diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2023-04-27 11:40:09 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2023-04-27 11:40:09 +0200 |
| commit | fa685c87eaa9888a4278f39bb2b815673589dced (patch) | |
| tree | 05d74cb4a09a889b0bc8a936a1fbc2472c50efbe /gnu/packages/bioinformatics.scm | |
| parent | 133957f7bb81d9c9f33216ea8afe649866267b5e (diff) | |
gnu: freebayes: Update to 1.3.7.
* gnu/packages/bioinformatics.scm (freebayes): Update to 1.3.7.
[arguments]: Do not use "grep -P" in tests; drop trailing #T.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 27 |
1 files changed, 12 insertions, 15 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 113bdc5675..181e68b44b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17339,7 +17339,7 @@ manipulations on VCF files.") (define-public freebayes (package (name "freebayes") - (version "1.3.5") + (version "1.3.7") (source (origin (method git-fetch) (uri (git-reference @@ -17347,12 +17347,7 @@ manipulations on VCF files.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "1l0z88gq57kva677a6xri5g9k2d9h9lk5yk1q2xmq64wqhv7dvc3")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file-recursively "contrib/htslib") - #t)))) + (base32 "163nd1xkq547za80khlys4qkgal64f3sgl6ap3yvik68r0rgyisv")))) (build-system meson-build-system) (inputs (list fastahack htslib smithwaterman tabixpp vcflib)) @@ -17392,25 +17387,27 @@ manipulations on VCF files.") (substitute* '("src/BedReader.cpp" "src/BedReader.h") (("../intervaltree/IntervalTree.h") "IntervalTree.h")) + ;; We don't have Perl support in grep -E. + (substitute* '("test/t/01_call_variants.t" + "test/t/01b_call_variants.t") + (("grep -P") "grep -E") + (("\\\\t") " ")) (substitute* "meson.build" ;; Our pkg-config file is vcflib.pc (("libvcflib") "vcflib") - (("vcflib_inc,") "")) - #t))) + (("vcflib_inc,") ""))))) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (mkdir-p "test/test-simple-bash") (copy-recursively (assoc-ref inputs "test-simple-bash-src") - "test/test-simple-bash") - #t)) + "test/test-simple-bash"))) ;; The slow tests take longer than the specified timeout. ,@(if (any (cute string=? <> (%current-system)) '("armhf-linux" "aarch64-linux")) '((replace 'check - (lambda* (#:key tests? #:allow-other-keys) - (when tests? - (invoke "meson" "test" "--timeout-multiplier" "5")) - #t))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "meson" "test" "--timeout-multiplier" "5"))))) '())))) (home-page "https://github.com/freebayes/freebayes") (synopsis "Haplotype-based variant detector") |