[PATCH] Add FASTX Toolkit.

[PATCH] Add FASTX Toolkit.

[Ricardo Wurmus]

[-- Attachment #1: Type: text/plain, Size: 424 bytes --]

Hi Guix,

attached are patches to add fastx-toolkit, and its dependency
libgtextutils.

"fastx-toolkit" installs three m4 files to "$out/share/aclocal", and
libgtextutils installs an empty "$out/share/aclocal" directoy.  I
reported this upstream, but I did not add a phase to remove these files,
because I think it's not a big deal.  Is this okay or should I modify
the sources to avoid installing these files?

~~ Ricardo


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-Add-libgtextutils.patch --]
[-- Type: text/x-patch, Size: 1992 bytes --]

From 673f316fd41b0d0d7679a7a69ed4755923873653 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 14 Apr 2015 16:35:30 +0200
Subject: [PATCH 1/2] gnu: Add libgtextutils.

* gnu/packages/textutils.scm (libgtextutils): New variable.
---
 gnu/packages/textutils.scm | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)

diff --git a/gnu/packages/textutils.scm b/gnu/packages/textutils.scm
index d6cc577..2f367ce 100644
--- a/gnu/packages/textutils.scm
+++ b/gnu/packages/textutils.scm
@@ -23,6 +23,7 @@
   #:use-module (guix download)
   #:use-module (guix git-download)
   #:use-module (guix build-system gnu)
+  #:use-module (gnu packages autotools)
   #:use-module (gnu packages python))
 
 (define-public recode
@@ -122,3 +123,33 @@ libenca and several charset conversion libraries and tools.")
 normalization, case-folding, and other operations for data in the UTF-8
 encoding, supporting Unicode version 7.0.")
     (license license:expat)))
+
+(define-public libgtextutils
+  (package
+    (name "libgtextutils")
+    (version "0.7")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append
+             "https://github.com/agordon/libgtextutils/releases/download/"
+             version "/libgtextutils-" version ".tar.gz"))
+       (sha256
+        (base32 "0jiybkb2z58wa2msvllnphr4js2hvjvh988pavb3mzkgr6ihwbkr"))))
+    (build-system gnu-build-system)
+    (arguments
+     '(#:phases
+       (alist-cons-after
+        'unpack 'autoreconf
+        (lambda _ (zero? (system* "autoreconf" "-vif")))
+        %standard-phases)))
+    (native-inputs
+     `(("autoconf" ,autoconf)
+       ("automake" ,automake)
+       ("libtool" ,libtool)))
+    (home-page "http://hannonlab.cshl.edu/fastx_toolkit")
+    (synopsis "Gordon's text utils library")
+    (description
+     "libgtextutils is a text utilities library used by the fastx toolkit from
+the Hannon Lab.")
+    (license license:agpl3+)))
-- 
2.1.0


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #3: 0002-gnu-Add-FASTX-Toolkit.patch --]
[-- Type: text/x-patch, Size: 2474 bytes --]

From 1d386b93064eb839e0156938ac38919daa654839 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Tue, 14 Apr 2015 16:36:30 +0200
Subject: [PATCH 2/2] gnu: Add FASTX Toolkit.

* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
---
 gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++
 1 file changed, 33 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 615d70d..0239e97 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -41,6 +41,7 @@
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages swig)
   #:use-module (gnu packages tbb)
+  #:use-module (gnu packages textutils)
   #:use-module (gnu packages vim)
   #:use-module (gnu packages xml)
   #:use-module (gnu packages zip))
@@ -473,6 +474,38 @@ file formats including SAM/BAM, Wiggle/BigWig, BED, GFF/GTF, VCF.")
 other types of unwanted sequence from high-throughput sequencing reads.")
     (license license:expat)))
 
