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Adding and updating dependencies

Adding new operating system packages

Update 'Install operating system packages' in docs/user/install.md:

  • Add an entry for the package to the 'Package Links' table.
  • Add commands to the 'Install on Ubuntu' and 'Install on CentOS' subsections.
  • Add commands to the 'Check packages have installed' subsection.

Add commands to "quick install scripts" (see current content of scripts for what is expected):

  • bash/install-ubuntu.sh
  • bash/install-centos.sh
  • bash/environment-tables.sh, add commands to capture versions of any command-line tools and echo these in a tabular format.

Follow Updating Dependencies overview tables.

Consider, and discuss with the team, the implications of these changes on Related riboviz repositories.

Adding tools not available as operating system packages

Update 'Install tools not available as operating system packages' in docs/user/install.md:

  • Add an entry for the package to the 'Package Links' table.
  • Add a new subsection describing how to download, build, configure, install and check the package.
  • If the new tool needs the PATH configured or other environment variables set, then update commands in setenv.sh in 'Create setenv.sh to configure paths'.

Add commands to "quick install scripts" (see current content of scripts for what is expected):

  • bash/install-tools.sh, also update commands to create setenv.sh, if applicable.
  • bash/environment-tables.sh, add commands to capture versions of any command-line tools and echo these in a tabular format.

Follow Updating Dependencies overview tables.

Consider, and discuss with the team, the implications of these changes on Related riboviz repositories.

Adding Python packages

Update 'Install Python packages' in docs/user/install.md or docs/developer/install.md (depending on whether the package is for all users or for developers only):

  • Add an entry for the package to the 'Package Links' table.
  • Add commands to the 'Install' commands.
  • For user-specific packages, add commands to the 'Check packages have installed command-line tools' commands, if applicable.

Add commands to "quick install scripts" (see current content of scripts for what is expected):

  • bash/install-py.sh
  • bash/environment-tables.sh, add conda package names to CONDA_LIST or pip package names to PIP_LIST.

Follow Updating Dependencies overview tables.

Consider, and discuss with the team, the implications of these changes on Related riboviz repositories.

Adding R packages

Update 'Install R and packages required by R packages to be installed' in docs/user/install.md:

  • Add commands to install any operating system packages to 'Install on Ubuntu' and 'Install on CentOS' subsections.

Update 'Install R packages' in docs/user/install.md or docs/developer/install.md (depending on whether the package is for all users or for developers only):

  • Add an entry for the package to the 'Package Links' table.
  • Add commands to the 'Install in R' commands.
  • For Bioconductor sub-packages, add commands to the 'For example, for R 3.5 or R 3.6, install in R' and 'For example, for R 3.4, install in R' commands.

Add commands to "quick install scripts" (see current content of scripts for what is expected):

  • bash/install-r-ubuntu.sh, commands to install Ubuntu packages.
  • bash/install-r-centos.sh, commands to install CentOS packages.
  • bash/install-r.R, commands to install R packages.
  • bash/install-r-3.4-bioconductor.R, commands to install Bioconductor sub-packages under R 3.4.
  • bash/install-r-3.5-bioconductor.R, commands to install Bioconductor sub-packages under R 3.5+.
  • bash/environment-tables.sh, add package names R_LIST.

Follow Updating Dependencies overview tables.

Consider, and discuss with the team, the implications of these changes on Related riboviz repositories.

Updating existing dependencies

Run through the section corresponding to the nature of the dependency being updated and make any required updates to documentation and scripts:

Follow Updating Dependencies overview tables.

Consider, and discuss with the team, the implications of these changes on Related riboviz repositories.

Updating Dependencies overview tables

To update the 'Dependencies overview' tables in docs/user/install.md:

  • Run:
$ source bash/environment-tables.sh
  • Copy the Markdown tables that are output and paste into docs/user/install.md.

Consider also the implications on Related riboviz repositories.