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Refgenie bowtie indexes

This repository contains necessary files to build and archive reference genome assets to serve with refgenieserver. The whole process is scripted, starting from this repository. From here, we download the input data (FASTA files), use refgenie build to create all of these assets in a local refgenie instance, and then use refgenieserver archive to build the server archives, and finally serve them with a refgenieserver instance by calling refgenieserver serve.

How to add an asset

  1. Add a line for each genome in genome_descriptions.csv.
  2. Add a line for each asset in assets.csv.
  3. Add any required build inputs (links to files, parameters, etc) to recipe_inputs.csv

Deploying assets onto the server

Setup

In this guide we'll use environment variables to keep track of where stuff goes.

  • BASEDIR points to our parent folder where we'll do all the building/archiving
  • GENOMES points to pipeline output (referenced in the project config)
  • REFGENIE_RAW points to a folder where the downloaded raw files are kept
  • REFGENIE points to the refgenie config file
  • REFGENIE_ARCHIVE points to the location where we'll store the actual archives
export SERVERNAME=btref.databio.org
export BASEDIR=$PROJECT/deploy/$SERVERNAME
export BASEDIR=$HOME/refgenie_test # For local testing

export GENOMES=$BASEDIR/genomes
export REFGENIE_RAW=$BASEDIR/refgenie_$SERVERNAME
export REFGENIE=$BASEDIR/$SERVERNAME/config/refgenie_config.yaml
export REFGENIE_ARCHIVE=$GENOMES/archive
mkdir -p $BASEDIR
cd $BASEDIR

To start, clone this repository:

cp -R $CODE/$SERVERNAME . # For local testing
<!-- git clone git@github.com:refgenie/$SERVERNAME.git -->

Step 1: Download input files

Many of the assets require some input files, and we have to make sure we have those files locally. In the recipe_inputs.csv file, we have entered these files as remote URLs, so the first step is to download them. We have created a subproject called getfiles for this: To programmatically download all the files required by refgenie build, run from this directory using looper:

cd $SERVERNAME
mkdir -p $REFGENIE_RAW
looper run asset_pep/refgenie_build_cfg.yaml -p local --amend getfiles --sel-attr asset --sel-incl fasta

Check the status with looper check --use-pipesat:

--use-pipesat option is required as of early 2021. Might not be required if you're running later on.

looper check asset_pep/refgenie_build_cfg.yaml --amend getfiles --sel-attr asset --sel-incl fasta --use-pipestat

Step 2: Refgenie genome configuration file initialization

This repository comes with a genome configuration file already defined in \config directory, but if you have not initialized refgenie yet or want to start over, then first you can initialize the config like this:

refgenie init -c config/refgenie_config.yaml -f $GENOMES -u http://awspds.refgenie.databio.org/refgenomes.databio.org/ -a $GENOMES/archive -b refgenie_config_archive.yaml

Step 3: Build assets

Once files are present locally, we can run refgenie build on each asset specified in the sample_table (assets.csv). We have to submit fasta assets first:

looper run asset_pep/refgenie_build_cfg.yaml -p bulker_local --sel-attr asset --sel-incl fasta

This will create one job for each asset. Monitor job progress with:

grep CANCELLED ../genomes/submission/*.log
ll ../genomes/submission/*.log
grep error ../genomes/submission/*.log
grep maximum ../genomes/submission/*.log

ll ../genomes/data/*/*/*/_refgenie_build/*.flag
ll ../genomes/data/*/*/*/_refgenie_build/*failed.flag
ll ../genomes/data/*/*/*/_refgenie_build/*completed.flag
ll ../genomes/data/*/*/*/_refgenie_build/*running.flag
ll ../genomes/data/*/*/*/_refgenie_build/*completed.flag | wc -l
cat ../genomes/submission/*.log

To run all the asset types:

looper run asset_pep/refgenie_build_cfg.yaml -p bulker_local

Step 4. Archive assets

Assets are built locally now, but to serve them, we must archive them using refgenieserver. The general command is refgenieserver archive -c <path/to/genomes.yaml>. Since the archive process is generally lengthy, it makes sense to submit this job to a cluster. We can use looper to do that.

To start over completely, remove the archive config file with:

rm config/refgenie_config_archive.yaml

Then submit the archiving jobs with looper run

looper run asset_pep/refgenieserver_archive_cfg.yaml -p bulker_local --sel-attr asset --sel-incl fasta

Check progress with:

ll ../genomes/archive_logs/submission/*.log
grep Wait ../genomes/archive_logs/submission/*.log
grep Error ../genomes/archive_logs/submission/*.log
cat ../genomes/archive_logs/submission/*.log

Step 5. Upload archives to S3

Now the archives should be built, so we'll sync them to AWS. Use the refgenie credentials (here added with --profile refgenie, which should be preconfigured with aws configure)

aws s3 sync $REFGENIE_ARCHIVE s3://awspds.refgenie.databio.org/btref.databio.org/ --profile refgenie

Step 6. Deploy server

Now everything is ready to deploy. If using refgenieserver directly, you'll run refgenieserver serve config/refgenieserver_archive_cfg. We're hosting this repository on AWS and use GitHub Actions to trigger trigger deploy jobs to push the updates to AWS ECS whenever a change is detected in the config file.

ga -A; gcm "Deploy to ECS"; gpoh