Unverified Commit c82b723b authored by Ricardo Wurmus's avatar Ricardo Wurmus
Browse files

gnu: Add megadepth.

* gnu/packages/bioinformatics.scm (megadepth): New variable.
parent f9e5d04f
......@@ -14999,6 +14999,71 @@ collapsing the single-cell tracks to pseudo-bulk tracks) to capture distinct
cross-cluster accessibility profiles.")
(license license:gpl3+)))
 
(define-public megadepth
(package
(name "megadepth")
(version "1.1.1")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/ChristopherWilks/megadepth")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"0hj69d2dgmk2zwgazik7xzc04fxxlk93p888kpgc52fmhd95qph7"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #false ; some tests seem to require connection to
; www.ebi.ac.uk; this may be caused by htslib.
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'prepare-CMakeLists.txt
(lambda _
(rename-file "CMakeLists.txt.ci" "CMakeLists.txt")
(substitute* "CMakeLists.txt"
(("`cat ../VERSION`") ,version)
(("target_link_libraries\\(megadepth_static") "#")
(("target_link_libraries\\(megadepth_statlib") "#")
(("add_executable\\(megadepth_static") "#")
(("add_executable\\(megadepth_statlib") "#"))
(substitute* "tests/test.sh"
;; Disable remote test
(("./megadepth http://stingray.cs.jhu.edu/data/temp/test.bam") "#")
;; Prior to installation the binary's name differs from what
;; the test script assumes.
(("./megadepth") "../build/megadepth_dynamic"))))
(replace 'check
(lambda* (#:key tests? #:allow-other-keys)
(when tests?
(with-directory-excursion "../source"
(invoke "bash" "tests/test.sh" "use-local-test-data")))))
(replace 'install
(lambda* (#:key outputs #:allow-other-keys)
(let ((bin (string-append (assoc-ref outputs "out") "/bin")))
(mkdir-p bin)
(copy-file "megadepth_dynamic"
(string-append bin "/megadepth"))))))))
(native-inputs
`(("diffutils" ,diffutils)
("perl" ,perl)
("grep" ,grep)))
(inputs
`(("curl" ,curl)
("htslib" ,htslib)
("libdeflate" ,libdeflate)
("libbigwig" ,libbigwig)
("zlib" ,zlib)))
(home-page "https://github.com/ChristopherWilks/megadepth")
(synopsis "BigWig and BAM/CRAM related utilities")
(description "Megadepth is an efficient tool for extracting coverage
related information from RNA and DNA-seq BAM and BigWig files. It supports
reading whole-genome coverage from BAM files and writing either indexed TSV or
BigWig files, as well as efficient region coverage summary over intervals from
both types of files.")
(license license:expat)))
(define-public r-ascat
(package
(name "r-ascat")
......
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