| Message ID | 20190518172640.7165-2-mail@ambrevar.xyz |
|---|---|
| State | Accepted |
| Headers | show |
| Series | Package freebayes | expand |
| Context | Check | Description |
|---|---|---|
| cbaines/applying patch | success | Successfully applied |
Pierre Neidhardt <mail@ambrevar.xyz> writes: > * gnu/packages/bioinformatics.scm (smithwaterman): New variable. […] > + ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. > + (license (list license:gpl2 license:expat))))) If the licensing terms are unclear we should not include this package. -- Ricardo
https://github.com/ekg/smithwaterman/issues/9#issuecomment-493694384 Between the two licenses it's GPL2. The expat license text just hasn't been removed. On August 8, 2019 2:30:24 PM UTC, Ricardo Wurmus <rekado@elephly.net> wrote: > >Pierre Neidhardt <mail@ambrevar.xyz> writes: > >> * gnu/packages/bioinformatics.scm (smithwaterman): New variable. >[…] >> + ;; The licensing terms are unclear: >https://github.com/ekg/smithwaterman/issues/9. >> + (license (list license:gpl2 license:expat))))) > >If the licensing terms are unclear we should not include this package. > >-- >Ricardo
Efraim Flashner <efraim@flashner.co.il> writes: > https://github.com/ekg/smithwaterman/issues/9#issuecomment-493694384 > > Between the two licenses it's GPL2. The expat license text just hasn't been removed. Okay, that makes sense.
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 244741854d..1bf33853b0 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14869,3 +14869,33 @@ might be caused by ATAC-seq library prep or sequencing. The main program, (description "This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) + +(define-public smithwaterman + ;; TODO: Upgrading smithwaterman breaks FreeBayes. + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) + (package + (name "smithwaterman") + (version (string-append "0-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/smithwaterman/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "smithwaterman" bin))))))) + (home-page "https://github.com/ekg/smithwaterman") + (synopsis "Implementation of the Smith-Waterman algorithm") + (description "Implementation of the Smith-Waterman algorithm.") + ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. + (license (list license:gpl2 license:expat)))))