pgx-main from prod added

pgx-main/README.md

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+## Set up PGx server
+
+### Install python 3.8 (incl.pandas), docker, aws, java, samtools
+
+### Clone this and additional repos
+```bash
+git clone git@bitbucket.org:quantgene/pgx-engine-wrapper.git
+git clone git@bitbucket.org:quantgene/pgx-engine.git
+git clone https://github.com/SBIMB/StellarPGx.git pgx-main
+```
+
+### Prepare main directory
+```bash
+cp -r pgx-engine-wrapper/* pgx-main/
+mv pgx-main/test3.bed pgx-main/resources/cyp2d6/cyp_hg38/test3.bed
+mkdir pgx-main/pgx_results
+rm pgx-main/data/*
+```
+
+### Place fasta files into pgx-main directory
+(`hg38.fa`, `hg38.fa.fai`). For example:
+```bash
+scp root@139.162.190.87:~/ajit/resources/hg38\* pgx-main/
+```
+
+### Install nexflow
+
+```bash
+curl -fsSL get.nextflow.io | bash
+```
+
+Move the `nextflow` launcher (installed in your current directory) to a directory in your `$PATH` e.g. `/bin`
+
+```bash
+mv nextflow /bin
+```
+
+(The full Nextflow documentation can be found [here](https://www.nextflow.io))
+
+
+### Docker: StellarPGx
+```bash
+docker pull twesigomwedavid/stellarpgx-dev:latest
+```
+
+### Docker: PGx Engine
+```bash
+cd pgx-engine
+docker build -t pgx .
+docker run -d -p 5000:5000 --name pgx-api pgx
+docker stop pgx-api
+cd ..
+```
+
+## Run Entire PGx Pipeline
+
+Change directory: `cd pgx-main`
+
+The main script to run is: `get_pgx_result.sh`.
+The input can be either a text file or standard input: each line should contain an s3 path to a vcf file. The location of the corresponding bam file is inferred.
+The output folders will all be in `pgx_results/`. A diplotype/rsid overview is given in `pgx_diplotypes_rsids.tsv`.
+The `output.json` for each sample is stored in the same s3 location as the vcf with the filename `<sample.json>`.
+The entire pgx output for a sample is uploaded to s3 in the same location as the bam file with the name `<sample>_pgx_result.tar.gz`.