* [PATCH] gnu: Add ParDRe.
@ 2016-05-23 9:09 Ricardo Wurmus
2016-05-23 9:29 ` Roel Janssen
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2016-05-23 9:09 UTC (permalink / raw)
To: guix-devel
* 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
^ permalink raw reply related [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add ParDRe.
2016-05-23 9:09 [PATCH] gnu: Add ParDRe Ricardo Wurmus
@ 2016-05-23 9:29 ` Roel Janssen
2016-05-23 9:32 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Roel Janssen @ 2016-05-23 9:29 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add ParDRe.
2016-05-23 9:29 ` Roel Janssen
@ 2016-05-23 9:32 ` Ricardo Wurmus
2016-05-23 10:57 ` Ricardo Wurmus
0 siblings, 1 reply; 4+ messages in thread
From: Ricardo Wurmus @ 2016-05-23 9:32 UTC (permalink / raw)
To: Roel Janssen; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 4+ messages in thread
* Re: [PATCH] gnu: Add ParDRe.
2016-05-23 9:32 ` Ricardo Wurmus
@ 2016-05-23 10:57 ` Ricardo Wurmus
0 siblings, 0 replies; 4+ messages in thread
From: Ricardo Wurmus @ 2016-05-23 10:57 UTC (permalink / raw)
To: Roel Janssen; +Cc: guix-devel
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
^ permalink raw reply [flat|nested] 4+ messages in thread
end of thread, other threads:[~2016-05-23 10:57 UTC | newest]
Thread overview: 4+ messages (download: mbox.gz / follow: Atom feed)
-- links below jump to the message on this page --
2016-05-23 9:09 [PATCH] gnu: Add ParDRe Ricardo Wurmus
2016-05-23 9:29 ` Roel Janssen
2016-05-23 9:32 ` Ricardo Wurmus
2016-05-23 10:57 ` Ricardo Wurmus
Code repositories for project(s) associated with this public inbox
https://git.savannah.gnu.org/cgit/guix.git
This is a public inbox, see mirroring instructions
for how to clone and mirror all data and code used for this inbox;
as well as URLs for read-only IMAP folder(s) and NNTP newsgroup(s).