Thanks Ricardo.
On 11/12/15 01:54, Ricardo Wurmus wrote:
Ben Woodcroft <[email protected]> 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.
I hadn't before, so I thought you were right, but that seems not to make
any difference. I'm now running this daemon version, which I did using
./pre-inst-env make install, then updating the root's profile. I also
had to chown root:root /var/guix/profiles/per-user/root
root@u:~# ls -lh /root/.guix-profile/bin/guix-daemon
lrwxrwxrwx 2 root guix-builder 78 Jan 1 1970
/root/.guix-profile/bin/guix-daemon ->
/gnu/store/9da6v59j0lb9rf7fc559g5f1q1qn8qxg-guix-0.9.0.5c36edc/bin/guix-daemon
I got the same errors as before. Any ideas?
The rest looks good to me. Thanks!
Thanks for the comments, updated patch attached.
ben
>From d6ed5bb4ed94c999ba579aa015fa93d970b2f398 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <[email protected]>
Date: Thu, 10 Dec 2015 20:56:52 +1000
Subject: [PATCH] gnu: Add snap-aligner.
* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
---
gnu/packages/bioinformatics.scm | 36 ++++++++++++++++++++++++++++++++++++
1 file changed, 36 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 35cec1e..be8b65b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2792,6 +2792,42 @@ BioPython in a convenient way. Instead of having a big mess of scripts, there
is one that takes arguments.")
(license license:gpl3)))
+(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"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32
+ "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))))
+ (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)
+ (install-file "snap-aligner" bin)
+ (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)))
+
(define-public star
(package
(name "star")
--
2.5.0
