WIP packages

WIP packages

[Pjotr Prins]

Just for the record, we have working packages in our 'incubator':

  https://github.com/genenetwork/guix-bioinformatics/tree/master/gn/packages

We currently have the following packages created for
http://genenetwork.org/ (some are written by Roel and Dennis, see the
commit log):

gn/packages/ruby.scm: bio-vcf
gn/packages/ruby.scm: bio-table
gn/packages/sparql-query.scm: sparql-query
gn/packages/python.scm: python-flask-sqlalchemy
gn/packages/python.scm: python2-flask-sqlalchemy
gn/packages/python.scm: python-xlsxwriter
gn/packages/python.scm: python2-xlsxwriter
gn/packages/python.scm: python-rdflib-jsonld
gn/packages/python.scm: python2-rdflib-jsonld
gn/packages/python.scm: python-rdflib-4.2
gn/packages/python.scm: python2-rdflib-4.2
gn/packages/python.scm: python-avro
gn/packages/python.scm: python2-avro
gn/packages/python.scm: python-shellescape
gn/packages/python.scm: python2-shellescape
gn/packages/python.scm: python-mysqlclient
gn/packages/python.scm: python2-mysqlclient
gn/packages/python.scm: python2-htmlgen-gn
gn/packages/python.scm: python2-pil
gn/packages/python.scm: python2-piddle-gn
gn/packages/python.scm: python2-parallel
gn/packages/python.scm: python2-numarray
gn/packages/mongodb.scm: mongodb
gn/packages/statistics.scm: r-acepack
gn/packages/statistics.scm: r-latticeextra
gn/packages/statistics.scm: r-formula
gn/packages/statistics.scm: r-hmisc
gn/packages/statistics.scm: r-iterators
gn/packages/statistics.scm: r-fastcluster
gn/packages/statistics.scm: r-dynamictreecut
gn/packages/statistics.scm: r-rcppeigen
gn/packages/statistics.scm: r-matrix
gn/packages/statistics.scm: r-graphics
gn/packages/statistics.scm: r-lmmlite
gn/packages/statistics.scm: pylmm-gn2
gn/packages/elixir.scm: elixir
gn/packages/cwl.scm: python-cwltool
gn/packages/cwl.scm: python2-cwltool
gn/packages/cwl.scm: python-schema-salad
gn/packages/cwl.scm: python2-schema-salad
gn/packages/4store.scm: 4store

Incomplete (but almost there)

gn/packages/arrayfire.scm: arrayfire
gn/packages/arrayfire.scm: glfw
gn/packages/arrayfire.scm: clBLAS
gn/packages/arrayfire.scm: clFFT
gn/packages/arrayfire.scm: compute
gn/packages/arrayfire.scm: ocl-icd
gn/packages/arrayfire.scm: opencl-headers
gn/packages/tcl.scm: environment-modules

If anyone is interested to run with one of these in main line, feel
free to help.

Pj.

Re: WIP packages

[Ricardo Wurmus]

Pjotr Prins <pjotr.public12@thebird.nl> writes:

> gn/packages/statistics.scm: r-acepack
> gn/packages/statistics.scm: r-latticeextra
> gn/packages/statistics.scm: r-formula
> gn/packages/statistics.scm: r-hmisc
> gn/packages/statistics.scm: r-iterators
> gn/packages/statistics.scm: r-fastcluster
> gn/packages/statistics.scm: r-dynamictreecut
> gn/packages/statistics.scm: r-rcppeigen
> gn/packages/statistics.scm: r-matrix
> gn/packages/statistics.scm: r-graphics
> gn/packages/statistics.scm: r-lmmlite

I think I’ve packaged a couple of these, too.

I think that “matrix” and “graphics” are standard packages that are part
of the default R installation, though.

I also have an incomplete patch to provide a recursive importer for
CRAN/bioconductor packages.  If you plan to package more R stuff and I’m
slow to finish the importer patch, let me know and I can give you an
early copy.  It really makes packaging large dependency trees much
easier.

~~ Ricardo