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| author | Ricardo Wurmus <rekado@elephly.net> | 2018-10-11 16:12:11 +0200 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2018-10-11 16:12:11 +0200 |
| commit | e8a7eab169b84ef66c0fb39b3f20ec8af047d5c0 (patch) | |
| tree | 132892721448038e201e6a8dfb3c70662aa771dd | |
| parent | a8fa86c47781e3e5f6cb58468446ede59b3ba3f4 (diff) | |
gnu: kallisto: Update to 0.44.0.
* gnu/packages/bioinformatics.scm (kallisto): Update to 0.44.0.
[source]: Fetch from git.
[arguments]: Add build phase to use htslib from Guix.
[inputs]: Add htslib.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 34 |
1 files changed, 27 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index ed713cd144..91bb94c549 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -11735,19 +11735,39 @@ using nucleotide or amino-acid sequence data.") (define-public kallisto (package (name "kallisto") - (version "0.43.1") + (version "0.44.0") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/pachterlab/" - "kallisto/archive/v" version ".tar.gz")) - (file-name (string-append name "-" version ".tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/pachterlab/kallisto.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 (base32 - "03j3iqhvq7ya3c91gidly3k3jvgm97vjq4scihrlxh315j696r11")))) + "0nj382jiywqnpgvyhichajpkkh5r0bapn43f4dx40zdaq5v4m40m")))) (build-system cmake-build-system) - (arguments `(#:tests? #f)) ; no "check" target + (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\\)") "")) + #t))))) (inputs `(("hdf5" ,hdf5) + ("htslib" ,htslib) ("zlib" ,zlib))) (home-page "http://pachterlab.github.io/kallisto/") (synopsis "Near-optimal RNA-Seq quantification") |