Running Icarust on singularity issue (`could not read config.ini`)

[lborcard]

Dear Team,

I am trying to run icarust in a singularity image from the pulled docker image but I am encountering an issue with the config.ini files that is not found :

singularity exec -B ./configs/:/configs -B ./squiggle_arrs/:/squiggle_arrs -B ./output/:/tmp --network-args "portmap=10000:10001/tcp" icarust_latest.sif icarust -s /configs/config_dnar10_barcoded.toml -vv

Error: "couldn't read config.ini: No such file or directory (os error 2)"

I mount the config file properly and they are present in the image in /configs/

best,

Loïc

[Adoni5]

Hi Loïc,

Can you try, passing icarust -c /configs/config.ini -s /configs/config_dnar10_barcoded.toml -vv?

[lborcard]

This is what I am getting

[2024-06-20T15:45:05Z INFO icarust::impl_services::data: 307 ] Fetching barcode squiggle for barcode Barcode01 at static/barcode_squiggle/Barcode01_1_R10.squiggle.npy
thread 'main' panicked at src/impl_services/data.rs:288:77:
called `Result::unwrap()` on an `Err` value: Io(Os { code: 2, kind: NotFound, message: "No such file or directory" })
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

[lborcard]

when I run ls /configs/config.ini it can be found, I tried chmod the folder containing it but it did not help

[lborcard]

closing it since I can use the docker version

[Adoni5]

Hi @lborcard - please reopen this if you have any issues using the docker version!

[lborcard]

I finally decided to use the version from the github and not a container version. Thank you for the message!