Containerization

.gitignore

@@ -7,3 +7,4 @@
 /test
 *test*
 *lock
+*crt

Cargo.toml

@@ -1,8 +1,8 @@
 [workspace]
 
+
 members = [ "all_sample_hamming_dist", "all_sample_nt_diffs",
     "mutations_of_interest_table", "plots", "check_chemistry",
-]
 
 [workspace.dependencies]
 clap = { version = "4", features = ["derive"] }
@@ -11,4 +11,7 @@ either = "1"
 zoe = { version = "0.0.19", default-features = false, features = [
     "multiversion",
 ] }
+
+[profile.release]
+strip = true
 csv = "1.3.1"

Dockerfile

@@ -0,0 +1,61 @@
+# Create an argument to pull a particular version of an image
+
+####################################################################################################
+# BASE IMAGE
+####################################################################################################
+FROM rustlang/rust:nightly-alpine AS builder
+
+
+# Required certs for apk update
+COPY ca.crt /root/ca.crt
+
+# Put certs in /etc/ssl/certs location
+RUN cat /root/ca.crt >> /etc/ssl/certs/ca-certificates.crt
+
+RUN apk update && apk add --no-cache build-base
+
+
+WORKDIR /app
+
+# Copy all scripts to docker images
+COPY . .
+
+# This build step will cache the dependencies
+RUN cargo build --release
+
+
+FROM alpine:latest as deploy
+
+# May only be required for WSL.
+# Required certs for apk update
+COPY ca.crt /root/ca.crt
+
+# Put certs in /etc/ssl/certs location
+RUN cat /root/ca.crt >> /etc/ssl/certs/ca-certificates.crt
+
+# Install system libraries of general use
+RUN apk update && apk add --no-cache \
+    bash \
+    && rm -rf /var/lib/{apt,dpkg,cache,log} \
+    && rm /root/ca.crt
+
+WORKDIR /app
+
+COPY --from=builder \
+    /app/target/release/mutations_of_interest_table \
+    /app/target/release/all_sample_nt_diffs \
+    /app/target/release/all_sample_hamming_dist \
+    /app/target/release/plots \
+    /app/target/release/check_chemistry /app/
+
+# Create working directory variable
+ENV WORKDIR=/data
+
+# Set up volume directory in docker
+VOLUME ${WORKDIR}
+
+# Set up working directory in docker
+WORKDIR ${WORKDIR}    
+
+# Export project directory to PATH
+ENV PATH "$PATH:/app"

docker-compose.yml

@@ -0,0 +1,18 @@
+x-rust-image: &rust-image mira-oxide/rust-nightly
+
+x-data-volume: &data-volume
+  type: bind
+  source: /home/xpa3/mira-oxide/test
+  target: /data
+
+services:
+  mira-oxide:
+    container_name: mira-oxide
+    image: mira-oxide:latest
+    build:
+      context: .
+      dockerfile: Dockerfile
+    restart: always
+    volumes:
+      - *data-volume
+    command: tail -f /dev/null