Roel Janssen <r...@gnu.org> writes: > From c934cee6c84a39de36ecb4c3a85340ff025b1343 Mon Sep 17 00:00:00 2001 > From: Roel Janssen <r...@gnu.org> > Date: Tue, 22 Mar 2016 15:50:12 +0100 > Subject: [PATCH 6/8] gnu: Add fastahack.
> * gnu/packages/bioinformatics.scm (fastahack): New variable. > --- > gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ > 1 file changed, 34 insertions(+) > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 261660f..9cbde46 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4951,3 +4951,37 @@ combinatorial configurations.\" G Ehrlich - Journal of > the ACM (JACM), > (description "A program to compare version strings. It intends to be a > replacement for strverscmp.") > (license license:gpl3+)))) > + > +(define-public fastahack > + (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) > + (package > + (name "fastahack") > + (version (string-append "0-1." (string-take commit 7))) > + (source (origin > + (method url-fetch) > + (uri (string-append "https://github.com/ekg/fastahack/archive/"; > + commit ".tar.gz")) > + (file-name (string-append name "-" version > "-checkout.tar.gz")) I don’t think we should add “checkout” here. > + (sha256 > + (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2")))) > + (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 "fastahack" bin))))))) > + (home-page "https://github.com/ekg/fastahack";) > + (synopsis "Program for indexing and sequence extraction from > FASTA files") This sounds a bit off. It’s “indexing of ... FASTA files” (not “from”) but “sequence extraction from FASTA files”. Maybe dropping “Program for” would help here: “Index and extract sequences from FASTA files” What do you think? > + (description "Fastahack is a small application for indexing and > extracting > +sequences and subsequences from FASTA files. The included Fasta.cpp library > +provides a FASTA reader and indexer that can be embeddedinto applications > which > +would benefit from directly reading subsequences from FASTA files. The > library > +automatically handles index file generation and use.") “embeddedinto” should be split. I would drop mention of “Fasta.cpp” – or is this really the name of the library? > + ;; 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 before we use the license of this code and ignore the parent project’s license. Here’s a license problem, though. The files “Fasta.h” and “Fasta.cpp” contain notices like this: > // *************************************************************************** > // FastaIndex.h (c) 2010 Erik Garrison <erik.garri...@bc.edu> > // Marth Lab, Department of Biology, Boston College > // All rights reserved. > // --------------------------------------------------------------------------- > // Last modified: 5 February 2010 (EG) > // --------------------------------------------------------------------------- “disorder.c” has license GPLv2+. There’s a bug report mentioning this problem here: https://github.com/ekg/fastahack/issues/8 As it is now we cannot include this in Guix upstream unless the non-free files are removed in a snippet. ~~ Ricardo
