Another cool feature to demo to Ridha

README.md

@@ -28,3 +28,7 @@ You can serve the documentation locally by running:
     mkdocs serve
 
 Once the environment is created and dependencies installed, you only need to activate it in the future.
+
+## Resources
+
+- `mkdocs` docs: https://www.mkdocs.org/

docs/franklin/software/alphafold.md

@@ -0,0 +1,35 @@
+# :material-molecule: :material-dna: Alphafold
+
+Franklin has a deployment of deepmind's [alphafold](https://github.com/google-deepmind/alphafold) as well as its databases compiled from source[^1].
+The databases are located at `/share/databases/alphafold`; this directory is exported as `$ALPHAFOLD_DB_ROOT` when the module is loaded.
+
+This is _not_ a docker deployment.
+As such, many of the examples provided online need to be slightly modified.
+The main script supplied by the alphafold package is `run_alphafold.py`, which is the script that the docker container calls internally.
+All the same command line arguments that can be passed to alphafold's `run_docker.py` script can be passed to `run_alphafold.py`, but the latter requires all the database locations be supplied:
+
+```bash
+run_alphafold.py \
+--data_dir="$ALPHAFOLD_DB_ROOT" \
+--uniref90_database_path=$ALPHAFOLD_DB_ROOT/uniref90/uniref90.fasta \
+--mgnify_database_path=$ALPHAFOLD_DB_ROOT/mgnify/mgy_clusters_2022_05.fa \
+--template_mmcif_dir=$ALPHAFOLD_DB_ROOT/pdb_mmcif/mmcif_files \
+--obsolete_pdbs_path=$ALPHAFOLD_DB_ROOT/pdb_mmcif/obsolete.dat \
+--bfd_database_path=$ALPHAFOLD_DB_ROOT/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt \
+--uniref30_database_path=$ALPHAFOLD_DB_ROOT/uniref30/UniRef30_2021_03 \
+--pdb70_database_path=$ALPHAFOLD_DB_ROOT/pdb70/pdb70 \
+[OTHER ARGS]
+```
+
+Because this is annoying, we have supplied a wrapper script named `alphafold-wrapped` with our module that passes these common options for you.
+Any of the arguments not passed above will be passed along to the `run_alphafold.py` script; for example:
+
+```bash
+alphafold-wrapped \
+--output_dir=[OUTPUTS] \
+--fasta_paths=[FASTA INPUTS] \
+--max_template_date=2021-11-01 \
+--use_gpu_relax=true
+```
+
+[^1]: Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., … Hassabis, D. (2021). Highly accurate protein structure prediction with AlphaFold. Springer Science and Business Media LLC. [https://doi.org/10.1038/s41586-021-03819-2](https://doi.org/10.1038/s41586-021-03819-2)

docs/franklin/storage.md

@@ -9,4 +9,4 @@ Research data should be stored on lab storage allocations.
 These allocations are mounted at `/group/[PI_GROUP_NAME]`. N
 ote that these directories are mounted as-needed, so your particular allocation might not show up when you run `ls /group`; you will need to access the path directly.
 You can find your PI group name by running `groups`: this will output your user name and a name ending in `grp`.
-The latter corresponds to the directory name under `/group`, unless otherwise requested by your PI.
+The latter corresponds to the directory name under `/group`, unless otherwise requested by your PI.

mkdocs.yml

@@ -1,7 +1,7 @@
 site_name: HPC Core Facility Cluster Documentation
 site_url: http://docs.hpc.ucdavis.edu
 repo_url: https://github.com/ucdavis/hpccf-docs
-copyright: Copyright © 2023 The Regents of the University of California, Davis
+copyright: Copyright © 2023-24 The Regents of the University of California, Davis
 
 nav:
   - About: index.md
@@ -33,6 +33,7 @@ nav:
       - Software:
         - Modules: franklin/software/modules.md
         - cryo-EM: franklin/software/cryoem.md
+        - alphafold: franklin/software/alphafold.md
       - Job Scheduling: franklin/scheduling.md
       - Resources: franklin/resources.md
       - Storage: farm/storage.md
@@ -45,6 +46,7 @@ markdown_extensions:
   - attr_list
   - admonition
   - md_in_html
+  - footnotes
   - pymdownx.arithmatex:
       generic: true
   - pymdownx.details