diff mbox

gnu: Add Infernal.

Message ID 20160902133514.26930-1-ricardo.wurmus@mdc-berlin.de
State New
Headers show

Commit Message

Ricardo Wurmus Sept. 2, 2016, 1:35 p.m. UTC
* gnu/packages/bioinformatics.scm (infernal): New variable.
---
 gnu/packages/bioinformatics.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

Comments

David Thompson Sept. 2, 2016, 1:44 p.m. UTC | #1
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
Ricardo Wurmus Sept. 2, 2016, 2:12 p.m. UTC | #2
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
Efraim Flashner Sept. 5, 2016, 9:32 a.m. UTC | #3
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.
Ricardo Wurmus Sept. 5, 2016, 9:45 a.m. UTC | #4
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
diff mbox

Patch

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")