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cschin / Peregrine

Peregrine: Fast Genome Assembler Using SHIMMER Index
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docker errors #3

Closed bitcometz closed 5 years ago

bitcometz commented 5 years ago

Hello，

I docker run -i -t cschin/peregrine '/bin/bash' and met this errors: /opt/entry.sh: line 4: pg_run.py: command not found

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cschin commented 5 years ago

@bitcometz the DockerHub build system or my build script for it might have some issue. Try this build docker run -i -t cschin/peregrine:0.1.5.2 '/bin/bash'. (The latest will reserved for development, using a tagged version is better.)

a-khalak commented 5 years ago

@bitcometz @cschin The container is currently configured to launch pg_run.py based on the Dockerfile. Therefore, you can't launch a bash shell into the container to poke around until it is already running an assembly.

cschin commented 5 years ago

@sifta Thanks. I saw similar thing before. I think the DockerHub auto-build set-up has some issue now. I had to push the tagged build to override the DockerHub once before. I like to investigate what is going some time later.

cschin commented 5 years ago

@sifta I think the last commit fixed the real problem. I am closing this issue now.

@bitcometz as mentioned by @sifta the default "entrypoint" for the docker image is to run pg_run.py. This the canonical way to launch the assembler:

find /wd/chm13-fastq/ -name "*.fastq" | sort > chm13-seqdata.lst 

docker run -it -v /wd:/wd --user $(id -u):$(id -g) cschin/peregrine:0.1.5.0 asm \
    /wd/chm13-seqdata.lst 24 24 24 24 24 24 24 24 24 \ 
    --with-consensus --shimmer-r 3 --best_n_ovlp 8 \ 
    --output /wd/chm13-asm-r3-pg0.1.5.0

Please read the README to adjust the concurrence setup for your computing node. Depending on the amount of memory and CPUs that you have, you will need to adjust those for the optimized performance.