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quinlan-lab / STRling

Detect novel (and reference) STR expansions from short-read data
MIT License
61 stars 9 forks source link

Binary build error #101

Closed hdashnow closed 2 years ago

hdashnow commented 2 years ago

@brentp I'm having some trouble compiling the binaries. Following these instructions: https://strling.readthedocs.io/en/latest/contribute.html

stack trace: (most recent call last)
argparse.nim(881, 23)    tmpmkParser
argparse.nim(724, 31)    mkParser
argparse.nim(587, 36)    genParseProcs
macrohelp.nim(60, 8)     parentOf
/scratch/ucgd/lustre-work/quinlan/u6026198/git/STRling/src/strpkg/genome_strs.nim(172, 20) template/generic instantiation of `newParser` from here
/uufs/chpc.utah.edu/common/HIPAA/u6026198/.nimble/pkgs/argparse-0.7.1/argparse/macrohelp.nim(60, 8) Error: node not found: EXTRA
error compiling code
brentp commented 2 years ago

Hi, I get a successful compile for 06c0820 with:

singularity run --bind $(pwd):/load --bind /home  'docker://brentp/musl-hts-nim:v0.3.17' /usr/local/bin/nsb -n strling.nimble -s src/strling.nim -- -d:danger -d:release -d:debug

which is what's shown in that page (adjusted for my own paths). But, as a side node: adding -d:debug removes the effects of -d:danger and -d:release. Can you show the full command that you are running?

brentp commented 2 years ago

On 2nd look, maybe your $HOME nim stuff on the host is still getting into the container. You can try adding, e.g.:

singularity run --home /tmp/fake-home/ ...

to see if that helps. Also see --no-home option to singularity run.

hdashnow commented 2 years ago

Thanks @brentp, got it working!