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Re: bioinformatics.scm vs bioconductor.scm ?

From: zimoun
Subject: Re: bioinformatics.scm vs bioconductor.scm ?
Date: Tue, 18 Dec 2018 06:31:44 -0500

Dear Ricardo,

Thank you for your explanations.

> > And I am asking myself if a massive import from Bioconductor should be
> > possible ?
> Certainly!  I’ve done this before actually, but I hit two minor
> problems:
> 1. the bioconductor recursive importer does not *automatically* switch
>    to “CRAN mode” when a dependent package isn’t found on Bioconductor.
>    Not a big problem, but it means that teh import isn’t fully
>    automatic.

I am not sure to understand.
Is the bioconductor importer usable from `guix import` ?

I have tried once by hand; to understand step by step. :-)
Thank Pierre for the nice tutorial !
see the package definition below.

> 2. compiling big Guile modules (such as a future (gnu packages cran))
>    require lots of memory since Guile 2.2(?), so I didn’t add all these
>    packages.  This is a bug and we’d have to split the module, probably,
>    to work around it.

Ok, even if I have no clue to work around.

So as I need the FlowCore package to process data from cytometry, let
start my first attempt with this one. :-)

This package is on Bioconductor:
Then define the package by hand was straightforward! :-)
I am not sure to be compliant... Basically, I have just copied/pasted
the modules from bioinformatics.scm (or bioconductor.scm), then I have
look for if the dependency was already there. Missing r-corpcor from
CRAN, so `guix import cran`.

Hum, the package BiocGenerics needs the version >= 0.1.14, and it is
not defined in the package.
Then, the package grDevices, graphics, methods, stats, stats4 are
required (see bioconductor webpage) but not defined elsewhere. Is it
good ?

What is the convention about license ?
(license name) or (license license:name)

Well, then I have run guix package --install-from-file=my.scm and it
seems to works, I mean the first examples from the vignette do not
complain. ;-)

Thank you for any comment.

All the best


(define-module (gnu packages my-bioinformatics)
  #:use-module ((guix licenses) #:prefix license:)
  #:use-module (guix packages)
  #:use-module (guix utils)
  #:use-module (guix download)
  #:use-module (guix git-download)
  #:use-module (guix hg-download)
  #:use-module (guix build-system ant)
  #:use-module (guix build-system gnu)
  #:use-module (guix build-system cmake)
  #:use-module (guix build-system haskell)
  #:use-module (guix build-system ocaml)
  #:use-module (guix build-system perl)
  #:use-module (guix build-system python)
  #:use-module (guix build-system r)
  #:use-module (guix build-system ruby)
  #:use-module (guix build-system scons)
  #:use-module (guix build-system trivial)
  #:use-module (gnu packages)
  #:use-module (gnu packages autotools)
  #:use-module (gnu packages algebra)
  #:use-module (gnu packages base)
  #:use-module (gnu packages bash)
  #:use-module (gnu packages bison)
  #:use-module (gnu packages bioconductor)
  #:use-module (gnu packages bioinformatics)
  #:use-module (gnu packages boost)
  #:use-module (gnu packages check)
  #:use-module (gnu packages compression)
  #:use-module (gnu packages cpio)
  #:use-module (gnu packages cran)
  #:use-module (gnu packages curl)
  #:use-module (gnu packages documentation)
  #:use-module (gnu packages databases)
  #:use-module (gnu packages datastructures)
  #:use-module (gnu packages file)
  #:use-module (gnu packages flex)
  #:use-module (gnu packages gawk)
  #:use-module (gnu packages gcc)
  #:use-module (gnu packages gd)
  #:use-module (gnu packages gtk)
  #:use-module (gnu packages glib)
  #:use-module (gnu packages graph)
  #:use-module (gnu packages groff)
  #:use-module (gnu packages guile)
  #:use-module (gnu packages haskell)
  #:use-module (gnu packages haskell-check)
  #:use-module (gnu packages haskell-web)
  #:use-module (gnu packages image)
  #:use-module (gnu packages imagemagick)
  #:use-module (gnu packages java)
  #:use-module (gnu packages jemalloc)
  #:use-module (gnu packages dlang)
  #:use-module (gnu packages linux)
  #:use-module (gnu packages logging)
  #:use-module (gnu packages machine-learning)
  #:use-module (gnu packages man)
  #:use-module (gnu packages maths)
  #:use-module (gnu packages mpi)
  #:use-module (gnu packages ncurses)
  #:use-module (gnu packages ocaml)
  #:use-module (gnu packages pcre)
  #:use-module (gnu packages parallel)
  #:use-module (gnu packages pdf)
  #:use-module (gnu packages perl)
  #:use-module (gnu packages perl-check)
  #:use-module (gnu packages pkg-config)
  #:use-module (gnu packages popt)
  #:use-module (gnu packages protobuf)
  #:use-module (gnu packages python)
  #:use-module (gnu packages python-web)
  #:use-module (gnu packages readline)
  #:use-module (gnu packages ruby)
  #:use-module (gnu packages serialization)
  #:use-module (gnu packages shells)
  #:use-module (gnu packages statistics)
  #:use-module (gnu packages swig)
  #:use-module (gnu packages tbb)
  #:use-module (gnu packages tex)
  #:use-module (gnu packages texinfo)
  #:use-module (gnu packages textutils)
  #:use-module (gnu packages time)
  #:use-module (gnu packages tls)
  #:use-module (gnu packages vim)
  #:use-module (gnu packages web)
  #:use-module (gnu packages xml)
  #:use-module (gnu packages xorg)
  #:use-module (srfi srfi-1)
  #:use-module (ice-9 match))

