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03/06: gnu: Add intervaltree.
From: |
guix-commits |
Subject: |
03/06: gnu: Add intervaltree. |
Date: |
Thu, 9 Jan 2020 07:52:29 -0500 (EST) |
efraim pushed a commit to branch master
in repository guix.
commit de933b71ee0a15ca4b70c8a51920f1216dbf81f5
Author: Efraim Flashner <address@hidden>
AuthorDate: Wed Jan 8 11:55:17 2020 +0200
gnu: Add intervaltree.
* gnu/packages/bioinformatics.scm (intervaltree): New variable.
(vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
---
gnu/packages/bioinformatics.scm | 50 ++++++++++++++++++++++++++---------------
1 file changed, 32 insertions(+), 18 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f801639..6dc3131 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"
- branch master updated (1e3bbd9 -> 2604ecb), guix-commits, 2020/01/09
- 01/06: gnu: bwa: Install static library., guix-commits, 2020/01/09
- 04/06: gnu: fastahack: Update to 1.0.0., guix-commits, 2020/01/09
- 02/06: gnu: tabixpp: Update to 1.1.0., guix-commits, 2020/01/09
- 03/06: gnu: Add intervaltree.,
guix-commits <=
- 06/06: gnu: smithwaterman: Update to 0.0.0-2.2610e25., guix-commits, 2020/01/09
- 05/06: gnu: vcflib: Update to 1.0.1., guix-commits, 2020/01/09