* [PATCH] gnu: Add Infernal.
@ 2016-09-02 13:35 Ricardo Wurmus
2016-09-02 13:44 ` Thompson, David
0 siblings, 1 reply; 5+ messages in thread
From: Ricardo Wurmus @ 2016-09-02 13:35 UTC (permalink / raw)
To: guix-devel
* gnu/packages/bioinformatics.scm (infernal): New variable.
---
gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
1 file changed, 27 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 08c2545..1652f71 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4835,6 +4835,33 @@ data in the form of VCF files.")
;; at https://vcftools.github.io/license.html
(license license:lgpl3)))
+(define-public infernal
+ (package
+ (name "infernal")
+ (version "1.1.2")
+ (source (origin
+ (method url-fetch)
+ ;; There are no versioned tarballs
+ (uri (string-append "http://eddylab.org/software/infernal/"
+ "infernal-" version ".tar.gz"))
+ (sha256
+ (base32
+ "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
+ (build-system gnu-build-system)
+ (native-inputs
+ `(("perl" ,perl))) ; for tests
+ (home-page "http://eddylab.org/infernal/")
+ (synopsis "Inference of RNA alignments")
+ (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
+searching DNA sequence databases for RNA structure and sequence similarities.
+It is an implementation of a special case of profile stochastic context-free
+grammars called @dfn{covariance models} (CMs). A CM is like a sequence
+profile, but it scores a combination of sequence consensus and RNA secondary
+structure consensus, so in many cases, it is more capable of identifying RNA
+homologs that conserve their secondary structure more than their primary
+sequence.")
+ (license license:bsd-3)))
+
(define-public r-vegan
(package
(name "r-vegan")
--
2.9.3
^ permalink raw reply related [flat|nested] 5+ messages in thread* Re: [PATCH] gnu: Add Infernal.
2016-09-02 13:35 [PATCH] gnu: Add Infernal Ricardo Wurmus
@ 2016-09-02 13:44 ` Thompson, David
2016-09-02 14:12 ` Ricardo Wurmus
0 siblings, 1 reply; 5+ messages in thread
From: Thompson, David @ 2016-09-02 13:44 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
On Fri, Sep 2, 2016 at 9:35 AM, Ricardo Wurmus
<ricardo.wurmus@mdc-berlin.de> wrote:
> * gnu/packages/bioinformatics.scm (infernal): New variable.
> ---
> gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
> 1 file changed, 27 insertions(+)
>
> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> index 08c2545..1652f71 100644
> --- a/gnu/packages/bioinformatics.scm
> +++ b/gnu/packages/bioinformatics.scm
> @@ -4835,6 +4835,33 @@ data in the form of VCF files.")
> ;; at https://vcftools.github.io/license.html
> (license license:lgpl3)))
>
> +(define-public infernal
> + (package
> + (name "infernal")
> + (version "1.1.2")
> + (source (origin
> + (method url-fetch)
> + ;; There are no versioned tarballs
But the version appears in the URL?
> + (uri (string-append "http://eddylab.org/software/infernal/"
> + "infernal-" version ".tar.gz"))
> + (sha256
> + (base32
> + "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
> + (build-system gnu-build-system)
> + (native-inputs
> + `(("perl" ,perl))) ; for tests
> + (home-page "http://eddylab.org/infernal/")
> + (synopsis "Inference of RNA alignments")
> + (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
> +searching DNA sequence databases for RNA structure and sequence similarities.
> +It is an implementation of a special case of profile stochastic context-free
> +grammars called @dfn{covariance models} (CMs). A CM is like a sequence
> +profile, but it scores a combination of sequence consensus and RNA secondary
> +structure consensus, so in many cases, it is more capable of identifying RNA
> +homologs that conserve their secondary structure more than their primary
> +sequence.")
> + (license license:bsd-3)))
> +
> (define-public r-vegan
> (package
> (name "r-vegan")
> --
> 2.9.3
>
>
LGTM overall.
- Dave
^ permalink raw reply [flat|nested] 5+ messages in thread* Re: [PATCH] gnu: Add Infernal.
2016-09-02 13:44 ` Thompson, David
@ 2016-09-02 14:12 ` Ricardo Wurmus
2016-09-05 9:32 ` Efraim Flashner
0 siblings, 1 reply; 5+ messages in thread
From: Ricardo Wurmus @ 2016-09-02 14:12 UTC (permalink / raw)
To: Thompson, David; +Cc: guix-devel
Thompson, David <dthompson2@worcester.edu> writes:
> On Fri, Sep 2, 2016 at 9:35 AM, Ricardo Wurmus
> <ricardo.wurmus@mdc-berlin.de> wrote:
>> * gnu/packages/bioinformatics.scm (infernal): New variable.
>> ---
>> gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
>> 1 file changed, 27 insertions(+)
>>
>> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
>> index 08c2545..1652f71 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -4835,6 +4835,33 @@ data in the form of VCF files.")
>> ;; at https://vcftools.github.io/license.html
>> (license license:lgpl3)))
>>
>> +(define-public infernal
>> + (package
>> + (name "infernal")
>> + (version "1.1.2")
>> + (source (origin
>> + (method url-fetch)
>> + ;; There are no versioned tarballs
>
> But the version appears in the URL?
Sorry, this comment was supposed to be removed before sending out the
patch. Noticed it too late.
>> + (uri (string-append "http://eddylab.org/software/infernal/"
>> + "infernal-" version ".tar.gz"))
>> + (sha256
>> + (base32
>> + "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
>> + (build-system gnu-build-system)
>> + (native-inputs
>> + `(("perl" ,perl))) ; for tests
>> + (home-page "http://eddylab.org/infernal/")
>> + (synopsis "Inference of RNA alignments")
>> + (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
>> +searching DNA sequence databases for RNA structure and sequence similarities.
