diff options
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 50 |
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" |