>From ec580c06e33de844f6f6cb7c4fc3b44691e141fd Mon Sep 17 00:00:00 2001
From: Roel Janssen <r...@gnu.org>
Date: Thu, 10 Mar 2016 23:54:31 +0100
Subject: [PATCH] gnu: Add bioawk.
* gnu/packages/bioinformatics.scm (bioawk): New variable.
---
gnu/packages/bioinformatics.scm | 42 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 42 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d53dc9..d15e99d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -36,6 +36,7 @@
#:use-module (gnu packages autotools)
#:use-module (gnu packages algebra)
#:use-module (gnu packages base)
+ #:use-module (gnu packages bison)
#:use-module (gnu packages boost)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpio)
@@ -247,6 +248,47 @@ intervals from multiple files in widely-used genomic file formats such as BAM,
BED, GFF/GTF, VCF.")
(license license:gpl2)))
+(define-public bioawk
+ (package
+ (name "bioawk")
+ (version "1.0")
+ (source (origin
+ (method url-fetch)
+ (uri (string-append "https://github.com/lh3/bioawk/archive/v";
+ version ".tar.gz"))
+ (file-name (string-append name "-" version ".tar.gz"))
+ (sha256
+ (base32 "1daizxsk17ahi9n58fj8vpgwyhzrzh54bzqhanjanp88kgrz7gjw"))))
+ (build-system gnu-build-system)
+ (inputs
+ `(("zlib" ,zlib)))
+ (native-inputs
+ `(("bison" ,bison)))
+ (arguments
+ `(#:tests? #f ; There are no tests to run.
+ ;; Bison must generate files, before other targets can build.
+ #:parallel-build? #f
+ #:phases
+ (modify-phases %standard-phases
+ (delete 'configure) ; There is no configure phase.
+ (replace 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let* ((out (assoc-ref outputs "out"))
+ (bin (string-append out "/bin"))
+ (man (string-append out "/share/man/man1")))
+ (mkdir-p man)
+ (copy-file "awk.1" (string-append man "/bioawk.1"))
+ (install-file "bioawk" bin)))))))
+ (home-page "https://github.com/lh3/bioawk";)
+ (synopsis "AWK with bioinformatics extensions")
+ (description "Bioawk is an extension to Brian Kernighan's awk, adding the
+support of several common biological data formats, including optionally gzip'ed
+BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
+also adds a few built-in functions and a command line option to use TAB as the
+input/output delimiter. When the new functionality is not used, bioawk is
+intended to behave exactly the same as the original BWK awk.")
+ (license license:x11)))
+
(define-public python2-pybedtools
(package
(name "python2-pybedtools")
--
2.5.0
Dear Leo and Ricardo,
Thank you for reviewing this patch. I hope it is fine now.
Leo Famulari writes:
> On Tue, Mar 08, 2016 at 09:10:14PM +0100, Roel Janssen wrote:
>> From 990eda92a62dc25d0f5792437a82e119c5e3579f Mon Sep 17 00:00:00 2001
>> From: Roel Janssen <r...@gnu.org>
>> Date: Tue, 8 Mar 2016 21:06:53 +0100
>> Subject: [PATCH] gnu: Add bioawk.
>>
>> * gnu/packages/bioinformatics.scm (bioawk): New variable.
>
> Thanks for the patch!
>
> [...]
>
>> + (propagated-inputs
>> + `(("zlib" ,zlib)))
>
> I changed this to a plain input, and then checked the references of the
> resulting build, and zlib is referenced. Considering that, does it need
> to be propagated into the user's profile? Propagated inputs should be
> avoided if possible.
You're right. I simply get confused about inputs, native-inputs and
propagated-inputs.
I made it an input in my new patch.
>> + (native-inputs
>> + `(("bison" ,bison)))
>> + (arguments
>> + `(#:parallel-build? #f
>> + #:phases
>> + (modify-phases %standard-phases
>> + (delete 'configure)
>> + (delete 'check)
>
> Can you say why tests are disabled? It can be as simple as "no test
> suite" if that is accurate.
Sure.
>> + (replace
>> + 'install
>> + (lambda* (#:key outputs #:allow-other-keys)
>> + (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
>> + (install-file "bioawk" bin)))))))
>
> The git repo includes a manpage 'awk.1'. Can you send an updated patch
> that installs that as well?
I added it as bioawk.1 instead, to avoid confusion with awk.
Good catch!
Ricardo Wurmus writes:
> Roel Janssen <r...@gnu.org> writes:
>
>> Please let me know when something is wrong with the patch.
>
> In addition to Leo’s comments here are mine:
>
>> + (arguments
>> + `(#:parallel-build? #f
>
> Why is parallel-build disabled? Could you add a comment?
Sure.
>> + #:phases
>> + (modify-phases %standard-phases
>> + (delete 'configure)
>> + (delete 'check)
>
> We usually just do “#:tests? #f” with a comment, instead of deleting the
> “check” phase.
Sorry for the redundancy. I submitted two patches before receiving
comments about this. Fixed in my new patch, and I'll apply this in
future patches as well.
>> + (replace
>> + 'install
>
> Please put “'install” on the same line as “(replace”.
Should I do this for other (replace ...) as well? If I want to replace
the build phase, should I put it on the same line as well?
>> + (lambda* (#:key outputs #:allow-other-keys)
>> + (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
>> + (install-file "bioawk" bin)))))))
>> + (home-page "https://github.com/lh3/bioawk";)
>> + (synopsis "AWK with bioinformatics extensions")
>> + (description "Bioawk is an extension to Brian Kernighan's awk, adding
>> the
>> +support of several common biological data formats, including optionally
>> gzip'ed
>> +BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. It
>> +also adds a few built-in functions and an command line option to use TAB as
>> the
>
> “a command-line option”, not “an”
Good catch! Fixed in my new patch.
Kind regards,
Roel Janssen
