[PATCH] gnu: Add samtools

[PATCH] gnu: Add samtools

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it
---
 gnu-system.am                   |  1 +
 gnu/packages/bioinformatics.scm | 83 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 84 insertions(+)
 create mode 100644 gnu/packages/bioinformatics.scm

diff --git a/gnu-system.am b/gnu-system.am
index e923340..d4d0b51 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -45,6 +45,7 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/base.scm				\
   gnu/packages/bash.scm				\
   gnu/packages/bdw-gc.scm			\
+  gnu/packages/bioinformatics.scm		\
   gnu/packages/bittorrent.scm			\
   gnu/packages/bison.scm			\
   gnu/packages/boost.scm			\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
new file mode 100644
index 0000000..4d27b12
--- /dev/null
+++ b/gnu/packages/bioinformatics.scm
@@ -0,0 +1,83 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages bioinformatics)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python))
+
+(define-public samtools
+  (package
+    (name "samtools")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "mirror://sourceforge/samtools/"
+                       version "/samtools-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
+       #:phases
+       (alist-cons-after
+        'unpack
+        'patch-makefile-curses
+        (lambda _
+          (substitute* "Makefile"
+            (("-lcurses") "-lncurses")))
+        (alist-cons-after
+         'unpack
+         'patch-tests
+         (lambda* (#:key inputs #:allow-other-keys)
+           (let ((bash (assoc-ref inputs "bash")))
+             (substitute* "test/test.pl"
+               ;; The test script calls out to /bin/bash
+               (("/bin/bash")
+                (string-append bash "/bin/bash"))
+               ;; There are two failing tests upstream relating to the "stats"
+               ;; subcommand in test_usage_subcommand ("did not have Usage"
+               ;; and "usage did not mention samtools stats"), so we disable
+               ;; them.
+               (("(test_usage_subcommand\\(.*\\);)" cmd)
+                (string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
+         (alist-delete
+          'configure
+          %standard-phases)))))
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (inputs `(("ncurses" ,ncurses)
+              ("perl" ,perl)
+              ("python" ,python)
+              ("zlib" ,zlib)))
+    (home-page "http://samtools.sourceforge.net")
+    (synopsis "Efficient utilities on manipulating alignments in the SAM format")
+    (description
+     "Samtools implements various utilities for post-processing alignments in
+the SAM, BAM, and CRAM formats, including indexing, variant calling (in
+conjunction with bcftools), and a simple alignment viewer.")
+    (license license:expat)))
-- 
1.9.3

Re: [PATCH] gnu: Add samtools

[Ludovic Courtès]

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

> * gnu/packages/bioinformatics.scm: New file
> * gnu-system.am (GNU_SYSTEM_MODULES): Add it

Perfect!

[...]

> +    (synopsis "Efficient utilities on manipulating alignments in the SAM format")

What about “Utilities to manipulate nucleotide sequence alignments”, to
make it clearer that it’s bioinfo-related?

> +    (description
> +     "Samtools implements various utilities for post-processing alignments in
> +the SAM, BAM, and CRAM formats, including indexing, variant calling (in
> +conjunction with bcftools), and a simple alignment viewer.")

Likewise, maybe replace “alignments” with “nucleotide sequence
alignments” or something to that effect?

Thank you!

Ludo’.

Re: [PATCH] gnu: Add samtools

[Ricardo Wurmus]

[-- Attachment #1: Type: text/plain, Size: 768 bytes --]

Attached is an updated patch.

>> +    (synopsis "Efficient utilities on manipulating alignments in the SAM format")
>
> What about “Utilities to manipulate nucleotide sequence alignments”, to
> make it clearer that it’s bioinfo-related?

I chose to reword it as "Utilities to efficiently manipulate nucleotide
sequence alignments"; is this okay?

>> +    (description
>> +     "Samtools implements various utilities for post-processing alignments in
>> +the SAM, BAM, and CRAM formats, including indexing, variant calling (in
>> +conjunction with bcftools), and a simple alignment viewer.")
>
> Likewise, maybe replace “alignments” with “nucleotide sequence
> alignments” or something to that effect?

