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# Guix Rust Bootstrap
To develop code against rust you often need a recent edition of rust. With Guix this is possible because you don't depend on the underlying linux distribution to provide recent versions of glibc and other libraries. Here we have a recipe that should work anywhere on Linux.
I succeeded in running the latest Rust on Octopus and building packages with guix.
To make it work the following steps are required:
* Update guix with guix-pull if your guix is older than 3 months
* Unset GUIX_PROFILE on some systems
* Set your updated guix profile vars
* Create a container that has all dependencies for rust itself
* Run rustup
* Run cargo with LD_LIBRARY_PATH set to $GUIX_ENVIRONMENT/lib
# Get Guix updated
Important is to have a recent version of Guix. This is achieved with 'guix pull' and making sure it works.
```sh
mkdir -p ~/opt
guix pull -p ~/opt/guix-pull --url=https://codeberg.org/guix/guix
```
it takes a few minutes. Next set the environment
```sh
unset GUIX_PROFILE
. ~/opt/guix-pull/etc/profile
```
This will point the path to a recent guix. You can make sure with
```
guix describe
guix 772c456
repository URL: https://codeberg.org/guix/guix
branch: master
commit: 772c456717e755829397a6ff6dba4c1e135426d8
```
which can be validated against the Guix tree. Running
```sh
guix package -A rust
rust 1.85.1 rust-src,tools,out,cargo gnu/packages/rust.scm:1454:4
```
shows the current *stable* version in Guix. Now, of course, we want something more to get rust latest.
# Update Rust and Cargo to latest (stable)
The trick is to set up a container with Rust in your git working directory:
```
mkdir -p ~/.cargo ~/.rustup # to prevent rebuilds
guix shell --share=$HOME/.cargo --share=$HOME/.rustup -C -N -D -F -v 3 guix gcc-toolchain make libdeflate pkg-config xz coreutils sed zstd zlib nss-certs openssl curl
curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs | sh
. ~/.cargo/env
rustup default stable
```
Now rustc shows it is recent:
```
rustc --version
rustc 1.90.0 (1159e78c4 2025-09-14)
```
Next run 'cargo build' with:
```
env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib cargo build
Compiling libagc-sys v0.1.0 (/home/wrk/iwrk/opensource/code/pangenome/libagc-sys)
Finished 'dev' profile [unoptimized + debuginfo] target(s) in 0.06s
$ ./target/debug/libagc-sys
./target/debug/libagc-sys: error while loading shared libraries: libgcc_s.so.1: cannot open shared object file: No such file or directory
$ env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./target/debug/libagc-sys
Hello, world!
```
and your source should build and run. Note the libgcc_s.so.1 error.
## What if you get a libgcc or librt error?
The problem is that cargo picks up the wrong libgcc:
```
$ ls /gnu/store/*/lib/libgcc_s.so.1
/gnu/store/m2vhzr0dy352cn59sgcklcaykprrr4j6-gcc-14.3.0-lib/lib/libgcc_s.so.1
/gnu/store/rbs3nrx9z6sfawn3fa8r8z1kffdbnk8q-gcc-toolchain-15.2.0/lib/libgcc_s.so.1
/gnu/store/v3bq3shn333kh7m6gj3r58l0v7mkn4in-profile/lib/libgcc_s.so.1
/gnu/store/xm7i1gvi0i9pyndlkv627r08rsw1ny96-gcc-15.2.0-lib/lib/libgcc_s.so.1
```
This is because Guix itself builds on an older libgcc and librt. You need to tell it explicitly what library to load that built your cargo:
```
ldd ~/.cargo/bin/cargo
linux-vdso.so.1 (0x00007ffd409b2000)
libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007fd2cf433000)
librt.so.1 => /lib/librt.so.1 (0x00007fd2cf42e000)
```
in the container:
```
ls -l /lib/libgcc_s.so.1
lrwxrwxrwx 1 65534 overflow 82 Jan 1 1970 /lib/libgcc_s.so.1 -> /gnu/store/rbs3nrx9z6sfawn3fa8r8z1kffdbnk8q-gcc-toolchain-15.2.0/lib/libgcc_s.so.1
```
which happens to be the one in $GUIX_ENVIRONMENT/lib! So setting the library path solves it.
The reason that we don't get the automatically resolving libraries that you normally have in guix is that we have updated rust by *hand* using rustup. Guix has no control over this process.
# spoa-rs on octopus01
I just did above to build spoa-rs. Only had to add cmake to the shell packages.
# sweepga on octopus01
I just built sweepga. Only had the add clang to the shell:
```sh
guix shell --share=$HOME/.cargo --share=$HOME/.rustup -C -N -D -F -v 3 guix gcc-toolchain make libdeflate pkg-config xz coreutils sed zstd zlib nss-certs openssl curl zlib cmake clang
. ~/.cargo/env
env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib cargo build
env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib ./target/debug/sweepga
[sweepga::start::0.000*1.00] 2025-10-11 15:27:28 | ./target/debug/sweepga
[sweepga::detect::0.000*1.00] Using .1aln workflow (FastGA native format)
[sweepga] ERROR: No valid input provided
```
To run on the cluster you likely don't want to use the container. Make a note of GUIX_ENVIRONMENT:
```
echo $GUIX_ENVIRONMENT/
/gnu/store/6khi7iv7l75595hwlfc1nwmdcv72m24s-profile/
```
It has your libs! So, outsite the container you can run
```
export GUIX_ENVIRONMENT=/gnu/store/6khi7iv7l75595hwlfc1nwmdcv72m24s-profile
env LD_LIBRARY_PATH=$GUIX_ENVIRONMENT/lib /home/wrk/tmp/sweepga/target/debug/sweepga
```
# Updating the container
Now your build may fail because you miss a crucial library or tool. This is a feature of guix containers as it makes dependencies explicit.
Just add them to the guix shell command. Let's say we add zlib
```
guix shell --share=$HOME/.cargo --share=$HOME/.rustup -C -N -D -F -v 3 guix gcc-toolchain make libdeflate pkg-config xz coreutils sed zstd zlib nss-certs openssl curl zlib
```
# Troubleshooting
## Collisions
Guix may complain about collisions. These are mostly naming issues:
```
warning: collision encountered:
/gnu/store/nym6kiinrg2mb8z4lwnvfx5my8df9vrs-glibc-for-fhs-2.41/bin/ldd
/gnu/store/rbs3nrx9z6sfawn3fa8r8z1kffdbnk8q-gcc-toolchain-15.2.0/bin/ldd
warning: choosing /gnu/store/nym6kiinrg2mb8z4lwnvfx5my8df9vrs-glibc-for-fhs-2.41/bin/ldd
```
it will like one into your environment. You can still use both tools by using the full path and normally ignore the warning.
|
