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Re: bug? also [PATCH] Add snap-aligner.
From: |
Ricardo Wurmus |
Subject: |
Re: bug? also [PATCH] Add snap-aligner. |
Date: |
Thu, 10 Dec 2015 16:54:57 +0100 |
Ben Woodcroft <address@hidden> writes:
> I tried doing the check for reproducibility
> $ ./pre-inst-env guix build --rounds=3 snap-aligner
> but it only built once.
>
> $ ./pre-inst-env guix build --check snap-aligner
> ;;; note: source file /home/ben/git/guix/gnu/packages/bioinformatics.scm
> ;;; newer than compiled
> /home/ben/git/guix/gnu/packages/bioinformatics.go
> guix build: error: build failed: unsupported build mode
>
> Did I mess that up?
Have you restarted the daemon? Is it the latest version of the daemon?
It works for me after restarting the daemon.
> +(define-public snap-aligner
> + (package
> + (name "snap-aligner")
> + (version "1.0beta.18")
> + (source (origin
> + (method url-fetch)
> + (uri (string-append
> + "https://github.com/amplab/snap/archive/v"
> + version ".tar.gz"))
> + (sha256
> + (base32
> + "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))
> + (file-name (string-append name "-" version ".tar.gz"))))
Nit pick: I think it’s nicer to have “file-name” right after the
offending “uri” expression.
> + (build-system gnu-build-system)
> + (arguments
> + '(#:phases
> + (modify-phases %standard-phases
> + (delete 'configure)
> + (replace 'check (lambda _ (zero? (system* "./unit_tests"))))
> + (replace 'install
> + (lambda* (#:key outputs #:allow-other-keys)
> + (let* ((out (assoc-ref outputs "out"))
> + (bin (string-append out "/bin")))
> + (mkdir-p bin)
> + (copy-file "snap-aligner"
> + (string-append bin "/snap-aligner"))
> + (copy-file "SNAPCommand"
> + (string-append bin "/SNAPCommand"))))))))
Instead of “copy-file” (which requires repeating the target file name)
you can use this:
(install-file "SNAPCommand" bin)
> + (native-inputs
> + `(("zlib" ,zlib)))
> + (home-page "http://snap.cs.berkeley.edu/")
> + (synopsis "Short read DNA sequence aligner")
> + (description
> + "SNAP is a fast and accurate aligner for short DNA reads. It is
> +optimized for modern read lengths of 100 bases or higher, and takes advantage
> +of these reads to align data quickly through a hash-based indexing scheme.")
> + (license license:asl2.0)))
> +
The rest looks good to me. Thanks!
~~ Ricardo