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.
This commit is contained in:
Ricardo Wurmus 2018-10-11 16:12:11 +02:00
parent a8fa86c477
commit e8a7eab169
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@ -11735,19 +11735,39 @@ (define-public paml
(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")