Ben Woodcroft <b.woodcr...@uq.edu.au> writes: > From e24f4de21ee3c367c38e431626f4796795eb9e18 Mon Sep 17 00:00:00 2001 > From: Ben Woodcroft <donttrust...@gmail.com> > Date: Wed, 17 Jun 2015 11:49:27 +1000 > Subject: [PATCH] gnu: Add diamond. > > * gnu/packages/bioinformatics.scm (diamond): New variable. > --- > gnu/packages/bioinformatics.scm | 46 > +++++++++++++++++++++++++++++++++++++++++ > 1 file changed, 46 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 0d8a6d5..94db812 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm
Please add a copyright line for yourself to the top of the file. > @@ -28,6 +28,7 @@ > #:use-module (guix build-system python) > #:use-module (guix build-system trivial) > #:use-module (gnu packages) > + #:use-module (gnu packages algebra) > #:use-module (gnu packages base) > #:use-module (gnu packages boost) > #:use-module (gnu packages compression) > @@ -615,6 +616,51 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, > GFF/GTF, VCF.") > other types of unwanted sequence from high-throughput sequencing reads.") > (license license:expat))) > > +(define-public diamond > + (package > + (name "diamond") > + (version "0.7.9") > + (source (origin > + (method url-fetch) > + (uri > + (string-append > + "https://github.com/bbuchfink/diamond/archive/v"; version > ".tar.gz")) Please add: (file-name (string-append name "-" version ".tar.gz")) to this 'origin' form, because otherwise the filename of the source tarball in the store will be /gnu/store/…-v0.7.9.tar.gz without the name of the package. By default it is named based on the last path component of the source URI. > + (sha256 > + (base32 > + "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15")))) It would be good to remove the pre-compiled binary by adding the following snippet to the 'origin' form: --8<---------------cut here---------------start------------->8--- (snippet '(begin (delete-file "bin/diamond") #t)) --8<---------------cut here---------------end--------------->8--- > + (build-system gnu-build-system) > + (arguments > + '(#:tests? #f ;no "check" target > + #:phases Please use spaces instead of tabs, and align "#:phases" directly under "#:tests?". > + (alist-cons-after > + 'unpack 'enter-source-dir > + (lambda _ (chdir "src")) Phase procedures should return a boolean indicating whether the phase succeeded, but the return value of 'chdir' is unspecified. So you should add #t after (chdir "src"). > + (alist-replace > + 'install > + (lambda* (#:key outputs #:allow-other-keys) > + (let ((bin (string-append > + (assoc-ref outputs "out") "/bin"))) > + (mkdir-p bin) > + (copy-file "../bin/diamond" (string-append bin > "/diamond")))) Our convention is to have the body of a lambda indented two columns more than the lambda itself, so the open paren of the 'let' should be under the 'a' in 'lambda'. Add #t to the end. Please try to keep lines <= 80 columns. > + (alist-delete 'configure %standard-phases))))) It would also be good to use our new and improved 'modify-phases' syntax. Search for it in gnu/packages/*.scm for examples. > + (native-inputs > + `(("bc" ,bc))) > + (inputs > + `(("boost" ,boost) > + ("zlib" ,zlib))) > + (home-page "https://github.com/bbuchfink/diamond";) > + (synopsis "Accelerated BLAST compatible local sequence aligner") > + (description > + "DIAMOND is a BLAST-compatible local aligner for mapping protein and > +translated DNA query sequences against a protein reference database (BLASTP > +and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short Please put two spaces between sentences. > +reads at a typical sensitivity of 90-99% relative to BLAST depending on the > +data and settings.") > + (license (license:non-copyleft (string-append > "https://github.com/bbuchfink"; > + "/diamond/blob/v" > + version > + "/src/COPYING"))))) (license (license:non-copyleft "file://src/COPYING" "See src/COPYING in the distribution.")))) I wouldn't normally do this, but I went ahead and tested it with these changes and here's what it comes out to: --8<---------------cut here---------------start------------->8--- (define-public diamond (package (name "diamond") (version "0.7.9") (source (origin (method url-fetch) (uri (string-append "https://github.com/bbuchfink/diamond/archive/v"; version ".tar.gz")) (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 "0hfkcfv9f76h5brbyw9fyvmc0l9cmbsxrcdqk0fa9xv82zj47p15")) (snippet '(begin (delete-file "bin/diamond") #t)))) (build-system gnu-build-system) (arguments '(#:tests? #f ;no "check" target #:phases (modify-phases %standard-phases (add-after 'unpack 'enter-source-dir (lambda _ (chdir "src") #t)) (delete 'configure) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (mkdir-p bin) (copy-file "../bin/diamond" (string-append bin "/diamond")) #t)))))) (native-inputs `(("bc" ,bc))) (inputs `(("boost" ,boost) ("zlib" ,zlib))) (home-page "https://github.com/bbuchfink/diamond";) (synopsis "Accelerated BLAST compatible local sequence aligner") (description "DIAMOND is a BLAST-compatible local aligner for mapping protein and translated DNA query sequences against a protein reference database (BLASTP and BLASTX alignment mode). The speedup over BLAST is up to 20,000 on short reads at a typical sensitivity of 90-99% relative to BLAST depending on the data and settings.") (license (license:non-copyleft "file://src/COPYING" "See src/COPYING in the distribution.")))) --8<---------------cut here---------------end--------------->8--- but feel free to do it a bit differently :) Anyway, can you send an updated patch? Don't forget your copyright notice. Thanks! Mark
