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authorRicardo Wurmus <rekado@elephly.net>2018-10-11 16:12:11 +0200
committerRicardo Wurmus <rekado@elephly.net>2018-10-11 16:12:11 +0200
commite8a7eab169b84ef66c0fb39b3f20ec8af047d5c0 (patch)
tree132892721448038e201e6a8dfb3c70662aa771dd
parenta8fa86c47781e3e5f6cb58468446ede59b3ba3f4 (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.scm34
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")