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Author: chdominguez

README.md

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+# PredIG Docker and Singularity Documentation
+
+## Overview
+
+PredIG is a tool for protein immunogenicity prediction that can predict from various input formats including UniProt IDs and FASTA sequences.
+
+## Prerequisites
+
+1. Docker/Singularity installed on your system
+2. UniProt database file (uniprot_sprot.fasta)
+3. The PredIG Docker image:
+
+```bash
+docker pull bsceapm/predig:latest
+```
+
+## UniProt Database Setup
+
+1. Download the UniProt database file (uniprot_sprot.fasta) [Download here](https://ftp.ebi.ac.uk/pub/databases/uniprot/knowledgebase/uniprot_sprot.fasta.gz -O uniprot_sprot.fasta.gz)
+2. Place it in a directory that will be mounted to the container
+3. This directory must be bound to `/uniprot` when running the container
+
+## Basic Usage with Docker
+
+The container requires two volume bindings:
+
+- Your working directory to `/predig` (for input/output files)
+- UniProt database directory to `/uniprot`
+
+Basic command structure:
+
+```bash
+docker run -v /path/to/work/dir:/predig -v /path/to/uniprot/dir:/uniprot bsceapm/predig <input_file> --output <output_file> [options]
+```
+
+## Input Modes
+
+### 1. UniProt Mode (Default)
+
+Predict using UniProt.
+Example:
+
+```bash
+docker run -v ./my_data:/predig -v ./uniprot:/uniprot \
+ bsceapm/predig input_proteins.csv --output results.csv
+```
+
+### 2. Recombinant Mode
+
+Precit using recombinant sequences.
+Example:
+
+```bash
+docker run -v ./my_data:/predig -v ./uniprot:/uniprot \
+ bsceapm/predig input_sequences.csv --output results.csv --type recombinant
+```
+
+### 3. FASTA Mode
+
+Predict from FASTA input files. Requires an additional HLA alleles file.
+Example:
+
+```bash
+docker run -v ./my_data:/predig -v ./uniprot:/uniprot \
+ bsceapm/predig sequences.fasta --output results.csv --type fasta --alleles alleles.csv
+```
+
+## Command Arguments
+
+Required:
+
+- Input file: Path to the input file (relative to mounted directory)
+- `--output`: Name of the output file
+
+Optional:
+
+- `--type`: Input file type (uniprot, fasta, or recombinant)
+- `--model`: Prediction model (noncan, neoant, or path)
+- `--alleles`: Path to HLA alleles file (required for FASTA mode)
+- `--alpha`: Alpha parameter value
+- `--precursor-length`: Length of precursor sequence
+
+## Running with Singularity
+
+Singularity can run Docker containers directly, making it easy to use PredIG in HPC environments where Docker might not be available.
+
+### Converting Docker Image to Singularity
+
+1. Pull the Docker image and convert it to Singularity format:
+
+```bash
+singularity pull predig.sif docker://bsceapm/predig:latest
+```
+
+### Basic Usage with Singularity
+
+The command structure is similar to Docker, but uses Singularity bind syntax:
+
+```bash
+singularity run --bind /path/to/work/dir:/predig,/path/to/uniprot/dir:/uniprot \
+    predig.sif <input_file> --output <output_file> [options]
+```
+
+### Singularity Examples
+
+1. UniProt Mode:
+
+```bash
+singularity run --bind ./my_data:/predig,./uniprot:/uniprot \
+    predig.sif input_proteins.csv --output results.csv
+```
+
+2. Recombinant Mode:
+
+```bash
+singularity run --bind ./my_data:/predig,./uniprot:/uniprot \
+    predig.sif input_sequences.csv --output results.csv --type recombinant
+```
+
+3. FASTA Mode:
+
+```bash
+singularity run --bind ./my_data:/predig,./uniprot:/uniprot \
+    predig.sif sequences.fasta --output results.csv --type fasta --alleles alleles.csv
+```
+
+### Singularity Notes
+
+- Multiple bind paths are separated by commas in Singularity
+- The `.sif` file can be placed anywhere and called from any directory
+- All other functionality remains identical to the Docker version
+- File permissions are inherited from your user account, unlike Docker
+
+## Example File Formats
+
+### UniProt Mode Input Example
+
+CSV file with UniProt IDs:
+
+```
+UniProtID
+P01889
+P61769
+```
+
+### Recombinant Mode Input Example
+
+CSV file with protein sequences:
+
+```
+Sequence
+MALTLSFFVVLLLVG
+MLPGLALLLLAAWTARA
+```
+
+### FASTA Mode Input Example
+
+FASTA file (sequences.fasta):
+
+```
+>Protein1
+MALTLSFFVVLLLVG
+>Protein2
+MLPGLALLLLAAWTARA
+```
+
+Alleles file (alleles.csv):
+
+```
+Allele
+HLA-A*02:01
+HLA-B*07:02
+```
+
+## Notes
+
+- All input/output files must be in the directory mounted to `/predig`
+- The UniProt database file must be in the directory mounted to `/uniprot`
+- File paths in commands should be relative to the mounted directories
+- Output files will be created in your mounted working directory