checkM database handling via docker

checkM databases is not needed its included via docker
also i get errors

command:

nextflow run ../main.nf --ont nanopore/ --illumina fastq/ --assembler metaflye -profile docker

Error executing process > 'checkm_setup_db'

Caused by:
  Process `checkm_setup_db` terminated with an error exit status (127)

Command executed:

  if [ false == true ] ;
  then
      checkm data setRoot /home/christian/git_repositories/MUFFIN/wip/nextflow-autodownload-databases/checkm/checkm_data_2015_01_16.tar.gz ;
      echo '/home/christian/git_repositories/MUFFIN/wip/nextflow-autodownload-databases/checkm/checkm_data_2015_01_16.tar.gz' > path_db.txt;
  fi

  if [ false == false ] ;
  then
              path_db=$(dirname /home/christian/git_repositories/MUFFIN/wip/nextflow-autodownload-databases/checkm/checkm_data_2015_01_16.tar.gz);
              mkdir -p $path_db/db/;
              tar -xvf /home/christian/git_repositories/MUFFIN/wip/nextflow-autodownload-databases/checkm/checkm_data_2015_01_16.tar.gz -C $path_db/db/;
              checkm data setRoot $path_db/db;   
              echo $path_db/db > path_db.txt;
  fi

Command exit status:
  127

Command output:
  ./
  ./distributions/
  ./distributions/cd_dist.txt
  ./distributions/gc_dist.txt
  ./distributions/td_dist.txt
  ./genome_tree/
  ./genome_tree/genome_tree.derep.txt
  ./genome_tree/genome_tree.metadata.tsv
  ./genome_tree/missing_duplicate_genes_97.tsv
  ./genome_tree/missing_duplicate_genes_50.tsv
  ./genome_tree/genome_tree_reduced.refpkg/
  ./genome_tree/genome_tree_reduced.refpkg/CONTENTS.json
  ./genome_tree/genome_tree_reduced.refpkg/genome_tree.fasta
  ./genome_tree/genome_tree_reduced.refpkg/genome_tree.log
  ./genome_tree/genome_tree_reduced.refpkg/genome_tree.tre
  ./genome_tree/genome_tree_reduced.refpkg/phylo_modelJqWx6_.json
  ./genome_tree/genome_tree_full.refpkg/
  ./genome_tree/genome_tree_full.refpkg/CONTENTS.json
  ./genome_tree/genome_tree_full.refpkg/phylo_modelEcOyPk.json
  ./genome_tree/genome_tree_full.refpkg/genome_tree.fasta
  ./genome_tree/genome_tree_full.refpkg/genome_tree.log
  ./genome_tree/genome_tree_full.refpkg/genome_tree.tre
  ./genome_tree/genome_tree.taxonomy.tsv
  ./hmms/
  ./hmms/phylo.hmm
  ./hmms/phylo.hmm.ssi
  ./hmms/checkm.hmm
  ./hmms/checkm.hmm.ssi
  ./hmms_ssu/
  ./hmms_ssu/SSU_archaea.hmm
  ./hmms_ssu/SSU_bacteria.hmm
  ./hmms_ssu/SSU_euk.hmm
  ./hmms_ssu/createHMMs.py
  ./img/
  ./img/img_metadata.tsv
  ./pfam/
  ./pfam/Pfam-A.hmm.dat
  ./pfam/tigrfam2pfam.tsv
  ./selected_marker_sets.tsv
  ./taxon_marker_sets.tsv
  ./test_data/
  ./test_data/637000110.fna
  ./.dmanifest

Command error:
  WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap.
  .command.sh: line 13: checkm: command not found

Work dir:
  /home/christian/git_repositories/MUFFIN/wip/work/66/ee260da732c52e627289696047d007

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`

RVanDamme / MUFFIN

checkM database handling via docker #4