[PATCH] gnu: Add ParDRe.

[PATCH] gnu: Add ParDRe.

[Ricardo Wurmus]

* gnu/packages/bioinformatics.scm (pardre): New variable.
---
 gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 41 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 787f386..e681c56 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4111,6 +4111,47 @@ Needleman-Wunsch).")
     ;; Dual licensed; also includes public domain source.
     (license (list license:gpl3 license:bsd-2))))
 
+(define-public pardre
+  (package
+    (name "pardre")
+    (version "1.1.5")
+    (source
+     (origin
+       (method url-fetch)
+       (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
+                           version ".tar.gz"))
+       (sha256
+        (base32
+         "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy"))))
+    (build-system gnu-build-system)
+    (arguments
+     `(#:tests? #f ; no tests included
+       #:phases
+       (modify-phases %standard-phases
+         (delete 'configure)
+         (replace 'install
+           (lambda* (#:key outputs #:allow-other-keys)
+             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+               (mkdir-p bin)
+               (install-file "ParDRe" bin)
+               #t))))))
+    (inputs
+     `(("openmpi" ,openmpi)
+       ("zlib" ,zlib)))
+    (synopsis "Parallel tool to remove duplicate DNA reads ")
+    (description
+     "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
+Duplicate reads can be seen as identical or nearly identical sequences with
+some mismatches.  This tool will let the users to avoid the analysis of not
+necessary reads, reducing the time of subsequent procedures with the
+dataset (e.g., assemblies, mappings, etc.).  The tool is implemented with MPI
+in order to exploit the parallel capabilities of multicore clusters.  It is
+faster than multithreaded counterparts (end of 2015) for the same number of
+cores and, thanks to the message-passing technology, it can be executed on
+clusters.")
+    (home-page "https://sourceforge.net/projects/pardre/")
+    (license license:gpl3+)))
+
 (define-public bio-locus
   (package
     (name "bio-locus")
-- 
2.7.3

Re: [PATCH] gnu: Add ParDRe.

[Roel Janssen]

Ricardo Wurmus writes:

> * gnu/packages/bioinformatics.scm (pardre): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 41 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 787f386..e681c56 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -4111,6 +4111,47 @@ Needleman-Wunsch).")
>      ;; Dual licensed; also includes public domain source.
>      (license (list license:gpl3 license:bsd-2))))
>  
> +(define-public pardre
> +  (package
> +    (name "pardre")
> +    (version "1.1.5")
> +    (source
> +     (origin
> +       (method url-fetch)
> +       (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
> +                           version ".tar.gz"))
> +       (sha256
> +        (base32
> +         "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy"))))
> +    (build-system gnu-build-system)
> +    (arguments
> +     `(#:tests? #f ; no tests included
> +       #:phases
> +       (modify-phases %standard-phases
> +         (delete 'configure)
> +         (replace 'install
> +           (lambda* (#:key outputs #:allow-other-keys)
> +             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
> +               (mkdir-p bin)
> +               (install-file "ParDRe" bin)
> +               #t))))))
> +    (inputs
> +     `(("openmpi" ,openmpi)
> +       ("zlib" ,zlib)))
> +    (synopsis "Parallel tool to remove duplicate DNA reads ")

It would be nice to remove the space at the end of the synopsis.

> +    (description
> +     "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
> +Duplicate reads can be seen as identical or nearly identical sequences with
> +some mismatches.  This tool will let the users to avoid the analysis of not
> +necessary reads, reducing the time of subsequent procedures with the
> +dataset (e.g., assemblies, mappings, etc.).  The tool is implemented with MPI
> +in order to exploit the parallel capabilities of multicore clusters.  It is
> +faster than multithreaded counterparts (end of 2015) for the same number of
> +cores and, thanks to the message-passing technology, it can be executed on
> +clusters.")

Maybe transform:
"This tool will let the users to avoid the analysis of not necessary
reads, reducing the time of subsequent procedures with the dataset
(e.g., assemblies, mappings, etc.)."

into:
"This tool lets users avoid the analysis of unnecesarry reads, reducing
the time of subsequent procedures with the dataset (e.g., assemblies,
mappings, etc.)."

> +    (home-page "https://sourceforge.net/projects/pardre/")
> +    (license license:gpl3+)))
> +
>  (define-public bio-locus
>    (package
>      (name "bio-locus")

Kind regards,
Roel Janssen

Re: [PATCH] gnu: Add ParDRe.

[Ricardo Wurmus]

Roel Janssen <roel@gnu.org> writes:

> Ricardo Wurmus writes:
>
>> * gnu/packages/bioinformatics.scm (pardre): New variable.
>> ---
>>  gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
>>  1 file changed, 41 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 787f386..e681c56 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -4111,6 +4111,47 @@ Needleman-Wunsch).")
>>      ;; Dual licensed; also includes public domain source.
>>      (license (list license:gpl3 license:bsd-2))))
>>  
>> +(define-public pardre
>> +  (package
>> +    (name "pardre")
>> +    (version "1.1.5")
>> +    (source
>> +     (origin
>> +       (method url-fetch)
>> +       (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
>> +                           version ".tar.gz"))
>> +       (sha256
>> +        (base32
>> +         "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy"))))
>> +    (build-system gnu-build-system)
>> +    (arguments
>> +     `(#:tests? #f ; no tests included
>> +       #:phases
>> +       (modify-phases %standard-phases
>> +         (delete 'configure)
>> +         (replace 'install
>> +           (lambda* (#:key outputs #:allow-other-keys)
>> +             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
>> +               (mkdir-p bin)
>> +               (install-file "ParDRe" bin)
>> +               #t))))))
>> +    (inputs
>> +     `(("openmpi" ,openmpi)
>> +       ("zlib" ,zlib)))
>> +    (synopsis "Parallel tool to remove duplicate DNA reads ")
>
> It would be nice to remove the space at the end of the synopsis.

