On Wed, Apr 06, 2016 at 05:34:37PM +0200, Ricardo Wurmus wrote: > From 8cf38d1a43af8d89578e0604156d5097c88a212f Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus <[email protected]> > Date: Wed, 30 Mar 2016 12:23:51 +0200 > Subject: [PATCH 1/3] gnu: Add r-bsgenome-mmusculus-ucsc-mm9. > > * gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New > variable.
LGTM! > --- > gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ > 1 file changed, 31 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 9532e38..fd99ac4 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4943,6 +4943,37 @@ Stephens (1990).") > by UCSC (hg19, February 2009) and stored in Biostrings objects.") > (license license:artistic2.0))) > > +(define-public r-bsgenome-mmusculus-ucsc-mm9 > + (package > + (name "r-bsgenome-mmusculus-ucsc-mm9") > + (version "1.4.0") > + (source (origin > + (method url-fetch) > + ;; We cannot use bioconductor-uri here because this tarball is > + ;; located under "data/annotation/" instead of "bioc/". > + (uri (string-append "http://www.bioconductor.org/packages/"; > + "release/data/annotation/src/contrib/" > + "BSgenome.Mmusculus.UCSC.mm9_" > + version ".tar.gz")) > + (sha256 > + (base32 > + "1birqw30g2azimxpnjfzmkphan7x131yy8b9h85lfz5fjdg7841i")))) > + (properties > + `((upstream-name . "BSgenome.Mmusculus.UCSC.mm9"))) > + (build-system r-build-system) > + ;; As this package provides little more than a very large data file it > + ;; doesn't make sense to build substitutes. > + (arguments `(#:substitutable? #f)) > + (propagated-inputs > + `(("r-bsgenome" ,r-bsgenome))) > + (home-page > + "http://www.bioconductor.org/packages/BSgenome.Mmusculus.UCSC.mm9/";) > + (synopsis "Full genome sequences for Mouse") > + (description > + "This package provides full genome sequences for Mus musculus (Mouse) as > +provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") > + (license license:artistic2.0))) > + > (define-public r-motifrg > (package > (name "r-motifrg") > -- > 2.1.0 > > From 71eb33921e7179e04800554c775a321e1ecca297 Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus <[email protected]> > Date: Wed, 30 Mar 2016 12:24:16 +0200 > Subject: [PATCH 2/3] gnu: Add r-bsgenome-celegans-ucsc-ce6. > > * gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New > variable. > --- > gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ > 1 file changed, 32 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index fd99ac4..2fb1182 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -4974,6 +4974,38 @@ by UCSC (hg19, February 2009) and stored in Biostrings > objects.") > provided by UCSC (mm9, July 2007) and stored in Biostrings objects.") > (license license:artistic2.0))) > > +(define-public r-bsgenome-celegans-ucsc-ce6 > + (package > + (name "r-bsgenome-celegans-ucsc-ce6") > + (version "1.4.0") > + (source (origin > + (method url-fetch) > + ;; We cannot use bioconductor-uri here because this tarball is > + ;; located under "data/annotation/" instead of "bioc/". > + (uri (string-append "http://www.bioconductor.org/packages/"; > + "release/data/annotation/src/contrib/" > + "BSgenome.Celegans.UCSC.ce6_" > + version ".tar.gz")) > + (sha256 > + (base32 > + "0mqzb353xv2c3m3vkb315dkmnxkgczp7ndnknyhpgjlybyf715v9")))) > + (properties > + `((upstream-name . "BSgenome.Celegans.UCSC.ce6"))) > + (build-system r-build-system) > + ;; As this package provides little more than a very large data file it > + ;; doesn't make sense to build substitutes. > + (arguments `(#:substitutable? #f)) > + (propagated-inputs > + `(("r-bsgenome" ,r-bsgenome))) > + (home-page > + "http://www.bioconductor.org/packages/BSgenome.Celegans.UCSC.ce6/";) > + (synopsis "Full genome sequences for Worm") > + (description > + "This package provides full genome sequences for Caenorhabditis > +elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings > +objects.") > + (license license:artistic2.0))) > + > (define-public r-motifrg > (package > (name "r-motifrg") > -- > 2.1.0 > > From 6c2e98a5754c9959765774f8ef10feed6cbc1dbd Mon Sep 17 00:00:00 2001 > From: Ricardo Wurmus <[email protected]> > Date: Wed, 30 Mar 2016 12:24:44 +0200 > Subject: [PATCH 3/3] gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3. > > * gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3): > New variable. > --- > gnu/packages/bioinformatics.scm | 32 ++++++++++++++++++++++++++++++++ > 1 file changed, 32 insertions(+) > > diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm > index 2fb1182..01e9060 100644 > --- a/gnu/packages/bioinformatics.scm > +++ b/gnu/packages/bioinformatics.scm > @@ -5006,6 +5006,38 @@ elegans (Worm) as provided by UCSC (ce6, May 2008) and > stored in Biostrings > objects.") > (license license:artistic2.0))) > > +(define-public r-bsgenome-dmelanogaster-ucsc-dm3 > + (package > + (name "r-bsgenome-dmelanogaster-ucsc-dm3") > + (version "1.4.0") > + (source (origin > + (method url-fetch) > + ;; We cannot use bioconductor-uri here because this tarball is > + ;; located under "data/annotation/" instead of "bioc/". > + (uri (string-append "http://www.bioconductor.org/packages/"; > + "release/data/annotation/src/contrib/" > + "BSgenome.Dmelanogaster.UCSC.dm3_" > + version ".tar.gz")) > + (sha256 > + (base32 > + "19bm3lkhhkag3gnwp419211fh0cnr0x6fa0r1lr0ycwrikxdxsv8")))) > + (properties > + `((upstream-name . "BSgenome.Dmelanogaster.UCSC.dm3"))) > + (build-system r-build-system) > + ;; As this package provides little more than a very large data file it > + ;; doesn't make sense to build substitutes. > + (arguments `(#:substitutable? #f)) > + (propagated-inputs > + `(("r-bsgenome" ,r-bsgenome))) > + (home-page > + "http://www.bioconductor.org/packages/BSgenome.Dmelanogaster.UCSC.dm3/";) > + (synopsis "Full genome sequences for Fly") > + (description > + "This package provides full genome sequences for Drosophila > +melanogaster (Fly) as provided by UCSC (dm3, April 2006) and stored in > +Biostrings objects.") > + (license license:artistic2.0))) > + > (define-public r-motifrg > (package > (name "r-motifrg") > -- > 2.1.0 >
