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isugifNF / polishCLR

A nextflow pipeline for polishing CLR assemblies
https://isugifnf.github.io/polishCLR/
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Update: Dockerfile #47

Closed j23414 closed 2 years ago

j23414 commented 2 years ago

Description

@Sivanandan and I rebuilt docker image with following changes:

After pushing to DockerHub, and if tests pass, we can probably merge

Issues

Related to issue(s): https://github.com/isugifNF/polishCLR/issues/40 and maybe https://github.com/isugifNF/polishCLR/issues/26 although would need to check...

Testing

Assuming reviewer has a working install of docker and nextflow

# start docker deamon
docker pull csiva2022/polishclr:latest

# run interactive
docker run -it csiva2022/polishclr:latest bash

# test software dependencies
nextflow run isugifNF/polishCLR -r main \
  --check_software \
  -profile local

Can also check singularity

singularity pull polishclr.sif docker://csiva2022/polishclr:latest
singularity shell polishclr.sif
nextflow run isugifNF/polishCLR -r main \
  --check_software \
  -profile local
j23414 commented 2 years ago

Test worked on MacBook Pro (13-inch, 2016):

~ % docker run -it csiva2022/polishclr:latest bash
(base) root@7f06571221c6:/tmp# nextflow run isugifNF/polishCLR -r main \
  --check_software \
  -profile local
N E X T F L O W  ~  version 22.04.5
Pulling isugifNF/polishCLR ...
 downloaded from https://github.com/isugifNF/polishCLR.git
Launching `https://github.com/isugifNF/polishCLR` [lonely_cajal] DSL2 - revision: 1fb9a1938e [main]
executor >  local (1)
[11/96efae] process > check_software [100%] 1 of 1 ✔
executor >  local (1)
[11/96efae] process > check_software [100%] 1 of 1 ✔
===== Dependencies check =====
parallel   .... good.  GNU parallel 20160622
bzcat      .... good.  bzip2, a block-sorting file compressor. Version 1.0.8, 13-Jul-2019.
pigz       .... good.  pigz 2.6
meryl      .... good.  meryl 1.3
pbmm2      .... good.  pbmm2 1.9.0 Using: pbmm2 : 1.9.0 (commit v1.9.0) pbbam : 2.1.0 (commit v2.1.0) pbcopper : 2.0.0 (commit v2.0.0-54-g1ce9870) boost : 1.77 htslib : 1.15 minimap2 : 2.15 zlib : 1.2.11
minimap2   .... good.  2.24-r1122
samtools   .... good.  samtools 1.15.1
gcpp       .... good.  gcpp 2.0.2-2.0.2
bwa-mem2    .... good.  2.2.1
freebayes  .... good.  version: v1.3.6
bcftools   .... good.  bcftools 1.15.1
merfin     .... good.  merfin 1.0
pbcstat    .... good.  Usage: aa_pb [options] <PAF_FILE> ...
calcuts    .... good.  Usage: calcuts [<options>] <STAT> ...
split_fa   .... good.  Usage: split_fa [<options>] <STAT> ...
purge_dups .... good.  Version: 1.2.5
get_seqs   .... good.  Usage: get_seqs [<options>] <DUPs.BED> <FASTA>
gzip       .... good.  gzip 1.12
busco      .... good.  BUSCO 5.4.2

although we may need to deal with this issue at some point, maybe by recommending rosetta. Although I mainly imagine polishCLR being run in an HPC/cloud environment.