(define-public r-corpcor
   (name "r-corpcor")
   (version "1.6.9")
     (method url-fetch)
     (uri (cran-uri "corpcor" version))
   (build-system r-build-system)
    "Efficient Estimation of Covariance and (Partial) Correlation")
    "Implements a James-Stein-type shrinkage estimator for the
covariance matrix, with separate shrinkage for variances and
correlations.  The details of the method are explained in Schafer and
Strimmer (2005) <DOI:10.2202/1544-6115.1175> and Opgen-Rhein and
Strimmer (2007) <DOI:10.2202/1544-6115.1252>.  The approach is both
computationally as well as statistically very efficient, it is
applicable to \"small n, large p\" data, and always returns a positive
definite and well-conditioned covariance matrix.  In addition to
inferring the covariance matrix the package also provides shrinkage
estimators for partial correlations and partial variances.  The
inverse of the covariance and correlation matrix can be efficiently
computed, as well as any arbitrary power of the shrinkage correlation
matrix.  Furthermore, functions are available for fast singular value
decomposition, for computing the pseudoinverse, and for checking the
rank and positive definiteness of a matrix.")
   (license license:gpl3+)))

(define-public r-flowcore
    (name "r-flowcore")
    (version "1.48.0")
       (method url-fetch)
       (uri (bioconductor-uri "flowCore" version))
    (build-system r-build-system)
       ("r-biobase" ,r-biobase)
       ("r-biocgenerics" ,r-biocgenerics)
       ("r-biocmanager" ,r-biocmanager)
       ("r-bh" ,r-bh)
       ("r-graph" ,r-graph)
       ("r-rrcov" ,r-rrcov)
       ("r-r-utils" ,r-r-utils)
       ("r-corpcor" ,r-corpcor)
       ("r-rcpp" ,r-rcpp)
       ("r-matrixstats" ,r-matrixstats)
       ("r-mass" ,r-mass)
     `(("zlib" ,zlib)))
    (home-page "";)
    (synopsis "Basic structures for flow cytometry data")
     "Provides S4 data structures and basic functions to deal with
flow cytometry data.")
    (license license:artistic2.0)))

;;BiocGenerics(>= 0.1.14),
;; grDevices,
;; graphics, methods,
;; stats, stats4,


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