[PATCH] Add MOSAIK.

[PATCH] Add MOSAIK.

[Ricardo Wurmus]

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From 2f5755ddad550cf811f97ad6889eea2a7171a1c3 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 16 Oct 2015 17:41:07 +0200
Subject: [PATCH] gnu: Add MOSAIK.

* gnu/packages/bioinformatics.scm (mosaik): 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 069e52f..e339a70 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2248,6 +2248,52 @@ viewer.")
                                    (string-append bin "/samtools")))))
            (delete 'patch-tests)))))))
 
+(define-public mosaik
+  (let ((commit "5c25216d"))
+    (package
+      (name "mosaik")
+      (version "2.2.30")
+      (source (origin
+                ;; There are no release tarballs nor tags.
+                (method git-fetch)
+                (uri (git-reference
+                      (url "https://github.com/wanpinglee/MOSAIK.git")
+                      (commit commit)))
+                (file-name (string-append name "-" version))
+                (sha256
+                 (base32
+                  "17gj3s07cm77r41z92awh0bim7w7q7fbn0sf5nkqmcm1vw052qgw"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:tests? #f ; no tests
+         #:make-flags (list "CC=gcc")
+         #:phases
+         (modify-phases %standard-phases
+           (replace 'configure
+                    (lambda _ (chdir "src") #t))
+           (replace 'install
+                    (lambda* (#:key outputs #:allow-other-keys)
+                      (let ((bin (string-append (assoc-ref outputs "out")
+                                                "/bin")))
+                        (mkdir-p bin)
+                        (copy-recursively "../bin" bin)
+                        #t))))))
+      (inputs
+       `(("perl" ,perl)
+         ("zlib" ,zlib)))
+      (home-page "https://code.google.com/p/mosaik-aligner/")
+      (synopsis "Map nucleotide sequence reads to reference genomes")
+      (description
+       "MOSAIK is a program for mapping second and third-generation sequencing
+reads to a reference genome.  MOSAIK can align reads generated by all the
+major sequencing technologies, including Illumina, Applied Biosystems SOLiD,
+Roche 454, Ion Torrent and Pacific BioSciences SMRT.")
+      ;; MOSAIK is released under the GPLv2+ with the exception of third-party
+      ;; code released into the public domain:
+      ;; 1. fastlz by Ariya Hidayat - http://www.fastlz.org/
+      ;; 2. MD5 implementation - RSA Data Security, RFC 1321
+      (license (list license:gpl2+ license:public-domain)))))
+
 (define-public ngs-sdk
   (package
     (name "ngs-sdk")
-- 
2.1.0

Re: [PATCH] Add MOSAIK.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 2f5755ddad550cf811f97ad6889eea2a7171a1c3 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 16 Oct 2015 17:41:07 +0200
> Subject: [PATCH] gnu: Add MOSAIK.
>
> * gnu/packages/bioinformatics.scm (mosaik): New variable.

LGTM, thanks!

Ludo'.

Re: [PATCH] Add MOSAIK.

[Andreas Enge]

Mosaik fails on all architectures except for x86_64. Should it be disabled
or are there configure flags to make it work elsewhere?

Andreas

Re: [PATCH] Add MOSAIK.

[Ricardo Wurmus]

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> Mosaik fails on all architectures except for x86_64. Should it be disabled
> or are there configure flags to make it work elsewhere?

I think this is caused by ‘includes/linux.inc’, which is unconditionally
included by default.

Disabling the line

    include includes/$(BLD_PLATFORM).inc

should be sufficient to fix this.

Alternatively, we could set BLD_PLATFORM (to something other than just
“linux” on non-x86_64) and patch “include” to read “-include”, so that
it doesn’t cause an error when the file does not exist.

That’s what the attached patch does.


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From 156df9fcf8a7b9a5f61b29db366f6b780082c81a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 23 Oct 2015 10:35:00 +0200
Subject: [PATCH] gnu: mosaik: Enable optimizations only on x86_64.

* gnu/packages/bioinformatics.scm (mosaik)[arguments]: Set BLD_PLATFORM
  make flag; add build phase to make include optional.
---
 gnu/packages/bioinformatics.scm | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e1ae107..6424dde 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2266,9 +2266,21 @@ viewer.")
       (build-system gnu-build-system)
       (arguments
        `(#:tests? #f ; no tests
-         #:make-flags (list "CC=gcc")
+         #:make-flags
+         (list "CC=gcc"
+               (string-append "BLD_PLATFORM="
+                              (let ((system ,(or (%current-target-system)
+                                                 (%current-system))))
+                                (if (string-prefix? "x86_64" system)
+                                    "linux"
+                                    system))))
          #:phases
          (modify-phases %standard-phases
+           (add-after 'unpack 'make-optimization-optional
+            (lambda _
+              (substitute* "src/Makefile"
+                (("^include") "-include"))
+              #t))
            (replace 'configure
                     (lambda _ (chdir "src") #t))
            (replace 'install
-- 
2.1.0

Re: [PATCH] Add MOSAIK.

[Efraim Flashner]

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On Fri, 23 Oct 2015 10:42:49 +0200
Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> wrote:

> > Mosaik fails on all architectures except for x86_64. Should it be disabled
> > or are there configure flags to make it work elsewhere?  
> 
> I think this is caused by ‘includes/linux.inc’, which is unconditionally
> included by default.
> 
> Disabling the line
> 
>     include includes/$(BLD_PLATFORM).inc
> 
> should be sufficient to fix this.
> 
> Alternatively, we could set BLD_PLATFORM (to something other than just
> “linux” on non-x86_64) and patch “include” to read “-include”, so that
> it doesn’t cause an error when the file does not exist.
> 
> That’s what the attached patch does.
> 

I ran `./pre-inst-env guix build -s i686-linux mosaik` and the build failed for me.

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Re: [PATCH] Add MOSAIK.

[Ricardo Wurmus]

Efraim Flashner <efraim@flashner.co.il> writes:

> On Fri, 23 Oct 2015 10:42:49 +0200
> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> wrote:
>
>> > Mosaik fails on all architectures except for x86_64. Should it be disabled
>> > or are there configure flags to make it work elsewhere?  
>> 
>> I think this is caused by ‘includes/linux.inc’, which is unconditionally
>> included by default.
>> 
>> Disabling the line
>> 
>>     include includes/$(BLD_PLATFORM).inc
>> 
>> should be sufficient to fix this.
>> 
>> Alternatively, we could set BLD_PLATFORM (to something other than just
>> “linux” on non-x86_64) and patch “include” to read “-include”, so that
>> it doesn’t cause an error when the file does not exist.
>> 
>> That’s what the attached patch does.
>> 
>
> I ran `./pre-inst-env guix build -s i686-linux mosaik` and the build failed for me.

I can confirm this.  Too bad.  The reason is that “ssw.c” uses macros
from emmintrin.h that are always inlined.  Inlining fails here due to
“target specific option mismatch”.

Does this only happen when cross-compiling or will this also happen if
it’s built natively on i686?

~~ Ricardo

Re: [PATCH] Add MOSAIK.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> Efraim Flashner <efraim@flashner.co.il> writes:

[...]

>> I ran `./pre-inst-env guix build -s i686-linux mosaik` and the build failed for me.
>
> I can confirm this.  Too bad.  The reason is that “ssw.c” uses macros
> from emmintrin.h that are always inlined.  Inlining fails here due to
> “target specific option mismatch”.
>
> Does this only happen when cross-compiling or will this also happen if
> it’s built natively on i686?

It happens natively: The -s above does a native build (for
cross-compilation, it’s --target, which must be passed a full GNU
triplet.)

Ludo’.