Running the test profile fails, unable to find docker image

[chasemc]

The versioned docker images for the "mock" test run aren't available on dockerhub so the pipeline fails.

It might be easier to just change the nextflow module for those to take the "latest" docker image so that it doesn't haven't to be synced?

Error executing process > 'AUTOMETA:CREATE_MOCK:GET_GENOMES_FOR_MOCK (fetching 3 genomes)'

Caused by:
  Process `AUTOMETA:CREATE_MOCK:GET_GENOMES_FOR_MOCK (fetching 3 genomes)` terminated with an error exit status (125)

Command executed:

  curl -s https://ftp.ncbi.nlm.nih.gov/genomes/ASSEMBLY_REPORTS/assembly_summary_refseq.txt > assembly_report.txt
  
  grep -E "GCF_000734955.1|GCF_900448115.1|GCF_015751765.1" assembly_report.txt |\
      awk -F '\t' '{print $20}' |\
      sed 's,https://,rsync://,' |\
          xargs -n 1 -I {}                 rsync -am                     --exclude='*_rna_from_genomic.fna.gz'                     --exclude='*_cds_from_genomic.fna.gz'                     --include="*_genomic.fna.gz"                     --include="*_protein.faa.gz"                     --include='*/'                     --exclude='*' {} .
  
  # "clean_mock_data.sh" is here: ~/Autometa/bin/clean_mock_data.sh
  clean_mock_data.sh

Command exit status:
  125

Command output:
  (empty)

Command error:
  Unable to find image 'jasonkwan/autometa-nf-modules-get_genomes_for_mock:2.1.0' locally
  docker: Error response from daemon: manifest for jasonkwan/autometa-nf-modules-get_genomes_for_mock:2.1.0 not found: manifest unknown: manifest unknown.
  See 'docker run --help'.

Work dir:
  /home/chase/work/b4/39a48d8ca92a6c4caa0d90bf851e05

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

It might be easier to just change the nextflow module for those to take the "latest" docker image so that it doesn't haven't to be synced?

---

To get the pipeline to work in the meantime:

# Navigate to an empty directory and then: (if necessary, change the '2.1.0' to the current Autometa release)

git clone git@github.com:KwanLab/Autometa.git
cd Autometa
cd docker/modules

# One or both of of these may take a while to build
docker build -t jasonkwan/autometa-nf-modules-get_genomes_for_mock:2.1.0 -f get_genomes_for_mock.Dockerfile .
docker build -t jasonkwan/autometa-nf-modules-mock_data_reporter:2.1.0 -f mock_data_reporter.Dockerfile .

# Now run the test 
nextflow run KwanLab/Autometa -profile test,docker