diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 32 |
1 files changed, 8 insertions, 24 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 10ecac18ae..748b1901b6 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15416,7 +15416,7 @@ output of segemehl is a SAM or BAM formatted alignment file.") (define-public kallisto (package (name "kallisto") - (version "0.48.0") + (version "0.50.1") (source (origin (method git-fetch) (uri (git-reference @@ -15425,31 +15425,15 @@ output of segemehl is a SAM or BAM formatted alignment file.") (file-name (git-file-name name version)) (sha256 (base32 - "0wx1ndmhndsd60952piaa925lk8bjr59d2yr1m2hcsqcb6cdjwpn")) - (modules '((guix build utils))) - (snippet - '(delete-file-recursively "ext/htslib/")))) + "0zfs79mv75599cf9d7d3c5a3s8idgz9qvl4qfzhvhbd87y3dv7p0")))) (build-system cmake-build-system) (arguments - `(#:tests? #f ; no "check" target - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'do-not-use-bundled-htslib - (lambda _ - (substitute* "CMakeLists.txt" - (("^ExternalProject_Add" m) - (string-append "if (NEVER)\n" m)) - (("^\\)") - (string-append ")\nendif(NEVER)")) - (("include_directories\\(\\$\\{htslib_PREFIX.*" m) - (string-append "# " m))) - (substitute* "src/CMakeLists.txt" - (("target_link_libraries\\(kallisto kallisto_core pthread \ -\\$\\{CMAKE_CURRENT_SOURCE_DIR\\}/../ext/htslib/libhts.a\\)") - "target_link_libraries(kallisto kallisto_core pthread hts)") - (("include_directories\\(\\.\\./ext/htslib\\)") ""))))))) - (inputs - (list hdf5 htslib-1.9 zlib)) + (list + #:tests? #false ;no "check" target + ;; The build system attempts to link libbifrost.a into the kallisto + ;; executable before the library has been built. + #:parallel-build? #false)) + (inputs (list hdf5 zlib)) (home-page "https://pachterlab.github.io/kallisto/") (synopsis "Near-optimal RNA-Seq quantification") (description |