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-rw-r--r--gnu/packages/bioinformatics.scm50
1 files changed, 32 insertions, 18 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f801639472..6dc313199b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -13384,6 +13384,36 @@ reference transcripts provided in a annotation file (also in GTF/GFF3 format).
license:expat ;license for gffcompare
license:artistic2.0))))) ;license for gclib
+(define-public intervaltree
+ (let ((commit "b90527f9e6d51cd36ecbb50429e4524d3a418ea5"))
+ (package
+ (name "intervaltree")
+ (version (git-version "0.0.0" "1" commit))
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/ekg/intervaltree/")
+ (commit commit)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "0rgv6q5fl4x5d74n6p5wvdna6zmbdbqpb4jqqh6vq3670gn08xad"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:tests? #f ; No tests.
+ #:make-flags (list (string-append "PREFIX=" (assoc-ref %outputs "out"))
+ "DESTDIR=\"\"")
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure)))) ; There is no configure phase.
+ (home-page "https://github.com/ekg/intervaltree")
+ (synopsis "Minimal C++ interval tree implementation")
+ (description "An interval tree can be used to efficiently find a set of
+numeric intervals overlapping or containing another interval. This library
+provides a basic implementation of an interval tree using C++ templates,
+allowing the insertion of arbitrary types into the tree.")
+ (license license:expat))))
+
(define-public python-intervaltree
(package
(name "python-intervaltree")
@@ -15086,15 +15116,7 @@ library automatically handles index file generation and use.")
("fsom-src" ,(package-source fsom))
("filevercmp-src" ,(package-source filevercmp))
("fastahack-src" ,(package-source fastahack))
- ("intervaltree-src"
- ,(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/ekg/intervaltree/")
- (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
- (file-name "intervaltree-src-checkout")
- (sha256
- (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))))
+ ("intervaltree-src" ,(package-source intervaltree))))
(arguments
`(#:tests? #f ; no tests
#:phases
@@ -15181,15 +15203,7 @@ manipulations on VCF files.")
("fsom-src" ,(package-source fsom))
("filevercmp-src" ,(package-source filevercmp))
("fastahack-src" ,(package-source fastahack))
- ("intervaltree-src"
- ,(origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/ekg/intervaltree/")
- (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838")))
- (file-name "intervaltree-src-checkout")
- (sha256
- (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj"))))
+ ("intervaltree-src" ,(package-source intervaltree))
;; These submodules are needed to run the tests.
("bash-tap-src" ,(package-source bash-tap))
("test-simple-bash-src"