Build custom docker images to biocontainers

For the custom tools that we use in zarp we should open PRs to build images to bio containers. These are:

• zgtf
• zpca
• merge_kallisto
• multiqc-plugins
• tin_score_calculation

I think an easy way to solve the issue is to upload them first to bioconda. This is mentioned in the bioconda website:

Each package added to Bioconda also has a corresponding Docker BioContainer automatically created and uploaded to Quay.io. A list of these and other containers can be found at the Biocontainers Registry.

So we need to solve #97 (closed) first

added Blocked To Do pipeline labels

added Doing label and removed To Do label

assigned to @gypas

removed Blocked label

marked the checklist item zpca as completed

So, for zpca we have the following:

• conda: https://anaconda.org/bioconda/zpca
  Note: You need to specify both conda-forge and bioconda as channels in order to work. In the link this is not mentioned.
• docker image from biocontainers: https://quay.io/repository/biocontainers/zpca Note: In Snakefile specify it like this: docker://quay.io/biocontainers/zpca:0.8.2--pyh3252c3a_0
• singularity image from galaxy: https://depot.galaxyproject.org/singularity/zpca%3A0.8.2--pyh3252c3a_0

mentioned in commit 0718c5da

mentioned in merge request !81 (merged)

mentioned in issue #159 (closed)

marked the checklist item zgtf as completed

• zpca: docker://quay.io/biocontainers/zpca:0.8.3.post1--pyh5e36f6f_0
• zgtf: docker://quay.io/biocontainers/zgtf:0.1.1--pyh5e36f6f_0
• merge_kallisto: docker://quay.io/biocontainers/r-merge-kallisto:0.6--hdfd78af_0
• tin-score-calculation: docker://quay.io/biocontainers/tin-score-calculation:0.4--pyh5e36f6f_0
• multiqc-plugins: docker://quay.io/biocontainers/zavolan-multiqc-plugins:1.3--pyh5e36f6f_0

marked the checklist item merge_kallisto as completed

marked the checklist item tin_score_calculation as completed

marked the checklist item multiqc-plugins as completed

Fixed in !81 (merged) !85 (merged) !86 (merged) !87 (merged) !88 (merged)

closed

mentioned in issue #145 (closed)