MAX_HEAP calculation fails if `bc` is not available

GooglingTheCancerGenome / sv-callers

Snakemake-based workflow for detecting structural variants in genomic data

https://research-software.nl/software/sv-callers

Apache License 2.0

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MAX_HEAP calculation fails if `bc` is not available #44

Closed annawoodard closed 4 years ago

annawoodard commented 4 years ago

The gridss rule for me is failing with

Invalid maximum heap size: -Xmx0g

This seems to be because bc is not available in my path. It is available on conda-forge, so could be included in environment.yaml.

arnikz commented 4 years ago

Thanks @annawoodard for reporting this. AFAIK bc is so common in major Linux distros that I didn't think of it as an extra dependency:) Btw. which distro did you use? Currently, it's included in the Docker images used for CI tests (see [1] and [2]), perhaps it should be part of the wf dependencies instead.

annawoodard commented 4 years ago

I agree @arnikz, I was surprised it was missing. I am running on a cluster running Ubuntu 16.04.6 (admittedly a bit long in the tooth, but an LTS release which doesn't reach EOL until 2021).

docker run -it --rm ubuntu:xenial-20200903
root@9399d786521e:/# bc
bash: bc: command not found

arnikz commented 4 years ago

Fixed CI (#46).