did not mention samtools stats"), so we disable - ;; them. - (("(test_usage_subcommand\\(.*\\);)" cmd) - (string-append "unless ($subcommand eq 'stats') {" cmd "};"))))) + 'unpack 'patch-tests + (lambda _ + (substitute* "test/test.pl" + ;; The test script calls out to /bin/bash + (("/bin/bash") (which "bash"))) + #t) (alist-cons-after 'install 'install-library (lambda* (#:key outputs #:allow-other-keys) @@ -2443,7 +2428,7 @@ distribution, coverage uniformity, strand specificity, etc.") (install-file file include)) (scandir "." (lambda (name) (string-match "\\.h$" name)))) #t)) - (alist-delete 'configure %standard-phases)))))) + %standard-phases))))) (native-inputs `(("pkg-config" ,pkg-config))) (inputs `(("ncurses" ,ncurses) ("perl" ,perl) |