Docker runs example and quits

[scharch]

This is probably a dumb "I don't know how to use Docker" question, but I when try to enter the Docker container, I can't get an interactive session. What am I doing wrong?

schrammca@cogsworth $> docker run -it -v /home/schrammca/2016201_Rv217/20170427/:/data quay.io/matsengrp/linearham

scons: Reading SConscript files ...
Mkdir("output")
scons: done reading SConscript files.
scons: Building targets ...
git rev-parse --verify HEAD >> output/git.log && git describe --dirty >> output/git.log
lib/partis/bin/partis annotate --all-seqs-simultaneous --infname data/liao_dataset.fasta --parameter-dir output/parameter_dir --locus igh --extra-annotation-columns linearham-info --outfname output/partis_run.yaml > output/partis_run.stdout.log
scons: done building targets.
scons: Reading SConscript files ...
scons: done reading SConscript files.
scons: Building targets ...
scripts/parse_cluster.py output/partis_run.yaml --indel-reversed-seqs --fasta-output-file output/cluster-0/cluster_seqs.fasta --yaml-output-file output/cluster-0/cluster.yaml
 only one annotation in partis output file. Using it.
  writing 313 sequences to output/cluster-0/cluster_seqs.fasta
scripts/generate_revbayes_rev_file.py templates/revbayes_template.rev --fasta-path output/cluster-0/cluster_seqs.fasta --mcmc-iter 25 --mcmc-thin 1 --tune-iter 0 --tune-thin 100 --num-rates 4 --seed 0 --output-path output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/revbayes_run.rev
lib/revbayes/projects/cmake/rb output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/revbayes_run.rev > output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/revbayes_run.stdout.log
_build/linearham/linearham --pipeline --yaml-path output/cluster-0/cluster.yaml --cluster-ind 0 --hmm-param-dir output/parameter_dir/hmm/hmms --seed 0 --num-rates 4 --input-path output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/revbayes_run.trees --output-path output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/lh_revbayes_run.trees
Rscript --slave --vanilla scripts/run_bootstrap_asr_ess.R output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/lh_revbayes_run.trees output/cluster-0/cluster_seqs.fasta 0.1 0.05 1 0 output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.trees output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.log output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.ess
scripts/tabulate_naive_probs.py output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.trees --output-base output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/aa_naive_seqs
scripts/tabulate_lineage_probs.py output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.trees output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/aa_naive_seqs.fasta --seed-seq KC576081.1 --pfilters 0.1 --output-base output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/lineage_KC576081.1/aa_lineage_seqs
scripts/write_lh_annotations.py output/cluster-0/cluster.yaml output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_run.log --output-base output/cluster-0/mcmciter25_mcmcthin1_tuneiter0_tunethin100_numrates4_rngseed0/burninfrac0.1_subsampfrac0.05/linearham_annotations
git rev-parse --verify HEAD >> output/git.log && git describe --dirty >> output/git.log
scons: done building targets.

schrammca@cogsworth $> 

[psathyrella]

You should add /bin/bash to the command -- look in the partis install docs for some details

[eharkins]

We should probably have some instructions in the README on how to run with Docker.

The implicit command is to run the linearham test command and then clean up

To run anything else, you just need to specify a command after quay.io/matsengrp/linearham, e.g. /bin/bash as Duncan said:

docker run -it -v /home/schrammca/2016201_Rv217/20170427/:/data quay.io/matsengrp/linearham /bin/bash

[scharch]

Awesome, thanks

[nannabarnkob]

Hi all! As someone who has never used docker before trying to run your image, it would have saved me a few hours if I had known to add bash after (didn't think to look in closed issues for this...) 👍

[psathyrella]

Hi @nannabarnkob sorry about that! But thanks for adding the feedback, we really appreciate it, and we'll use it to update the docs.