bug? also [PATCH] Add snap-aligner.

bug? also [PATCH] Add snap-aligner.

[Ben Woodcroft]

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Hey,

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?

Thanks,
ben

[-- Attachment #2: 0001-gnu-Add-snap-aligner.patch --]
[-- Type: text/x-patch, Size: 2345 bytes --]

From 6dd854282c75c30b8ae8eb922a2bc65a5be599c0 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
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 | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 35cec1e..836b4fa 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2792,6 +2792,44 @@ 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"))
+              (sha256
+               (base32
+                "1vnsjwv007k1fl1q7d681kbwn6bc66cgw6h16hym6gvyy71qv2ly"))
+              (file-name (string-append name "-" version ".tar.gz"))))
+    (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"))))))))
+    (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

Re: bug? also [PATCH] Add snap-aligner.

[Ricardo Wurmus]

Ben Woodcroft <b.woodcroft@uq.edu.au> 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

Re: bug? also [PATCH] Add snap-aligner.

[Ben Woodcroft]

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Thanks Ricardo.

On 11/12/15 01:54, Ricardo Wurmus wrote:
> Ben Woodcroft <b.woodcroft@uq.edu.au> 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

[-- Attachment #2: 0001-gnu-Add-snap-aligner.patch --]
[-- Type: text/x-patch, Size: 2232 bytes --]

From d6ed5bb4ed94c999ba579aa015fa93d970b2f398 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <donttrustben@gmail.com>
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

Re: bug? also [PATCH] Add snap-aligner.

[Ludovic Courtès]

Ben Woodcroft <b.woodcroft@uq.edu.au> skribis:

> $ ./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

This error indicates that the daemon ‘guix build’ is talking to is too
“old” (that is, more than a week old ;-)) and doesn’t support this build
mode.

It comes from:

  http://git.savannah.gnu.org/cgit/guix.git/tree/guix/store.scm#n667

The solution is to build, install, and run the daemon from current
‘master’.

HTH!

Ludo’.

Re: bug? also [PATCH] Add snap-aligner.

[Ricardo Wurmus]

Ben Woodcroft <b.woodcroft@uq.edu.au> writes:

> Thanks for the comments, updated patch attached.

I made a tiny modification (ended the install phase with #t) and
pushed.  Thanks!

~~ Ricardo