I agree.  See attached patch.


[-- Attachment #2: 0001-gnu-Add-samtools.patch --]
[-- Type: text/x-patch, Size: 4587 bytes --]

From c4cae6d77e00491cfd78fe03da8ab617bc1732f2 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Thu, 11 Dec 2014 15:48:22 +0100
Subject: [PATCH] gnu: Add samtools

* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it
---
 gnu-system.am                   |  1 +
 gnu/packages/bioinformatics.scm | 84 +++++++++++++++++++++++++++++++++++++++++
 2 files changed, 85 insertions(+)
 create mode 100644 gnu/packages/bioinformatics.scm

diff --git a/gnu-system.am b/gnu-system.am
index e923340..d4d0b51 100644
--- a/gnu-system.am
+++ b/gnu-system.am
@@ -45,6 +45,7 @@ GNU_SYSTEM_MODULES =				\
   gnu/packages/base.scm				\
   gnu/packages/bash.scm				\
   gnu/packages/bdw-gc.scm			\
+  gnu/packages/bioinformatics.scm		\
   gnu/packages/bittorrent.scm			\
   gnu/packages/bison.scm			\
   gnu/packages/boost.scm			\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
new file mode 100644
index 0000000..6f6178a
--- /dev/null
+++ b/gnu/packages/bioinformatics.scm
@@ -0,0 +1,84 @@
+;;; GNU Guix --- Functional package management for GNU
+;;; Copyright © 2014 Ricardo Wurmus <rekado@elephly.net>
+;;;
+;;; This file is part of GNU Guix.
+;;;
+;;; GNU Guix is free software; you can redistribute it and/or modify it
+;;; under the terms of the GNU General Public License as published by
+;;; the Free Software Foundation; either version 3 of the License, or (at
+;;; your option) any later version.
+;;;
+;;; GNU Guix is distributed in the hope that it will be useful, but
+;;; WITHOUT ANY WARRANTY; without even the implied warranty of
+;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+;;; GNU General Public License for more details.
+;;;
+;;; You should have received a copy of the GNU General Public License
+;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
+
+(define-module (gnu packages bioinformatics)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix packages)
+  #:use-module (guix download)
+  #:use-module (guix build-system gnu)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages compression)
+  #:use-module (gnu packages ncurses)
+  #:use-module (gnu packages perl)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python))
+
+(define-public samtools
+  (package
+    (name "samtools")
+    (version "1.1")
+    (source
+     (origin
+       (method url-fetch)
+       (uri
+        (string-append "mirror://sourceforge/samtools/"
+                       version "/samtools-" version ".tar.bz2"))
+       (sha256
+        (base32
+         "1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
+       #:phases
+       (alist-cons-after
+        'unpack
+        'patch-makefile-curses
+        (lambda _
+          (substitute* "Makefile"
+            (("-lcurses") "-lncurses")))
+        (alist-cons-after
+         'unpack
+         'patch-tests
+         (lambda* (#:key inputs #:allow-other-keys)
+           (let ((bash (assoc-ref inputs "bash")))
+             (substitute* "test/test.pl"
+               ;; The test script calls out to /bin/bash
+               (("/bin/bash")
+                (string-append bash "/bin/bash"))
+               ;; There are two failing tests upstream relating to the "stats"
+               ;; subcommand in test_usage_subcommand ("did not have Usage"
+               ;; and "usage did not mention samtools stats"), so we disable
+               ;; them.
+               (("(test_usage_subcommand\\(.*\\);)" cmd)
+                (string-append "unless ($subcommand eq 'stats') {" cmd "};")))))
+         (alist-delete
+          'configure
+          %standard-phases)))))
+    (native-inputs `(("pkg-config" ,pkg-config)))
+    (inputs `(("ncurses" ,ncurses)
+              ("perl" ,perl)
+              ("python" ,python)
+              ("zlib" ,zlib)))
+    (home-page "http://samtools.sourceforge.net")
+    (synopsis "Utilities to efficiently manipulate nucleotide sequence alignments")
+    (description
+     "Samtools implements various utilities for post-processing nucleotide
+sequence alignments in the SAM, BAM, and CRAM formats, including indexing,
+variant calling (in conjunction with bcftools), and a simple alignment
+viewer.")
+    (license license:expat)))
-- 
1.9.3