>> +It is an implementation of a special case of profile stochastic context-free
>> +grammars called @dfn{covariance models} (CMs). A CM is like a sequence
>> +profile, but it scores a combination of sequence consensus and RNA secondary
>> +structure consensus, so in many cases, it is more capable of identifying RNA
>> +homologs that conserve their secondary structure more than their primary
>> +sequence.")
>> + (license license:bsd-3)))
>> +
>> (define-public r-vegan
>> (package
>> (name "r-vegan")
>> --
>> 2.9.3
>>
>>
>
> LGTM overall.
Okay, will push in a moment (after removing the wrong comment).
Thanks for taking a look!
~~ Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread* Re: [PATCH] gnu: Add Infernal.
2016-09-02 14:12 ` Ricardo Wurmus
@ 2016-09-05 9:32 ` Efraim Flashner
2016-09-05 9:45 ` Ricardo Wurmus
0 siblings, 1 reply; 5+ messages in thread
From: Efraim Flashner @ 2016-09-05 9:32 UTC (permalink / raw)
To: Ricardo Wurmus; +Cc: guix-devel
[-- Attachment #1: Type: text/plain, Size: 2940 bytes --]
On Fri, Sep 02, 2016 at 04:12:21PM +0200, Ricardo Wurmus wrote:
>
> Thompson, David <dthompson2@worcester.edu> writes:
>
> > On Fri, Sep 2, 2016 at 9:35 AM, Ricardo Wurmus
> > <ricardo.wurmus@mdc-berlin.de> wrote:
> >> * gnu/packages/bioinformatics.scm (infernal): New variable.
> >> ---
> >> gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
> >> 1 file changed, 27 insertions(+)
> >>
> >> diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
> >> index 08c2545..1652f71 100644
> >> --- a/gnu/packages/bioinformatics.scm
> >> +++ b/gnu/packages/bioinformatics.scm
> >> @@ -4835,6 +4835,33 @@ data in the form of VCF files.")
> >> ;; at https://vcftools.github.io/license.html
> >> (license license:lgpl3)))
> >>
> >> +(define-public infernal
> >> + (package
> >> + (name "infernal")
> >> + (version "1.1.2")
> >> + (source (origin
> >> + (method url-fetch)
> >> + ;; There are no versioned tarballs
> >
> > But the version appears in the URL?
>
> Sorry, this comment was supposed to be removed before sending out the
> patch. Noticed it too late.
>
> >> + (uri (string-append "http://eddylab.org/software/infernal/"
> >> + "infernal-" version ".tar.gz"))
> >> + (sha256
> >> + (base32
> >> + "0sr2hiz3qxfwqpz3whxr6n82p3x27336v3f34iqznp10hks2935c"))))
> >> + (build-system gnu-build-system)
> >> + (native-inputs
> >> + `(("perl" ,perl))) ; for tests
> >> + (home-page "http://eddylab.org/infernal/")
> >> + (synopsis "Inference of RNA alignments")
> >> + (description "Infernal (\"INFERence of RNA ALignment\") is a tool for
> >> +searching DNA sequence databases for RNA structure and sequence similarities.
> >> +It is an implementation of a special case of profile stochastic context-free
> >> +grammars called @dfn{covariance models} (CMs). A CM is like a sequence
> >> +profile, but it scores a combination of sequence consensus and RNA secondary
> >> +structure consensus, so in many cases, it is more capable of identifying RNA
> >> +homologs that conserve their secondary structure more than their primary
> >> +sequence.")
> >> + (license license:bsd-3)))
> >> +
> >> (define-public r-vegan
> >> (package
> >> (name "r-vegan")
> >> --
> >> 2.9.3
> >>
> >>
> >
> > LGTM overall.
>
> Okay, will push in a moment (after removing the wrong comment).
> Thanks for taking a look!
>
> ~~ Ricardo
>
After checking the hydra logs I removed support for armhf and mips,
since they lack the necessary hardware features to build the package.
--
Efraim Flashner <efraim@flashner.co.il> אפרים פלשנר
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^ permalink raw reply [flat|nested] 5+ messages in thread* Re: [PATCH] gnu: Add Infernal.
2016-09-05 9:32 ` Efraim Flashner
@ 2016-09-05 9:45 ` Ricardo Wurmus
0 siblings, 0 replies; 5+ messages in thread
From: Ricardo Wurmus @ 2016-09-05 9:45 UTC (permalink / raw)
To: Efraim Flashner; +Cc: guix-devel
Efraim Flashner <efraim@flashner.co.il> writes:
> On Fri, Sep 02, 2016 at 04:12:21PM +0200, Ricardo Wurmus wrote:
>>
>> Thompson, David <dthompson2@worcester.edu> writes:
>>
>> > On Fri, Sep 2, 2016 at 9:35 AM, Ricardo Wurmus
>> > <ricardo.wurmus@mdc-berlin.de> wrote:
>> >> * gnu/packages/bioinformatics.scm (infernal): New variable.
[...]
> After checking the hydra logs I removed support for armhf and mips,
> since they lack the necessary hardware features to build the package.
Thank you. My apologies for not detecting this earlier.
~~ Ricardo
^ permalink raw reply [flat|nested] 5+ messages in thread
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2016-09-02 13:35 [PATCH] gnu: Add Infernal Ricardo Wurmus
2016-09-02 13:44 ` Thompson, David
2016-09-02 14:12 ` Ricardo Wurmus
2016-09-05 9:32 ` Efraim Flashner
2016-09-05 9:45 ` Ricardo Wurmus
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