futurile/guix-play
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

gnu: Add intervaltree.

Browse Source 
* gnu/packages/bioinformatics.scm (intervaltree): New variable.
(vcflib, freebayes)[native-inputs]: Use packaged intervaltree's source.
This commit is contained in:
Efraim Flashner 2020-01-08 11:55:17 +02:00
parent 612d6a8e5b
commit de933b71ee
No known key found for this signature in database
GPG Key ID: 41AAE7DCCA3D8351
1 changed files with 32 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

50
gnu/packages/bioinformatics.scm
View File

@ -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"