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authorRicardo Wurmus <rekado@elephly.net>2022-06-01 00:14:30 +0200
committerRicardo Wurmus <rekado@elephly.net>2022-06-01 00:17:05 +0200
commitb279e778ab510e7a789205fe11107daac85147f4 (patch)
tree87d2be4856d9e150529dfe6550e62a428c24c500
parent95792a26c3a0b8f3cd54bc5f490ec28085ad01f1 (diff)
gnu: Add sylamer.
* gnu/packages/bioinformatics.scm (sylamer): New variable.
-rw-r--r--gnu/packages/bioinformatics.scm41
1 files changed, 41 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 679b5af4a2..7059be7d24 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13674,6 +13674,47 @@ some of the details of opening and jumping in tabix-indexed files.")
;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9.
(license (list license:gpl2 license:expat)))))
+(define-public sylamer
+ (package
+ (name "sylamer")
+ (version "18-131")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/micans/sylamer/")
+ (commit "aa75c3584797c0c15f860addb645f7bc1dd7627d")))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "1ddiwlrdghhb4574rvfw0brjp9gs5l6nfsy82h0m4mvz1dr3gkj5"))))
+ (build-system gnu-build-system)
+ (arguments
+ (list
+ #:tests? #f ; no test target
+ #:make-flags
+ #~(list (string-append "GSLPREFIX=" #$(this-package-input "gsl")))
+ #:phases
+ '(modify-phases %standard-phases
+ (replace 'configure
+ (lambda* (#:key outputs #:allow-other-keys)
+ (substitute* "Makefile"
+ (("cp sylamer \\$\\(HOME\\)/local/bin")
+ (string-append "install -D -t " (assoc-ref outputs "out")
+ "/bin sylamer")))
+ (install-file "Makefile" "src")
+ (chdir "src"))))))
+ (inputs (list gsl zlib))
+ (home-page "https://www.ebi.ac.uk/research/enright/software/sylamer")
+ (synopsis "Asses microRNA binding and siRNA off-target effects")
+ (description "Sylamer is a system for finding significantly over or
+under-represented words in sequences according to a sorted gene list.
+Typically it is used to find significant enrichment or depletion of microRNA
+or siRNA seed sequences from microarray expression data. Sylamer is extremely
+fast and can be applied to genome-wide datasets with ease. Results are
+plotted in terms of a significance landscape plot. These plots show
+significance profiles for each word studied across the sorted genelist.")
+ (license license:gpl3+)))
+
(define-public multichoose
(package
(name "multichoose")