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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 65 |
1 files changed, 65 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b74d8925db..c3ab0ce354 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -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") |