env

#!/bin/bash

[ -f "$PWD/.env.local" ] && source "$PWD/.env.local"

# pick up all the things in bin/
export MAFFT_BINARIES="$PWD/bin"

export WORKDIR=${WORKDIR:=/fs/project/PAS1604/pipeline/dev}

# genback data
export PHYLOGATR_GENBANK_DIR="${PHYLOGATR_GENBANK_DIR:=/fs/project/PAS1604/genbank}"

# gbif
export PHYLOGATR_GBIF_ID="${GBIF_ID:=0147211-200613084148143}"
export PHYLOGATR_GBIF_DIR="${PHYLOGATR_GBIF_DIR:=.}"
_PHYLOGATR_GBIF_RAW="$PHYLOGATR_GBIF_DIR/occurrence.txt"
export PHYLOGATR_GBIF_RAW="${PHYLOGATR_GBIF_RAW:=$_PHYLOGATR_GBIF_RAW}"
export PHYLOGATR_GBIF_FILTERED="${PHYLOGATR_GBIF_FILTERED:=$PHYLOGATR_GBIF_RAW.filtered}"
export PHYLOGATR_GBIF_EXPANDED="${PHYLOGATR_GBIF_EXPANDED:=$PHYLOGATR_GBIF_FILTERED.expanded}"

# bold data
export PHYLOGATR_BOLD_DIR="${PHYLOGATR_BOLD_DIR:=/fs/project/PAS1604/bold}"

# other stuff
export PHYLOGATR_METRIC_FILE="${PHYLOGATR_METRIC_FILE:=$WORKDIR/metrics.yml}"
export PHYLOGATR_RUBY_VERSION="${PHYLOGATR_RUBY_VERSION:=2.5}"
export PHYLOGATR_ENV="${PHYLOGATR_ENV:=development}"