easyconfigs/foss-2019a/ELIC_R-1-foss-2019a-R-3.6.0.eb

easyblock = 'Bundle'

name = 'ELIC_R'
version = '1'
versionsuffix = '-R-%(rver)s'

homepage = 'https://gogs.elic.ucl.ac.be'
description = """This repo provides additional Python and R extensions for ELIC ecosystem."""

toolchain = {'name': 'foss', 'version': '2019a'}

dependencies = [
    ('R', '3.6.0'),
    ('GEOS', '3.7.2', '-Python-3.7.2'),
    ('GDAL', '3.0.0', '-Python-3.7.2'),
]

exts_default_options = {
    'source_urls': [
        'https://cran.r-project.org/src/contrib/Archive/%(name)s',  # package archive
        'https://cran.r-project.org/src/contrib/',  # current version of packages
        'https://cran.freestatistics.org/src/contrib',  # mirror alternative for current packages
    ],
    'source_tmpl': '%(name)s_%(version)s.tar.gz'
}

exts_defaultclass = 'RPackage'
exts_filter = ("R -q --no-save", "library(%(ext_name)s)")

# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends
# !! order of packages is important !!
# packages updated on Sept 25th 2018
exts_list = [
    ('rgdal', '1.4-4'),
    ('gdalUtils', '2.0.1.14'),
    ('ncdf4', '1.16.1'),
    ('gdtools', '0.1.9'),
    ('leaflet', '2.0.2'),
    ('satellite', '1.0.1'),
    ('sf', '0.7-4'),
    ('svglite', '1.2.2'),
    ('leafem', '0.0.1'),
    ('leafpop', '0.0.1'),
    ('mapview', '2.7.0'),
    ('MuMIn', '1.43.6'),
    ('BayesianTools', '0.1.6'),
]

modextrapaths = {'R_LIBS': ''}

postinstallcmds = [
    "cd %(installdir)s && " +
    'Rscript -e "install.packages(\'gstat\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'RNetCDF\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'ggmap\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'automap\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'clhs\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'rasterVis\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'reporttools\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'remotes\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'spatstat\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'rgeos\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'RandomFieldsUtils\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'RandomFields\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'spptest\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'GET\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "library(remotes); install_github(\'myllym/GET\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'shinydashboard\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'rsconnect\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'package_vector\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'tidyverse\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'tidyr\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'R.utils\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'shiny\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'shinythemes\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'shinyFiles\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'RColorBrewer\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'rworldmap\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'rworldxtra\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'colourpicker\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'maptools\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'colorRamps\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'mapdata\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'mapproj\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'FNN\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'countriesHigh\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'remotes\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'RPostgreSQL\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'getPass\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'rpostgis\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'aws.s3\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'stringdist\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'fuzzyjoin\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')" ; Rscript -e "install.packages(\'cmsaf\', repos=\'https://www.freestatistics.org/cran/\', lib=\'%(installdir)s\')"'
]

sanity_check_paths = {
    'files': [],
    'dirs': ['ncdf4', 'sf', 'mapview'],
}

moduleclass = 'numlib'