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