[PATCH] gnu: Add kaiju.

[PATCH] gnu: Add kaiju.

[Roel Janssen]

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Dear Guix,

Here's a patch for kaiju.  A C++ program without any dependencies, plus
some additional scripts that need perl.

Kind regards,
Roel Janssen


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From ed45f47f7514faf10710b41a7d5e9cdaa8217c70 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 1 Jun 2017 15:01:51 +0200
Subject: [PATCH] gnu: Add kaiju.

* gnu/packages/bioinformatics (kaiju): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ec69f50..a8ad424 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3214,6 +3214,43 @@ data.")
     (supported-systems '("x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public kaiju
+  (package
+    (name "kaiju")
+    (version "1.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/bioinformatics-centre/kaiju/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; There are no tests.
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'build 'move-to-src-dir
+           (lambda _ (chdir "src") #t))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               (mkdir-p bin)
+               (chdir "..")
+               (copy-recursively "bin" bin)
+               (copy-recursively "util" bin)))))))
+    (inputs
+     `(("perl" ,perl)))
+    (home-page "http://kaiju.binf.ku.dk/")
+    (synopsis "Fast and sensitive taxonomic classification for metagenomics")
+    (description "Kaiju is a program for sensitive taxonomic classification
+of high-throughput sequencing reads from metagenomic whole genome sequencing
+experiments.")
+    (license license:gpl3+)))
+
 (define-public macs
   (package
     (name "macs")
-- 
2.7.4

bug#27181: [PATCH] gnu: Add kaiju.

[Roel Janssen]

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Dear Guix,

Here's a patch for kaiju.  A C++ program without any dependencies, plus
some additional scripts that need perl.

Kind regards,
Roel Janssen


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From ed45f47f7514faf10710b41a7d5e9cdaa8217c70 Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Thu, 1 Jun 2017 15:01:51 +0200
Subject: [PATCH] gnu: Add kaiju.

* gnu/packages/bioinformatics (kaiju): New variable.
---
 gnu/packages/bioinformatics.scm | 37 +++++++++++++++++++++++++++++++++++++
 1 file changed, 37 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index ec69f50..a8ad424 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -3214,6 +3214,43 @@ data.")
     (supported-systems '("x86_64-linux"))
     (license license:bsd-3)))
 
+(define-public kaiju
+  (package
+    (name "kaiju")
+    (version "1.5.0")
+    (source (origin
+              (method url-fetch)
+              (uri (string-append
+                    "https://github.com/bioinformatics-centre/kaiju/archive/v"
+                    version ".tar.gz"))
+              (file-name (string-append name "-" version ".tar.gz"))
+              (sha256
+               (base32
+                "0afbfalfw9y39bkwnqjrh9bghs118ws1pzj5h8l0nblgn3mbjdks"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; There are no tests.
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (add-before 'build 'move-to-src-dir
+           (lambda _ (chdir "src") #t))
+         (replace 'install
+           (lambda* (#:key inputs outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               (mkdir-p bin)
+               (chdir "..")
+               (copy-recursively "bin" bin)
+               (copy-recursively "util" bin)))))))
+    (inputs
+     `(("perl" ,perl)))
+    (home-page "http://kaiju.binf.ku.dk/")
+    (synopsis "Fast and sensitive taxonomic classification for metagenomics")
+    (description "Kaiju is a program for sensitive taxonomic classification
+of high-throughput sequencing reads from metagenomic whole genome sequencing
+experiments.")
+    (license license:gpl3+)))
+
 (define-public macs
   (package
     (name "macs")
-- 
2.7.4

bug#27181: [PATCH] gnu: Add kaiju.

[Ludovic Courtès]

Hi Roel!

Roel Janssen <roel@gnu.org> skribis:

> From ed45f47f7514faf10710b41a7d5e9cdaa8217c70 Mon Sep 17 00:00:00 2001
> From: Roel Janssen <roel@gnu.org>
> Date: Thu, 1 Jun 2017 15:01:51 +0200
> Subject: [PATCH] gnu: Add kaiju.
>
> * gnu/packages/bioinformatics (kaiju): New variable.

[...]

> +       (modify-phases %standard-phases
> +         (delete 'configure)
> +         (add-before 'build 'move-to-src-dir
> +           (lambda _ (chdir "src") #t))
> +         (replace 'install
> +           (lambda* (#:key inputs outputs #:allow-other-keys)
> +             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
> +               (mkdir-p bin)
> +               (chdir "..")
> +               (copy-recursively "bin" bin)
> +               (copy-recursively "util" bin)))))))

Make sure to return #t at the end of the phase.  Otherwise LGTM!

Thanks,
Ludo’.

bug#27181: [PATCH] gnu: Add kaiju.

[Roel Janssen]

Ludovic Courtès writes:

> Hi Roel!
>
> Roel Janssen <roel@gnu.org> skribis:
>
>> From ed45f47f7514faf10710b41a7d5e9cdaa8217c70 Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <roel@gnu.org>
>> Date: Thu, 1 Jun 2017 15:01:51 +0200
>> Subject: [PATCH] gnu: Add kaiju.
>>
>> * gnu/packages/bioinformatics (kaiju): New variable.
>
> [...]
>
>> +       (modify-phases %standard-phases
>> +         (delete 'configure)
>> +         (add-before 'build 'move-to-src-dir
>> +           (lambda _ (chdir "src") #t))
>> +         (replace 'install
>> +           (lambda* (#:key inputs outputs #:allow-other-keys)
>> +             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
>> +               (mkdir-p bin)
>> +               (chdir "..")
>> +               (copy-recursively "bin" bin)
>> +               (copy-recursively "util" bin)))))))
>
> Make sure to return #t at the end of the phase.  Otherwise LGTM!

I added the #t to the end of the phase.

Thanks Ludo’! Pushed in b9a601d9db3aa1bdb877c0ac5e7f53077ee56185.

Kind regards,
Roel Janssen

Re: [PATCH] gnu: Add kaiju.

[Roel Janssen]

Roel Janssen writes:

> Dear Guix,
>
> Here's a patch for kaiju.  A C++ program without any dependencies, plus
> some additional scripts that need perl.
>
> Kind regards,
> Roel Janssen

This was supposed to go to guix-patches instead.  Sorry for the noise.