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scripts/deploy_all_pipelines.sh
View file @ 529c7455
......@@ -160,8 +160,8 @@ branch:|$branch
[[ $dryrun == false && $do_git_pull == true ]] && ( git -C $git_parent_dir clone --branch "$branch" "${repository_origin_urls[$pipeline]}" || die "Could not clone repository: $pipeline" )
[[ ! -d $pipeline_dir ]] && die "Directory was not created: $pipeline_dir"
## check status
"$pipeline_dir"/"${pipeline_setup_sh[$pipeline]}" --auto --status
## install mamba environment
"$pipeline_dir"/"${pipeline_setup_sh[$pipeline]}" --auto --mamba
return 0
}
......
static/pipelines.tsv
View file @ 529c7455
pipeline official_name repository_name repository_origin_url main_snakefile pipeline_py pipeline_setup_sh pipeline_wrapper_sh full_install_args
aquamis AQUAMIS AQUAMIS https://gitlab.com/bfr_bioinformatics/AQUAMIS.git Snakefile aquamis.py scripts/aquamis_setup.sh scripts/aquamis_wrapper.sh --mamba --databases --test_data
bakcharak BakCharak bakcharak https://gitlab.com/bfr_bioinformatics/bakcharak.git Snakefile bakcharak.py scripts/bakcharak_setup.sh scripts/bakcharak_wrapper.sh --mamba --databases --test_data
chewiesnake ChewieSnake chewieSnake https://gitlab.com/bfr_bioinformatics/chewieSnake.git chewieSnake_fromcontigs.smk chewieSnake.py scripts/chewieSnake_setup.sh scripts/chewieSnake_wrapper.sh --mamba --databases --test_data
pipeline official_name repository_name repository_origin_url main_snakefile pipeline_py pipeline_setup_sh pipeline_wrapper_sh install_args_full
aquamis AQUAMIS AQUAMIS https://gitlab.com/bfr_bioinformatics/AQUAMIS.git Snakefile aquamis.py scripts/aquamis_setup.sh scripts/aquamis_wrapper.sh --mamba --busco --databases --test_data
bakcharak BakCharak bakcharak https://gitlab.com/bfr_bioinformatics/bakcharak.git Snakefile bakcharak.py scripts/bakcharak_setup.sh scripts/bakcharak_wrapper.sh --mamba --amrfinder_update --databases --bakta light --test_data
chewiesnake ChewieSnake chewieSnake https://gitlab.com/bfr_bioinformatics/chewieSnake.git chewieSnake_fromcontigs.smk chewieSnake.py scripts/chewieSnake_setup.sh scripts/chewieSnake_wrapper.sh --mamba --databases
snippysnake snippySnake snippySnake https://gitlab.com/bfr_bioinformatics/snippySnake.git snippySnake.smk snippySnake.py scripts/snippySnake_setup.sh scripts/snippySnake_wrapper.sh --mamba --databases --test_data
milonga MiLongA milonga https://gitlab.com/bfr_bioinformatics/milonga pipeline.smk milonga.py scripts/milonga_setup.sh scripts/milonga_wrapper.sh --mamba --databases --test_data
milonga MiLongA milonga https://gitlab.com/bfr_bioinformatics/milonga pipeline.smk milonga.py scripts/milonga_setup.sh scripts/milonga_wrapper.sh --mamba --test_data --sra_toolkit