Good catch!

>> +    (description
>> +     "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
>> +Duplicate reads can be seen as identical or nearly identical sequences with
>> +some mismatches.  This tool will let the users to avoid the analysis of not
>> +necessary reads, reducing the time of subsequent procedures with the
>> +dataset (e.g., assemblies, mappings, etc.).  The tool is implemented with MPI
>> +in order to exploit the parallel capabilities of multicore clusters.  It is
>> +faster than multithreaded counterparts (end of 2015) for the same number of
>> +cores and, thanks to the message-passing technology, it can be executed on
>> +clusters.")
>
> Maybe transform:
> "This tool will let the users to avoid the analysis of not necessary
> reads, reducing the time of subsequent procedures with the dataset
> (e.g., assemblies, mappings, etc.)."
>
> into:
> "This tool lets users avoid the analysis of unnecesarry reads, reducing
> the time of subsequent procedures with the dataset (e.g., assemblies,
> mappings, etc.)."

Yes, I should change this to make this read like proper English :)
Thanks for taking a look!

~~ Ricardo

Re: [PATCH] gnu: Add ParDRe.

[Ricardo Wurmus]

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

> Roel Janssen <roel@gnu.org> writes:
>
>> Ricardo Wurmus writes:
>>
>>> * gnu/packages/bioinformatics.scm (pardre): New variable.
>>> ---
>>>  gnu/packages/bioinformatics.scm | 41 +++++++++++++++++++++++++++++++++++++++++
>>>  1 file changed, 41 insertions(+)
>>>
>>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>>> index 787f386..e681c56 100644
>>> --- a/gnu/packages/bioinformatics.scm
>>> +++ b/gnu/packages/bioinformatics.scm
>>> @@ -4111,6 +4111,47 @@ Needleman-Wunsch).")
>>>      ;; Dual licensed; also includes public domain source.
>>>      (license (list license:gpl3 license:bsd-2))))
>>>  
>>> +(define-public pardre
>>> +  (package
>>> +    (name "pardre")
>>> +    (version "1.1.5")
>>> +    (source
>>> +     (origin
>>> +       (method url-fetch)
>>> +       (uri (string-append "mirror://sourceforge/pardre/ParDRe-rel"
>>> +                           version ".tar.gz"))
>>> +       (sha256
>>> +        (base32
>>> +         "0zkyjzv4s8q2h5npalhirbk17r5b1h0n2a42mh7njzlf047h9bhy"))))
>>> +    (build-system gnu-build-system)
>>> +    (arguments
>>> +     `(#:tests? #f ; no tests included
>>> +       #:phases
>>> +       (modify-phases %standard-phases
>>> +         (delete 'configure)
>>> +         (replace 'install
>>> +           (lambda* (#:key outputs #:allow-other-keys)
>>> +             (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
>>> +               (mkdir-p bin)
>>> +               (install-file "ParDRe" bin)
>>> +               #t))))))
>>> +    (inputs
>>> +     `(("openmpi" ,openmpi)
>>> +       ("zlib" ,zlib)))
>>> +    (synopsis "Parallel tool to remove duplicate DNA reads ")
>>
>> It would be nice to remove the space at the end of the synopsis.
>
> Good catch!
>
>>> +    (description
>>> +     "ParDRe is a parallel tool to remove duplicate genetic sequence reads.
>>> +Duplicate reads can be seen as identical or nearly identical sequences with
>>> +some mismatches.  This tool will let the users to avoid the analysis of not
>>> +necessary reads, reducing the time of subsequent procedures with the
>>> +dataset (e.g., assemblies, mappings, etc.).  The tool is implemented with MPI
>>> +in order to exploit the parallel capabilities of multicore clusters.  It is
>>> +faster than multithreaded counterparts (end of 2015) for the same number of
>>> +cores and, thanks to the message-passing technology, it can be executed on
>>> +clusters.")
>>
>> Maybe transform:
>> "This tool will let the users to avoid the analysis of not necessary
>> reads, reducing the time of subsequent procedures with the dataset
>> (e.g., assemblies, mappings, etc.)."
>>
>> into:
>> "This tool lets users avoid the analysis of unnecesarry reads, reducing
>> the time of subsequent procedures with the dataset (e.g., assemblies,
>> mappings, etc.)."
>
> Yes, I should change this to make this read like proper English :)
> Thanks for taking a look!

Pushed with the fixed synopsis and with a couple of changes to the
description.

~~ Ricardo