diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 79 |
1 files changed, 79 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 674bbb107d..58cee5cbbe 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14118,6 +14118,85 @@ enrichment analysis (GSEA) calculation with or without the absolute filtering. absolute GSEA.") (license license:gpl2))) +(define-public jamm + (package + (name "jamm") + (version "1.0.7.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mahmoudibrahim/JAMM.git") + (commit (string-append "JAMMv" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0ls889jcma1ch9h21jjhnkadgszgqj41842hhcjh6cg88f85qf3i")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "JAMM.sh" + (("^sPath=.*") + (string-append ""))) + #t)) + (replace 'install + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (libexec (string-append out "/libexec/jamm")) + (bin (string-append out "/bin"))) + (substitute* '("JAMM.sh" + "SignalGenerator.sh") + (("^sPath=.*") + (string-append "sPath=\"" libexec "\"\n"))) + (for-each (lambda (file) + (install-file file libexec)) + (list "bincalculator.r" + "peakfinder.r" + "peakhelper.r" + "signalmaker.r" + "xcorr.r" + "xcorrhelper.r" + ;; Perl scripts + "peakfilter.pl" + "readshifter.pl")) + + (for-each + (lambda (script) + (chmod script #o555) + (install-file script bin) + (wrap-program (string-append bin "/" script) + `("PATH" ":" prefix + (,(string-append (assoc-ref inputs "coreutils") "/bin") + ,(string-append (assoc-ref inputs "gawk") "/bin") + ,(string-append (assoc-ref inputs "perl") "/bin") + ,(string-append (assoc-ref inputs "r-minimal") "/bin"))) + `("PERL5LIB" ":" prefix (,(getenv "PERL5LIB"))) + `("R_LIBS_SITE" ":" prefix (,(getenv "R_LIBS_SITE"))))) + (list "JAMM.sh" "SignalGenerator.sh"))) + #t))))) + (inputs + `(("bash" ,bash) + ("coreutils" ,coreutils) + ("gawk" ,gawk) + ("perl" ,perl) + ("r-minimal" ,r-minimal) + ;;("r-parallel" ,r-parallel) + ("r-signal" ,r-signal) + ("r-mclust" ,r-mclust))) + (home-page "https://github.com/mahmoudibrahim/JAMM") + (synopsis "Peak finder for NGS datasets") + (description + "JAMM is a peak finder for next generation sequencing datasets (ChIP-Seq, +ATAC-Seq, DNase-Seq, etc.) that can integrate replicates and assign peak +boundaries accurately. JAMM is applicable to both broad and narrow +datasets.") + (license license:gpl3+))) + (define-public ngless (package (name "ngless") |