[PATCH] gnu: Add bioawk.

[PATCH] gnu: Add bioawk.

[Roel Janssen]

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From 990eda92a62dc25d0f5792437a82e119c5e3579f Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@gnu.org>
Date: Tue, 8 Mar 2016 21:06:53 +0100
Subject: [PATCH] gnu: Add bioawk.

* gnu/packages/bioinformatics.scm (bioawk): New variable.
---
 gnu/packages/bioinformatics.scm | 38 ++++++++++++++++++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 5d53dc9..4ceec08 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -37,6 +37,7 @@
   #:use-module (gnu packages algebra)
   #:use-module (gnu packages base)
   #:use-module (gnu packages boost)
+  #:use-module (gnu packages bison)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages cpio)
   #:use-module (gnu packages curl)
@@ -247,6 +248,43 @@ 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)
+    (propagated-inputs
+     `(("zlib" ,zlib)))
+    (native-inputs
+     `(("bison" ,bison)))
+    (arguments
+     `(#:parallel-build? #f
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (delete 'check)
+         (replace
+          'install
+          (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
+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


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Dear Guix,

Here's a patch to add bioawk -- a version of awk specialized in
biological data formats.

Please let me know when something is wrong with the patch.

Kind regards,
Roel Janssen

Re: [PATCH] gnu: Add bioawk.

[Leo Famulari]

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 <roel@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.

> +    (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.

> +         (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?

> +    (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
> +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 Guix,
> 
> Here's a patch to add bioawk -- a version of awk specialized in
> biological data formats.
> 
> Please let me know when something is wrong with the patch.
> 
> Kind regards,
> Roel Janssen

Re: [PATCH] gnu: Add bioawk.

[Ricardo Wurmus]

Roel Janssen <roel@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?

> +       #:phases
> +       (modify-phases %standard-phases
> +         (delete 'configure)
> +         (delete 'check)

We usually just do “#:tests? #f” with a comment, instead of deleting the
“check” phase.

> +         (replace
> +          'install

Please put “'install” on the same line as “(replace”.

> +          (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”

Thanks!

~~ Ricardo

Re: [PATCH] gnu: Add bioawk.

[Roel Janssen]

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From ec580c06e33de844f6f6cb7c4fc3b44691e141fd Mon Sep 17 00:00:00 2001
From: Roel Janssen <roel@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


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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 <roel@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 <roel@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

Re: [PATCH] gnu: Add bioawk.

[Leo Famulari]

On Fri, Mar 11, 2016 at 12:00:11AM +0100, Roel Janssen wrote:
> Thank you for reviewing this patch.  I hope it is fine now.

Thanks for the revised patch!

Pushed as a0a71439fa3, adding a copyright line for you.

> > 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!

A good catch on your part as well!

Re: [PATCH] gnu: Add bioawk.

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:


>>> +         (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?

Yes, the phase name(s) should always be on the same line as the “verb”.

~~ Ricardo

Re: [PATCH] gnu: Add bioawk.

[Roel Janssen]

Ricardo Wurmus writes:

> Roel Janssen <roel@gnu.org> writes:
>
>
>>>> +         (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?
>
> Yes, the phase name(s) should always be on the same line as the “verb”.

I will do this in future patches.

Thanks.