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10/10: gnu: Add jamm.
From: |
Ricardo Wurmus |
Subject: |
10/10: gnu: Add jamm. |
Date: |
Wed, 14 Nov 2018 09:19:07 -0500 (EST) |
rekado pushed a commit to branch master
in repository guix.
commit ee66a13563dc0ca03865ec3d3d36f8c55e885ac0
Author: Ricardo Wurmus <address@hidden>
Date: Wed Nov 14 13:56:54 2018 +0100
gnu: Add jamm.
* gnu/packages/bioinformatics.scm (jamm): New variable.
---
gnu/packages/bioinformatics.scm | 79 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 79 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 674bbb1..58cee5c 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")
- branch master updated (51b262f -> ee66a13), Ricardo Wurmus, 2018/11/14
- 02/10: gnu: Add r-rjags., Ricardo Wurmus, 2018/11/14
- 05/10: gnu: Add r-acdm., Ricardo Wurmus, 2018/11/14
- 01/10: gnu: Add jags., Ricardo Wurmus, 2018/11/14
- 04/10: gnu: Add r-acd., Ricardo Wurmus, 2018/11/14
- 07/10: gnu: Add r-circular., Ricardo Wurmus, 2018/11/14
- 09/10: gnu: Add r-ouch., Ricardo Wurmus, 2018/11/14
- 06/10: gnu: Add r-overlap., Ricardo Wurmus, 2018/11/14
- 08/10: gnu: Add r-activity., Ricardo Wurmus, 2018/11/14
- 10/10: gnu: Add jamm.,
Ricardo Wurmus <=
- 03/10: gnu: Add r-abn., Ricardo Wurmus, 2018/11/14