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adds verkko #890

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Feb 28, 2024
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adds verkko #890

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891f093
adds verkko
Kincekara Feb 27, 2024
82c70ec
limit output in test
Kincekara Feb 28, 2024
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1 change: 1 addition & 0 deletions Program_Licenses.md
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Expand Up @@ -166,6 +166,7 @@ The licenses of the open-source software that is contained in these Docker image
| Trycycler | GNU GPLv3 | https://github.com/rrwick/Trycycler/blob/master/LICENSE |
| Unicycler | GNU GPLv3 | https://github.com/rrwick/Unicycler/blob/master/LICENSE |
| VADR | Public Domain | https://github.com/nawrockie/vadr/blob/master/LICENSE |
| Verkko | Public Domain | https://github.com/marbl/verkko/blob/master/README.licenses |
| VIBRANT | GNU GPLv3 | https://github.com/AnantharamanLab/VIBRANT/blob/master/LICENSE |
| VIGOR4 | GNU GPLv3 | https://github.com/JCVenterInstitute/VIGOR4/blob/master/LICENSE.txt |
| VirSorter2 | GNU GPLv2 | https://github.com/jiarong/VirSorter2/blob/master/LICENSE |
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1 change: 1 addition & 0 deletions README.md
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Expand Up @@ -272,6 +272,7 @@ To learn more about the docker pull rate limits and the open source software pro
| [Trycycler](https://hub.docker.com/r/staphb/trycycler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/trycycler)](https://hub.docker.com/r/staphb/trycycler) | <ul><li>0.3.1</li><li>0.3.2</li><li>0.3.3</li><li>0.5.0</li><li>0.5.3</li><li>0.5.4</li></ul> | https://github.com/rrwick/Trycycler |
| [Unicycler](https://hub.docker.com/r/staphb/unicycler/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/unicycler)](https://hub.docker.com/r/staphb/unicycler) | <ul><li>0.4.7</li><li>0.4.8</li><li>0.4.9</li><li>0.5.0</li></ul> | https://github.com/rrwick/Unicycler |
| [VADR](https://hub.docker.com/r/staphb/vadr/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/vadr)](https://hub.docker.com/r/staphb/vadr) | <ul><li>1.1</li><li>1.1.2</li><li>1.1.3</li><li>1.2</li><li>1.2.1</li><li>1.3 & SARS-CoV-2 models 1.3-1</li><li>1.3 & SARS-CoV-2 models 1.3-2</li><li>1.4 & SARS-CoV-2 models 1.3-2</li><li>1.4.1 & SARS-CoV-2 models 1.3-2</li><li>1.4.2 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1</li><li>1.5 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1</li><li>1.5.1 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2</li><li>1.6.3 & SARS-CoV-2 models 1.3-2, MPXV models 1.4.2-1, RSV models 1.5-2, Influenza v1.6.3-1</li></ul> | https://github.com/nawrockie/vadr (archived, now redirects to ncbi/vadr) </br>https://github.com/ncbi/vadr |
| [Verkko](https://hub.docker.com/r/staphb/verkko/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/verkko)](https://hub.docker.com/r/staphb/verkko) | <ul><li>[2.0](./verkko/2.0/)</li></ul> | https://github.com/marbl/verkko |
| [VIBRANT](https://hub.docker.com/r/staphb/vibrant/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/vibrant)](https://hub.docker.com/r/staphb/vibrant) | <ul><li>1.2.1</li></ul> | https://github.com/AnantharamanLab/VIBRANT |
| [VIGOR4](https://hub.docker.com/r/staphb/vigor4/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/vigor4)](https://hub.docker.com/r/staphb/vigor4) | <ul><li>4.1.20190131</li></ul> | https://github.com/JCVenterInstitute/VIGOR4 |
| [VirSorter2](https://hub.docker.com/r/staphb/virsorter2/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/virsorter2)](https://hub.docker.com/r/staphb/virsorter2/) | <ul><li>2.1</li></ul> | https://github.com/jiarong/VirSorter2 |
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50 changes: 50 additions & 0 deletions verkko/2.0/Dockerfile
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FROM mambaorg/micromamba:1.5.6 as app

ARG VERKKO_VER="2.0"

USER root

WORKDIR /

LABEL base.image="mambaorg/micromamba:1.5.6"
LABEL dockerfile.version="1"
LABEL software="Verkko"
LABEL software.version="${VERKKO_VER}"
LABEL description="Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads."
LABEL website="https://github.com/marbl/verkko"
LABEL license="https://github.com/marbl/verkko/blob/master/README.licenses"
LABEL maintainer="Kutluhan Incekara"
LABEL maintainer.email="[email protected]"

RUN apt-get update && apt-get install --no-install-recommends -y \
procps \
curl && \
apt-get autoclean && rm -rf /var/lib/apt/lists/*

RUN micromamba install --name base -c conda-forge -c bioconda verkko=${VERKKO_VER} && \
micromamba clean -a -y

ENV PATH="/opt/conda/bin/:${PATH}" \
LC_ALL=C.UTF-8

CMD [ "verkko", "--help" ]

WORKDIR /data

## Test ##
FROM app as test

ENV ENV_NAME="base"
ARG MAMBA_DOCKERFILE_ACTIVATE=1

RUN apt-get update && apt-get install --no-install-recommends -y curl

# test data
RUN curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_hifi_subset24x.fastq.gz -o hifi.fastq.gz &&\
curl -L https://obj.umiacs.umd.edu/sergek/shared/ecoli_ont_subset50x.fastq.gz -o ont.fastq.gz

# verkko test run
RUN verkko -d asm --hifi ./hifi.fastq.gz --nano ./ont.fastq.gz &&\
head asm/assembly.hifi-coverage.csv &&\
head asm/assembly.fasta
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This prints a lot to the screen. I have a hunch that head asm/assembly.fasta might the culprit. Can we try something like wc -l asm/assembly.fasta?

#11 225.4     resources: tmpdir=/tmp
#11 225.4 
#11 225.4 Reading graph from stdin
#11 225.4 [Tue Feb 27 17:49:59 2024]
#11 225.4 Finished job 0.
#11 225.4 64 of 64 steps (100%) done
#11 225.4 Complete log: .snakemake/log/2024-02-27T174614.567918.snakemake.log
#11 225.5 node	coverage	length
#11 225.5 utig4-0	23.78	3421198
#11 225.5 utig4-1	7.67	4526
#11 225.5 utig4-2	8.00	4518
#11 225.5 >contig-0000001
#11 225.5

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I think contig sequences are written in one line, so head gives a lot of outbut. I limit output with 1000 bytes. That should work.

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Thank you!

It's much easier to read now.


21 changes: 21 additions & 0 deletions verkko/2.0/README.md
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# Verkko container

Main tool: [verkko](https://github.com/marbl/verkko)

Code repository: https://github.com/marbl/verkko

Basic information on how to use this tool:
- executable: verkko
- help: --help
- version: --version
- description: Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads.

Full documentation: https://github.com/marbl/verkko

## Example Usage

```bash
verkko -d <work-directory> --hifi <hifi-read-files> [--nano <ont-read-files>]
```


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