Roel Janssen <r...@gnu.org> writes: > From e75aa388931c92657336c8a15f88b6a0273f5e02 Mon Sep 17 00:00:00 2001 > From: Roel Janssen <r...@gnu.org> > Date: Tue, 22 Mar 2016 15:01:37 +0100 > Subject: [PATCH 2/8] gnu: Add smithwaterman.
> * gnu/packages/bioinformatics.scm (smithwaterman): New variable. > --- > gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ > 1 file changed, 31 insertions(+) > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 6792be9..fa7ba24 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4830,3 +4830,34 @@ group or two ChIP groups run under different > conditions.") > (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 > + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) As there have been new commits since you posted this patch could you add a comment that explains why it should be this particular commit? Is it because this is the version of the submodule of vcflib? > + (package > + (name "smithwaterman") > + (version (string-append "0-1." (string-take commit 7))) > + (source (origin > + (method url-fetch) > + (uri (string-append "https://github.com/ekg/smithwaterman/archive/"; > + commit ".tar.gz")) > + (file-name (string-append name "-" version "-checkout.tar.gz")) > + (sha256 > + (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b")))) > + (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 "This package provides an implementation of the > Smith-Waterman > +algorithm.") > + ;; libdisorder is licensed GPLv2. The parent project (vcflib), of > which > + ;; this program is a submodule, is licensed MIT, which is the same as > + ;; the Expat license. > + (license (list license:gpl2 license:expat))))) As far as I can see the license is GPLv2+ as it doesn’t specifically restricts users to version 2. The license of the parent project doesn’t matter in this case, so “(license license:gpl2+)” would seem to be enough. ~~ Ricardo