Re: [PATCH] gnu: Add samtools

[Ludovic Courtès]

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

> Attached is an updated patch.
>
>>> +    (synopsis "Efficient utilities on manipulating alignments in the SAM format")
>>
>> What about “Utilities to manipulate nucleotide sequence alignments”, to
>> make it clearer that it’s bioinfo-related?
>
> I chose to reword it as "Utilities to efficiently manipulate nucleotide
> sequence alignments"; is this okay?

Sure.

> From c4cae6d77e00491cfd78fe03da8ab617bc1732f2 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 11 Dec 2014 15:48:22 +0100
> Subject: [PATCH] gnu: Add samtools
>
> * gnu/packages/bioinformatics.scm: New file
> * gnu-system.am (GNU_SYSTEM_MODULES): Add it

Applied, thank you!

And welcome aboard! ;-)

Ludo’.

Re: [PATCH] gnu: Add samtools

[Mark H Weaver]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> writes:
> From c4cae6d77e00491cfd78fe03da8ab617bc1732f2 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Thu, 11 Dec 2014 15:48:22 +0100
> Subject: [PATCH] gnu: Add samtools

This built successfully on x86_64, but on i686 its test suite shows 87
failures ("SAM files differ").  See:

  http://hydra.gnu.org/build/173180
  http://hydra.gnu.org/build/173180/log/raw

Would you be willing to investigate?  On your existing guix system, you
could start with:

  guix build --system=i686-linux --keep-failed

It fails similarly on mips64el, but that will be hard for you to debug
and probably not so important.

     Mark

Re: [PATCH] gnu: Add samtools

[Ricardo Wurmus]

Mark H Weaver writes:
> This built successfully on x86_64, but on i686 its test suite shows 87
> failures ("SAM files differ").  See:
>
>   http://hydra.gnu.org/build/173180
>   http://hydra.gnu.org/build/173180/log/raw

Apparently, these 87 test failures on non-64-bit architectures are
upstream problems with the test data for version 1.1.  According to the
developers the test data does not actually comply with the SAM specs,
see <https://github.com/samtools/samtools/pull/307> and the linked
discussion.

This has been fixed in later commits, but there hasn't been a new
release yet.

Can we disable the test suite for certain architectures?  Or would they
have to be disabled completely?

Re: [PATCH] gnu: Add samtools

[Ludovic Courtès]

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

> Can we disable the test suite for certain architectures?  Or would they
> have to be disabled completely?

Yes, just pass something like in ‘arguments’:

  #:tests? (not (string=? (or (%current-system) (%current-target-system))
                          "i686-linux"))

Also please add a comment above linking to the upstream bug report.

TIA,  :-)
Ludo’.

Re: [PATCH] gnu: Add samtools

[Mark H Weaver]

ludo@gnu.org (Ludovic Courtès) writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> Can we disable the test suite for certain architectures?  Or would they
>> have to be disabled completely?
>
> Yes, just pass something like in ‘arguments’:
>
>   #:tests? (not (string=? (or (%current-system) (%current-target-system))
>                           "i686-linux"))

Since it fails the same way on mips64el, I suggest this instead:

   #:tests? (string=? (or (%current-system) (%current-target-system))
                          "x86_64-linux")

> Also please add a comment above linking to the upstream bug report.

