Setting up the package requirements on Linux • hydrographr

Installation of the required GIS tools

If you do not have installed any of the GIS tools, please, install before using hydrographr. If you use Ubuntu you can copy-paste the commands below. If you use another Linux distribution, please, see the linked software webpage below for installation instruction.

Warning! Sometimes the installation does not work within a VPN connection. If you fail to fetch data from online repositories during the installation, please try deactivating your VPN connection.

Add the Ubuntugis repository

First, you have to add the “Ubuntugis” Personal Package Archive (PPA) to your system’s software sources to be able to install the GIS tools available from there.

# Add the Ubuntugis PPA
sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable

Next, you need to tell your system to pull down the latest list of software from each archive it knows about, including the PPA you just added:

# Update the packages list
sudo apt update

Now you are ready to installGDAL, GRASS GIS and GNU parallel. Copy and paste the commands below into your console and follow the instructions to install the tools.

GDAL

GDAL is a translator library for raster and vector geospatial data formats and comes with a variety of useful command line utilities for data translation and processing. For more information check the GDAL website.

# Install GDAL
sudo apt install gdal-bin python3-gdal

GRASS GIS

GRASS GIS is a powerful raster, vector, and geospatial processing engine including tools for terrain and ecosystem modeling, hydrology and the processing of satellite and aerial imagery. For more detailed installation instructions check the GRASS GIS users wiki or the GRASS GIS website. Please, make sure that you have grass8.2 installed.

# Install GRASS GIS
sudo apt-get install grass grass-core grass-dev grass-gui grass-doc

GRASS GIS addons

Copy-paste the commands below to install the required addons for GRASS GIS.

sudo apt install make

# Install GRASS GIS addons
export GRASSEXEC="grass --exec"
$GRASSEXEC  g.extension  extension=r.stream.distance
$GRASSEXEC  g.extension  extension=r.stream.order
$GRASSEXEC  g.extension  extension=r.stream.snap
$GRASSEXEC  g.extension  extension=r.stream.basins

GNU parallel

GNU parallel is a shell tool for executing jobs in parallel on multiple cores. For a faster processing, some of the hydrographr functions such as snap_to_subc_segment() and extract_zonal_stat() have GNU parallel implemented. For more information check the GNU parallel website.

# Download the latest version of GNU parallel 
wget http://ftp.gnu.org/gnu/parallel/parallel-latest.tar.bz2

# Unzip the the .tar file and create a new folder parallel-yyyymmdd
sudo tar xjf parallel-latest.tar.bz2
# Check folders and files in the directory and see the date of 
# latest version e.g. parallel-20221122
ls
# Move to the new created folder parallel-yyyymmdd
cd parallel-20221122

sudo ./configure && make
sudo make install
parallel --citation

#> Academic tradition requires you to cite works you base your article on.
#> If you use programs that use GNU Parallel to process data for an article in a
#> scientific publication, please cite:
#> 
#> @software{tange_2022_7347980,
#>       author       = {Tange, Ole},
#>       title        = {GNU Parallel 20221122 ('Херсо́н')},
#>       month        = Nov,
#>       year         = 2022,
#>       note         = {{GNU Parallel is a general parallelizer to run
#>                        multiple serial command line programs in parallel
#>                        without changing them.}},
#>       publisher    = {Zenodo},
#>       doi          = {10.5281/zenodo.7347980},
#>       url          = {https://doi.org/10.5281/zenodo.7347980}
#> }

#> (Feel free to use \nocite{tange_2022_7347980})

#> This helps funding further development; AND IT WON'T COST YOU A CENT.
#> If you pay 10000 EUR you should feel free to use GNU Parallel without citing.

#> More about funding GNU Parallel and the citation notice:
#> https://lists.gnu.org/archive/html/parallel/2013-11/msg00006.html
#> https://www.gnu.org/software/parallel/parallel_design.html#citation-notice
#> https://git.savannah.gnu.org/cgit/parallel.git/tree/doc/citation-notice-faq.txt

#> If you send a copy of your published article to tange@gnu.org, it will be
#> mentioned in the release notes of next version of GNU Parallel.
#> 
#> Type: 'will cite' and press enter.

will cite

#> Thank you for your support: You are the reason why there is funding to
#> continue maintaining GNU Parallel. On behalf of future versions of
#> GNU Parallel, which would not exist without your support:

#>  THANK YOU SO MUCH

#> It is really appreciated. The citation notice is now silenced.

Now type ctrl+z to exit the GNU parallel environment.

GNU bc

GNU bc (Basic Calculator) is an arbitrary precision numeric processing language, which is used in the function snap_to_subc_segment(). For more information check the GNU bc website.

# Install bc
sudo apt install bc

We recommend to reboot your computer after the installation.