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databio / bulker

Manager for multi-container computing environments
https://bulker.io
BSD 2-Clause "Simplified" License
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make 'bulker load' printout more concise #25

Closed stolarczyk closed 4 years ago

stolarczyk commented 4 years ago

after bulker load cmd execution lots of stuff is logged to the screen. Can this be more concise? What is more, some of the information does not make sense for a bulker newbie -- after each entry:

None
None found.

entire printout:

[mstolarczyk@MichalsMBP test_genomes]: bulker load refgenie -f /Users/mstolarczyk/Uczelnia/UVA/code/refgenie/refgenie_manifest.yaml
Using default config. No config found in env var: BULKERCFG
Bulker config: /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/bulker/templates/bulker_config.yaml
Executable template: /Library/Frameworks/Python.framework/Versions/3.6/lib/python3.6/site-packages/bulker/templates/docker_executable.jinja2
That manifest has already been loaded. Overwrite? [y/N] y
Removing all executables in: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
command: samtools
dockerargs: -i
docker_image: quay.io/biocontainers/samtools:1.9--h91753b0_8
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
command: bowtie2-build
docker_image: quay.io/biocontainers/bowtie2:2.3.5--py37he860b03_0
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
command: bwa
docker_image: quay.io/biocontainers/bwa:0.7.17--pl5.22.0_2
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
command: hisat2-build
docker_image: quay.io/biocontainers/hisat2:2.0.4--py35_0
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
command: bismark_genome_preparation
docker_image: quay.io/biocontainers/bismark:0.18.1--pl5.22.0
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
command: tabix
docker_image: quay.io/biocontainers/htslib:1.6--0
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
command: STAR
docker_image: biocontainers/rna-star:v2.5.2bdfsg-1-deb_cv1
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
{'protocol': None, 'namespace': 'biocontainers', 'image': 'rna-star', 'subimage': None, 'tag': 'v2.5.2bdfsg-1-deb_cv1'}
None found.
command: salmon
docker_image: quay.io/biocontainers/salmon:0.11.3--h86b036
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
command: kallisto
docker_image: quay.io/biocontainers/kallisto:0.42.4--2
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: docker_executable.jinja2
shell_template: docker_shell.jinja2
build_template: docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
Loading manifest: 'bulker/refgenie:default'. Activate with 'bulker activate bulker/refgenie:default'.
Commands available: samtools, bowtie2-build, bwa, hisat2-build, bismark_genome_preparation, tabix, STAR, salmon, kallisto
nsheff commented 4 years ago

are you using the dev branch? I might have left in some LOGGER messages, whoops.

I'll have to see what the "None" means because I don't get that. maybe because you have no bulker config set?

stolarczyk commented 4 years ago

are you using the dev branch?

yes

maybe because you have no bulker config set?

initializing the config does not change that:

[mstolarczyk@MichalsMBP test_genomes]: export BULKERCFG=$HOME/bulker_config.yaml 
[mstolarczyk@MichalsMBP test_genomes]: bulker init -c $BULKERCFG
Guessing container engine is docker.
Wrote new configuration file: /Users/mstolarczyk/bulker_config.yaml
[mstolarczyk@MichalsMBP test_genomes]: bulker load refgenie -f /Users/mstolarczyk/Uczelnia/UVA/code/refgenie/refgenie_manifest.yaml
Bulker config: /Users/mstolarczyk/bulker_config.yaml
Executable template: /Users/mstolarczyk/templates/docker_executable.jinja2
command: samtools
dockerargs: -i
docker_image: quay.io/biocontainers/samtools:1.9--h91753b0_8
volumes: ['/tmp']
envvars: ['DISPLAY']
default_crate_folder: /Users/mstolarczyk/bulker_crates
singularity_image_folder: /Users/mstolarczyk/simages
container_engine: docker
default_namespace: bulker
executable_template: templates/docker_executable.jinja2
shell_template: templates/docker_shell.jinja2
build_template: templates/docker_build.jinja2
crates:
  bulker:
    refgenie:
      default: /Users/mstolarczyk/bulker_crates/bulker/refgenie/default
None
None found.
...