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https://github.com/refgenie/plantref

Refgenieserver content repository for plant genomes server
https://github.com/refgenie/plantref

Last synced: about 2 months ago
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Refgenieserver content repository for plant genomes server

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README 

        
# plantref.databio.org server overview



This repository contains the files to build and archive genome assets to serve with [refgenieserver](https://github.com/refgenie/refgenieserver) at http://plantref.databio.org. 



The whole process is scripted, starting from this repository. From here, we do this basic workflow:



1. Download raw input files for assets (FASTA files, GTF files etc.)

2. Build assets with `refgenie build` in a local refgenie instance

3. Archive assets with `refgenieserver archive`

4. Deploy assets to active server on AWS.



# Adding an asset to this server



## Overview of metadata structure



The metadata is located in the [asset_pep](asset_pep) folder, which contains a [PEP](https://pep.databio.org) with metadata for each asset. The contents are:



- `assets.csv` - The primary sample_table. Each each row is an asset. 

- `recipe_inputs.csv` - The subsample_table. This provides a way to define each individual value passed to any of the 3 arguments of the `refgenie build` command: `--assets`, `--params`, and `--files`. 

- `refgenie_build_cfg.yaml` -- config file that defines a subproject (which is used to download the input data) and additional project settings.



## Step 1: Add the asset to the asset table.



To add an asset, you will need to add a row in `assets.csv`. Follow these directions:



- `genome` - the human-readable genome (namespace) you want to serve this asset under

- `asset` - the human-readble asset name you want to serve this asset under. It is identical to the asset recipe. Use `refgenie list` to see [available recipes](http://refgenie.databio.org/en/latest/build/)



Your asset will be retrievable from the server with `refgenie pull {genome}/{asset_name}`.



## Step 2: Add any required inputs to the recipe_inputs table



Next, we need to add the source for each item required by your recipe. You can see what the recipe requires by using `-q` or `--requirements`, like this: `refgenie build {genome}/{recipe} -q`. If your recipe doesn't require any inputs, then you're done. If it requires any inputs (which can be one or more of the following: *assets*, *files*, *parameters*), then you need to specify these in the `recipe_inputs.csv` table.



For each required input, you add a row to `recipe_inputs.csv`. Follow these directions:

- `sample_name` - must match the `genome` and `asset` value in the `assets.csv` file. Format it this way: `-`. This is how we match inputs to assets.



Next you will need to fill in 3 columns:

- `input_type` which is one of the following: *files*, *params* or *assets*

- `intput_id` must match the recipe requirement. Again, use `refgenie build / -q` to learn the ids

- `input_value` value for the input, e.g. URL in case of *files*



## Step 3: See if you did it well!



**Validate the PEP with [`eido`](http://eido.databio.org/en/latest/)**



The command below validates the PEP against a remote schema. Any PEP issues will result in a `ValidationError`:



```

eido validate refgenie_build_cfg.yaml -s http://schema.databio.org/refgenie/refgenie_build.yaml

```



# 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 BASEDIR=$HOME/code/sandbox/refgenie_deploy

#export REFGENIE_RAW=$BASEDIR/refgenie_raw

export SERVERNAME=plantref

export BASEDIR=$PROJECT/deploy/$SERVERNAME

export GENOMES=$BASEDIR/genomes

export REFGENIE_RAW=/project/shefflab/www/refgenie_$SERVERNAME

export REFGENIE=$BASEDIR/$SERVERNAME/config/refgenie_config.yaml

export REFGENIE_ARCHIVE=$GENOMES/archive

mkdir $BASEDIR

cd $BASEDIR

```



To start, clone this repository:



```

git clone [email protected]: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](http://looper.databio.org):



```

cd $SERVERNAME

mkdir -p $REFGENIE_RAW

looper run asset_pep/refgenie_build_cfg.yaml -p local --amend getfiles

```



Check for errors here:

```

grep checksum ../genomes/submission/*.log

```



## Step 2: Build assets



Once files are present locally, we can run `refgenie build` on each asset specified in the sample_table (`assets.csv`). If you have not initialized it, then first you must init the config:



```

refgenie init -c config/refgenie_config.yaml -f $GENOMES -u https://refgenie.s3.amazonaws.com -a $GENOMES/archive -b refgenie_config_archive.yaml

```



We have to submit fasta assets first:



```

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

```



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



```

looper check asset_pep/refgenie_build_cfg.yaml  # TODO: this doesn't work because the pipeline doesn't produce flags...



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_slurm

```



## Step 3. Archive assets



Assets are built locally now, but to serve them, we must archive them using `refgenieserver`. The general command is `refgenieserver archive -c `. Since the archive process is generally lengthy, it makes sense to submit this job to the cluster. We can use looper to that. To start over completely, remove the archive config file with: `rm config/refgenie_config_archive.yaml`



```

looper run asset_pep/refgenieserver_archive_cfg.yaml -p bulker_slurm --sel-attr asset --sel-incl fasta --lumpn 5



```



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

```



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 --profile refgenie

```



## Step 4. 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

```