* [PATCH] Add FASTX Toolkit.
@ 2015-04-14 14:39 Ricardo Wurmus
2015-04-15 20:05 ` Ludovic Courtès
0 siblings, 1 reply; 3+ messages in thread
From: Ricardo Wurmus @ 2015-04-14 14:39 UTC (permalink / raw)
To: Guix-devel
[-- 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
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[-- 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
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[-- 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
^ permalink raw reply related [flat|nested] 3+ messages in thread
* Re: [PATCH] Add FASTX Toolkit.
2015-04-14 14:39 [PATCH] Add FASTX Toolkit Ricardo Wurmus
@ 2015-04-15 20:05 ` Ludovic Courtès
2015-04-16 8:31 ` Ricardo Wurmus
0 siblings, 1 reply; 3+ messages in thread
From: Ludovic Courtès @ 2015-04-15 20:05 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: Guix-devel
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’.
^ permalink raw reply [flat|nested] 3+ messages in thread
* Re: [PATCH] Add FASTX Toolkit.
2015-04-15 20:05 ` Ludovic Courtès
@ 2015-04-16 8:31 ` Ricardo Wurmus
0 siblings, 0 replies; 3+ messages in thread
From: Ricardo Wurmus @ 2015-04-16 8:31 UTC (permalink / raw)
To: Ludovic Courtès; +Cc: Guix-devel
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
^ permalink raw reply [flat|nested] 3+ messages in thread
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2015-04-14 14:39 [PATCH] Add FASTX Toolkit Ricardo Wurmus
2015-04-15 20:05 ` Ludovic Courtès
2015-04-16 8:31 ` Ricardo Wurmus
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