+(define-public fastx-toolkit
+  (package
+    (name "fastx-toolkit")
+    (version "0.0.14")
+    (source (origin
+              (method url-fetch)
+              (uri
+               (string-append
+                "https://github.com/agordon/fastx_toolkit/releases/download/"
+                version "/fastx_toolkit-" version ".tar.bz2"))
+              (sha256
+               (base32
+                "01jqzw386873sr0pjp1wr4rn8fsga2vxs1qfmicvx1pjr72007wy"))))
+    (build-system gnu-build-system)
+    (inputs
+     `(("libgtextutils" ,libgtextutils)))
+    (native-inputs
+     `(("pkg-config" ,pkg-config)))
+    (home-page "http://hannonlab.cshl.edu/fastx_toolkit/")
+    (synopsis "Tools for FASTA/FASTQ file preprocessing")
+    (description
+     "The FASTX-Toolkit is a collection of command line tools for Short-Reads
+FASTA/FASTQ files preprocessing.
+
+Next-Generation sequencing machines usually produce FASTA or FASTQ files,
+containing multiple short-reads sequences.  The main processing of such
+FASTA/FASTQ files is mapping the sequences to reference genomes.  However, it
+is sometimes more productive to preprocess the files before mapping the
+sequences to the genome---manipulating the sequences to produce better mapping
+results.  The FASTX-Toolkit tools perform some of these preprocessing tasks.")
+    (license license:agpl3+)))
+
 (define-public flexbar
   (package
     (name "flexbar")
-- 
2.1.0

Re: [PATCH] Add FASTX Toolkit.

[Ludovic Courtès]

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

> "fastx-toolkit" installs three m4 files to "$out/share/aclocal", and
> libgtextutils installs an empty "$out/share/aclocal" directoy.  I
> reported this upstream, but I did not add a phase to remove these files,
> because I think it's not a big deal.  Is this okay or should I modify
> the sources to avoid installing these files?

What’s wrong with these files?  It looks fine to me, and it’s the
standard directory for Autoconf macros.  So no problem IMO.  :-)

> From 673f316fd41b0d0d7679a7a69ed4755923873653 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 14 Apr 2015 16:35:30 +0200
> Subject: [PATCH 1/2] gnu: Add libgtextutils.
>
> * gnu/packages/textutils.scm (libgtextutils): New variable.

[...]

> +     '(#:phases
> +       (alist-cons-after
> +        'unpack 'autoreconf
> +        (lambda _ (zero? (system* "autoreconf" "-vif")))

So there’s no ‘make dist’ tarball I suppose?

> +    (home-page "http://hannonlab.cshl.edu/fastx_toolkit")

Maybe the github.com URL?

> +    (synopsis "Gordon's text utils library")
> +    (description
> +     "libgtextutils is a text utilities library

Not satisfying but apparently there’s nothing in the REAME nor in the
doc so we’ll live with it.

> From 1d386b93064eb839e0156938ac38919daa654839 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Tue, 14 Apr 2015 16:36:30 +0200
> Subject: [PATCH 2/2] gnu: Add FASTX Toolkit.
>
> * gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.

LGTM!

Thanks,
Ludo’.

Re: [PATCH] Add FASTX Toolkit.

[Ricardo Wurmus]

Ludovic Courtès writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> "fastx-toolkit" installs three m4 files to "$out/share/aclocal", and
>> libgtextutils installs an empty "$out/share/aclocal" directoy.  I
>> reported this upstream, but I did not add a phase to remove these files,
>> because I think it's not a big deal.  Is this okay or should I modify
>> the sources to avoid installing these files?
>
> What’s wrong with these files?  It looks fine to me, and it’s the
> standard directory for Autoconf macros.  So no problem IMO.  :-)

They are not necessary to use fastx-toolkit, so I'd rather avoid the
clutter.  The author seems to agree and is willing to accept patches to
fix this.

>> +    (home-page "http://hannonlab.cshl.edu/fastx_toolkit")
>
> Maybe the github.com URL?

Okay.

I pushed the two commits with the suggested changes.  Thanks for the
review!

~~ Ricardo