This is a collection of READMEs generated during installation of software applications on Uppmax clusters. It is incomplete in terms of modules available on Uppmax, and the individual READMEs may also be incomplete in terms of what was actually done to install the modules. We are publicising these in the hopes that they can be helpful.

1. Clone the install methods git repo (git clone https://github.com/UPPMAX/install-methods.git)
2. Add the repo to your $PATH and source the uppmax_functions.sh file to get access to the functions.
3. Run run_makeroom with at least -t and -v, to generate a .sh (makeroom_toolname_version.sh) file that will create the directory structure needed in /sw
4. Run the .sh file created in the directory you are standing to create the directory structure (/sw/category/toolname/ and /sw/mf/common/category) and template files.
5. Put the source code for the program in /sw/category/toolname/version/src
6. Compile and/or install the tool in /sw/category/toolname/version/cluster/bin etc.
7. Edit the readme file, explaining how you did the installation, in /sw/category/toolname/toolname-version_install-README.md
8. Edit the template module file /sw/category/toolname/mf/version to do what you want when the module loads.
9. Copy the module file to the live location, /sw/mf/common/category/[section]/toolname
10. Run all_mflink toolname version to create links for all clusters to the module file in /sw/mf/common/category/[section]/toolname
11. Run fixup /sw/category/toolname/version /sw/mf/common/category/[section]/toolname to make sure the ownership and permissions are ok.

gather-READMEs.sh - bash script to scan installation directories, looking for README files having a particular filename format that we create during installation of tools

fixup - bash script fixing up permissions and group membership within installation trees; our local installation group is sw. With the -g option, this script will chmod g+s directories in the tree, too.

uppmax-functions.sh - bash helper functions for SLURM job viewing and various module-related tasks, mostly to do with setting up mf files for loading modules; the latter require appexpert privileges. Source these from .bashrc.

The directories contain software installations in major subject areas.

General applications.

Bioinformatics applications.

Libraries.

Compilers, interpreters, build tools.

These directories cover installations of databases updated either manually, or via update scripts.

Installation instructions for databases under /sw/data/uppnex/. Database directories containing *-install-README.md files are updated manually. Database directories containing *-db-README.md files and scripts (currently, Kraken, diamond_databases and RTG) are updated monthly via crontab entries.

Blast database updates are included here, and involve multiple scripts, crontab entries and a test directory. These are updated monthly via crontab entries.

Installation instructions for databases under other locations, currently just BUSCO lineage sets, which are kept in the module installation directory. These are updated monthly via crontab entries.