-
Notifications
You must be signed in to change notification settings - Fork 119
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
* adding verkko version 2.1 * Update Dockerfile - removed "cur"l from app - micromamba clean -afy --------- Co-authored-by: Kutluhan Incekara <[email protected]>
- Loading branch information
Showing
3 changed files
with
70 additions
and
1 deletion.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,48 @@ | ||
| FROM mambaorg/micromamba:1.5.8 as app | ||
|
|
||
| ARG VERKKO_VER="2.1" | ||
|
|
||
| USER root | ||
|
|
||
| WORKDIR / | ||
|
|
||
| LABEL base.image="mambaorg/micromamba:1.5.8" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Verkko" | ||
| LABEL software.version="${VERKKO_VER}" | ||
| LABEL description="Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi or Oxford Nanopore Duplex and Oxford Nanopore simplex reads." | ||
| LABEL website="https://github.com/marbl/verkko" | ||
| LABEL license="https://github.com/marbl/verkko/blob/master/README.licenses" | ||
| LABEL maintainer="Kutluhan Incekara" | ||
| LABEL maintainer.email="[email protected]" | ||
|
|
||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| procps &&\ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| RUN micromamba install --name base -c conda-forge -c bioconda verkko=${VERKKO_VER} && \ | ||
| micromamba clean -afy | ||
|
|
||
| ENV PATH="/opt/conda/bin/:${PATH}" \ | ||
| LC_ALL=C.UTF-8 | ||
|
|
||
| CMD [ "verkko", "--help" ] | ||
|
|
||
| WORKDIR /data | ||
|
|
||
| ## Test ## | ||
| FROM app as test | ||
|
|
||
| RUN verkko --help | ||
|
|
||
| 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 -c 1000 asm/assembly.fasta | ||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| # 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>] | ||
| ``` | ||
|
|
||
|
|