Docker/Conda

[vivekbhr]

For the first public release of our pipeline, we should make it independent using docker and conda.. Then we can also see whether we can add some some travis tests (issue #34) .

[dpryan79]

If you want to go the docker route we might as well switch to singularity instead and avoid the permissions issues.

[dpryan79]

We can use this as a list of any remaining rules that need to use conda after the hackathon. Of course if there are none left then someone please close this :)

[vivekbhr]

Rules remaining for condafication after hackathon :

• [x] macs2
• [x] macs2 QC (atac and chip)
• [x] DESeq2
• [x] CSAW

(@steffenheyne @katsikora please update)

[katsikora]

WGBS is all condified as of this afternoon it uses the FASTQ shared rule, the rest is in WGBS.snakefile under shared/rules

[dpryan79]

I'm working on macs2, macs2 QC, and CSAW, since those are needed in the ATAC-seq pipeline.

[dpryan79]

The following rules in develop still need to be moved to conda:

• [x] histoneHMM (histoneHMM.snakefile)
• [x] histoneHMM_out_gz (histoneHMM.snakefile)
• [x] MACS2 (MACS2.snakefile)
• [x] MACS2_peak_qc (MACS2.snakefile)
• [x] combine_sample_counts (scRNAseq.snakefile)
• [x] extract_scale_counts (scRNAseq.snakefile)
• [x] sc_bam_featureCounts_genomic (scRNAseq.snakefile)

So mostly ChIP-seq and some R code.

[vivekbhr]

I don't remember when we made HISAT2.snakefile, since HISAT2 was only used for RNA mapping..

[dpryan79]

I have a feeling that HISAT2.snakefile isn't imported anywhere any more. I'm checking into that now.

[steffenheyne]

HISAT2 RNAseq mapping is part of RNA_mapping.snakefile so I think as well that we can remove HISAT2.snakefile