chore: use system rocksdb libs, if available

.cargo/config.toml

@@ -1,3 +1,7 @@
 [target.thumbv7em-none-eabi]
 linker = "utils/alpine-linker-script.sh"
 #ar = "arm-none-eabi-ar"
+
+[env]
+ROCKSDB_LIB_DIR = "/usr/lib/"
+SNAPPY_LIB_DIR = "/usr/lib/"

README.md

@@ -39,6 +39,41 @@ The supported set slightly differs between import for GRCh37 and GRCh38.
 - gnomAD v3.1 mtDNA [`gnomad.genomes.v3.1.sites.chrM.vcf.bgz`](https://gnomad.broadinstitute.org/downloads#v3-mitochondrial-dna)
 - HelixMTdb `HelixMTdb_20200327.tsv`
 
+## Building from scratch
+To reduce compile times, we recommend using a pre-built version of `rocksdb`, either from the system package manager or e.g. via `conda`:
+
+```bash
+# Ubuntu
+sudo apt-get install librocksdb-dev
+
+# Conda
+conda install -c conda-forge rocksdb
+```
+
+In either case, either add
+```toml
+[env]
+ROCKSDB_LIB_DIR = "/usr/lib/" # in case of the system package manager, adjust the path accordingly for conda
+SNAPPY_LIB_DIR = "/usr/lib/"  # same as above
+```
+to `.cargo/config.toml` or set the environment variables `ROCKSDB_LIB_DIR` and `SNAPPY_LIB_DIR` to the appropriate paths:
+
+```bash
+export ROCKSDB_LIB_DIR=/usr/lib/
+export SNAPPY_LIB_DIR=/usr/lib/
+```
+
+By default, the environment variables are defined in the `.cargo/config.toml` as described above, i.e. may need adjustments if not using the system package manager.
+
+To build the project, run:
+```bash
+cargo build --release
+```
+
+To install the project locally, run:
+```bash
+cargo install --path .
+```
 ## Internal Notes
 
 ```

utils/docker/Dockerfile

@@ -4,63 +4,51 @@
 # mehari right now as both CLI and lib; we would have to use features to
 # untable the two.
 
-# Based on https://levelup.gitconnected.com/1940db638a6c
-#
 # We don't do cross compilation at the moment but build the dependencies first
 # anyway to get the ability to increment.
 
 # ---------------------------------------------------------------------------
 # Builder
 # ---------------------------------------------------------------------------
 
-# Pinning Rust version for now because of this issue:
-#
-# - https://github.com/rust-lang/rust/issues/95926
-FROM rust:1-bookworm AS builder
+# Use ubuntu:noble as the base image
+FROM ubuntu:noble AS builder
 
-# Build dependencies first.
-#
-# Install dependencies for compilation of C code (e.g., rocksdb).
+# Install Rust toolchain and dependencies for compilation of C code (e.g., rocksdb)
 RUN apt-get update && \
-    apt-get install -y clang
-# Add the needed Cargo components.
-RUN rustup component add rustfmt
+    apt-get install -y unzip wget curl build-essential clang librocksdb-dev libsqlite3-dev && \
+    curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh -s -- -y && \
+    . $HOME/.cargo/env && \
+    rustup component add rustfmt
+
 # Install build dependency `protoc`.
 COPY utils/install-protoc.sh /tmp
 RUN PREFIX=/usr/local bash /tmp/install-protoc.sh
 
-#### Now for the two-step building.
-####
-#### Set initial workdir.
-###WORKDIR /usr/src
-#### Create blank project.
-###RUN USER=root cargo new mehari
-#### We want dependencies cached, so copy those first.
-###COPY Cargo.toml Cargo.lock /usr/src/mehari/
 # Set the working directory.
 WORKDIR /usr/src/mehari
-#### This is a dummy build to get the dependencies cached.
-###RUN cargo build --release
-#
-# Now copy in the rest of the sources.
+
+# Copy in the rest of the sources.
 COPY build.rs Cargo.toml Cargo.lock /usr/src/mehari/
 COPY src /usr/src/mehari/src/
 COPY protos /usr/src/mehari/protos/
 COPY utils/alpine-linker-script.sh /usr/src/mehari/utils/
 RUN chmod a+rx /usr/src/mehari/utils/alpine-linker-script.sh
 COPY .cargo /usr/src/mehari/.cargo/
-## Touch main.rs to prevent cached release build.
+
+# Touch main.rs to prevent cached release build.
 RUN touch /usr/src/mehari/src/main.rs
-# This is the actual application build.
-RUN cargo build --release
+
+# Build the application
+RUN /root/.cargo/bin/cargo build --release
 
 # ---------------------------------------------------------------------------
 # Runtime
 # ---------------------------------------------------------------------------
 
-FROM debian:bookworm-slim AS runtime
+FROM ubuntu:noble AS runtime
 
-# Install dependencies (and cleanup afterwards)
+# Install dependencies (and cleanup afterward)
 RUN apt-get update && \
     apt-get install -y libsqlite3-0 && \
     apt-get clean autoclean && \
@@ -78,5 +66,6 @@ RUN chmod a+rx /entrypoint.sh
 
 # Set the entrypoint.
 ENTRYPOINT ["/bin/bash", "/entrypoint.sh"]
-# Set port to expose
+
+# Expose the application port
 EXPOSE 8080