     Thanks!
       Mark

Re: [PATCH] gnu: Add samtools

[Mark H Weaver]

Mark H Weaver <mhw@netris.org> writes:

> ludo@gnu.org (Ludovic Courtès) writes:
>
>> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>>
>>> Can we disable the test suite for certain architectures?  Or would they
>>> have to be disabled completely?
>>
>> Yes, just pass something like in ‘arguments’:
>>
>>   #:tests? (not (string=? (or (%current-system) (%current-target-system))
>>                           "i686-linux"))
>
> Since it fails the same way on mips64el, I suggest this instead:
>
>    #:tests? (string=? (or (%current-system) (%current-target-system))
>                           "x86_64-linux")

Oops, we forgot to mention that there should be a comma before that
first open paren, like this:

    #:tests? ,(string=? (or (%current-system) (%current-target-system))
                            "x86_64-linux")

>> Also please add a comment above linking to the upstream bug report.
>
>      Thanks!
>        Mark

Re: [PATCH] gnu: Add samtools

[Ricardo Wurmus]

[-- Attachment #1: Type: text/plain, Size: 842 bytes --]

>>>> Can we disable the test suite for certain architectures?  Or would they
>>>> have to be disabled completely?
>>
>> Since it fails the same way on mips64el, I suggest this instead:
>>
>>    #:tests? (string=? (or (%current-system) (%current-target-system))
>>                           "x86_64-linux")
>
> Oops, we forgot to mention that there should be a comma before that
> first open paren, like this:
>
>     #:tests? ,(string=? (or (%current-system) (%current-target-system))
>                             "x86_64-linux")

Attached is a patch that disables the tests on all systems but
x86_64-linux.  I'm unsure about the indentation, though.  Should the
compared string really be aligned with the arguments of `(or' (as shown
above), or rather aligned with `(or', the argument to `(string=?' (as in
the attached patch)?

-- rekado


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-samtools-disable-tests-for-non-64-bit-systems.patch --]
[-- Type: text/x-patch, Size: 1497 bytes --]

From c9846248c28f2c22660c156d4275326fe8afac80 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 15 Dec 2014 12:23:01 +0100
Subject: [PATCH] gnu: samtools: disable tests for non-64-bit systems

* gnu/packages/bioinformatics.scm (samtools): disable tests for all non-64-bit
  systems because of an upstream bug in the test data.
---
 gnu/packages/bioinformatics.scm | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bcc5d43..1f323eb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -111,7 +111,14 @@ BED, GFF/GTF, VCF.")
          "1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
+     `(;; There are 87 test failures when building on non-64-bit architectures
+       ;; due to invalid test data.  This has since been fixed upstream (see
+       ;; <https://github.com/samtools/samtools/pull/307>), but as there has
+       ;; not been a new release we disable the tests for all non-64-bit
+       ;; systems.
+       #:tests? ,(string=? (or (%current-system) (%current-target-system))
+                           "x86_64-linux")
+       #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (alist-cons-after
         'unpack
-- 
1.9.3

Re: [PATCH] gnu: Add samtools

[Ludovic Courtès]

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

>>>>> Can we disable the test suite for certain architectures?  Or would they
>>>>> have to be disabled completely?
>>>
>>> Since it fails the same way on mips64el, I suggest this instead:
>>>
>>>    #:tests? (string=? (or (%current-system) (%current-target-system))
>>>                           "x86_64-linux")
>>
>> Oops, we forgot to mention that there should be a comma before that
>> first open paren, like this:
>>
>>     #:tests? ,(string=? (or (%current-system) (%current-target-system))
>>                             "x86_64-linux")
>
> Attached is a patch that disables the tests on all systems but
> x86_64-linux.  I'm unsure about the indentation, though.  Should the
> compared string really be aligned with the arguments of `(or' (as shown
> above), or rather aligned with `(or', the argument to `(string=?' (as in
> the attached patch)?

The patch uses the right alignment.

When in doubt, you can check “Formatting Code” in ‘HACKING’ (although I
admit the style guidelines it refers to is quite verbose.)

> From c9846248c28f2c22660c156d4275326fe8afac80 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 15 Dec 2014 12:23:01 +0100
> Subject: [PATCH] gnu: samtools: disable tests for non-64-bit systems
>
> * gnu/packages/bioinformatics.scm (samtools): disable tests for all non-64-bit
>   systems because of an upstream bug in the test data.

Applied, thanks!

Ludo’.