Merge pull request #281 from ResearchComputing/alphfold_layla

Alphfold layla

docs/index.rst

@@ -159,6 +159,7 @@ Use of University of Colorado Research Computing resources, including (but not l
    software/GNUParallel
    software/vasp
    software/Containerizationon
+   software/alphafold
    software/spack
 
 .. toctree::

docs/software/alphafold.md

@@ -0,0 +1,79 @@
+# AlphaFold
+
+## AlphaFold Overview
+AlphaFold is a program to
+It is currently available as module on CURC Alpine. Please contact <rc-help@colorado.edu> if you would like to run AlphaFold on Blanca.
+
+## Running AlphaFold
+
+Load the default AlphaFold module:
+```
+module load alphafold
+```
+
+View run options:
+```
+run_alphafold
+```
+
+### AlphaFold Module
+
+Loading the AlphaFold module does the following:
+
+- redirects temporary files from `/tmp` to `/scratch/alpine/$USER`
+    - you can override this path by resetting TMPDIR *after* you load the module:
+        ```
+        module load alphafold
+        export TMPDIR=<path/of/your/choosing>
+        ```
+- activates the AlphaFold conda environment
+
+- sets `CURC_AF_DBS` and `CURC_AF_EXAMPLES` environment variables (see 'AlphaFold Databases' and 'AlphaFold Examples' sections, below`)
+
+- creates a shortcut to the AlphaFold script so you can run the program with `run_alphafold`
+
+
+### AlphaFold Databases
+The AlphaFold databases are located in `/gpfs/alpine1/datasets/bioinformatics/alphafold`. Note that this directory is not visible from a login node. Loading the AlphaFold module stores this path in `CURC_AF_DBS`.
+
+### AlphaFold Examples
+Several example fasta files are located in `/curc/sw/install/bio/alphafold/examples`. Loading the AlphaFold module stores this path in `CURC_AF_EXAMPLES`:
+
+```
+ls $CURC_AF_EXAMPLES
+dummy.fasta  multimer.fa  rcsb_pdb_7DDD.fasta  T1050.fasta
+```
+
+### Example Job Script
+
+This example job script below is saved in `/curc/sw/install/bio/alphafold/2.3.1`. You can copy it to any space you have write permissions and make the desired changes:
+```bash
+cd /projects/$USER
+cp /curc/sw/install/bio/alphafold/2.3.1/alphafold_alpine.sh .
+```
+
+``` bash
+#!/bin/bash
+
+#SBATCH --nodes=1
+#SBATCH --time=06:00:00
+#SBATCH --partition=aa100
+#SBATCH --qos=normal
+#SBATCH --gres=gpu:1
+#SBATCH --job-name=multimer_test
+#SBATCH --output=multimer_test_%j.out
+#SBATCH --ntasks=40
+#SBATCH --mail-type=ALL
+#SBATCH --mail-user=<your email address>
+
+module purge
+module load alphafold
+
+#change directory
+cd /projects/$USER
+
+#run AlphaFold
+run_alphafold -d $CURC_AF_DBS -o . -f $CURC_AF_EXAMPLES/dummy.fasta -t 2020-05-14 -m "monomer" -g true
+```
+### Using Precomputed MSA Option
+`-p true`