-
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.
* initial racon files * added builder and tests * added racon version 1.5.0 * added additional racon repo * add --no-install-recommends
- Loading branch information
Showing
4 changed files
with
106 additions
and
2 deletions.
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
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 +1,81 @@ | ||
| ARG RACON_VER="1.5.0" | ||
|
|
||
| # Use ubuntu as base image | ||
| FROM ubuntu:jammy as builder | ||
|
|
||
| ARG RACON_VER | ||
|
|
||
| RUN apt-get update && apt-get install --no-install-recommends -y \ | ||
| perl \ | ||
| default-jre \ | ||
| gnuplot \ | ||
| libgomp1 \ | ||
| maven \ | ||
| git \ | ||
| wget \ | ||
| python3 \ | ||
| build-essential \ | ||
| cmake \ | ||
| zlib1g-dev && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| # install racon | ||
| RUN wget https://github.com/lbcb-sci/racon/archive/refs/tags/${RACON_VER}.tar.gz && \ | ||
| tar -xvf ${RACON_VER}.tar.gz && \ | ||
| cd racon-${RACON_VER} && \ | ||
| mkdir build && \ | ||
| cd build && \ | ||
| cmake -DCMAKE_BUILD_TYPE=Release .. && \ | ||
| make | ||
|
|
||
| ENV PATH="/racon-${RACON_VER}/build/bin:${PATH}" | ||
|
|
||
| RUN racon_test | ||
|
|
||
| FROM ubuntu:jammy as app | ||
|
|
||
| ARG RACON_VER | ||
|
|
||
| # metadata | ||
| LABEL base.image="ubuntu:jammy" | ||
| LABEL version="1" | ||
| LABEL dockerfile.version="1" | ||
| LABEL software="Racon" | ||
| LABEL software.version="${RACON_VER}" | ||
| LABEL description="Long read assembly and polishing tools" | ||
| LABEL website="https://github.com/lbcb-sci/racon" | ||
| LABEL license="https://github.com/lbcb-sci/racon/blob/master/LICENSE" | ||
| LABEL maintainer="Erin Young" | ||
| LABEL maintainer.email="[email protected]" | ||
|
|
||
| # install python | ||
| RUN apt-get update && apt-get install -y \ | ||
| procps \ | ||
| wget \ | ||
| python3 && \ | ||
| apt-get autoclean && rm -rf /var/lib/apt/lists/* | ||
|
|
||
| COPY --from=builder /racon-${RACON_VER}/build/bin/* /usr/local/bin/ | ||
|
|
||
| RUN mkdir /data | ||
|
|
||
| WORKDIR /data | ||
|
|
||
| # set perl locale settings | ||
| ENV PATH=${PATH} LC_ALL=C | ||
|
|
||
| CMD racon --help | ||
|
|
||
| FROM app as test | ||
|
|
||
| RUN racon --help && racon --version | ||
|
|
||
| COPY --from=builder /racon-${RACON_VER}/test/data/* /test/ | ||
|
|
||
| WORKDIR /test | ||
|
|
||
| RUN wget -q https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.paf && \ | ||
| wget -q https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz && \ | ||
| wget -q https://github.com/nf-core/test-datasets/raw/modules/data/genomics/prokaryotes/bacteroides_fragilis/nanopore/fastq/test.fastq.gz && \ | ||
| racon -t 2 test.fastq.gz genome.paf genome.fna.gz > test_polished.fasta && \ | ||
| head test_polished.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 +1,23 @@ | ||
| # racon container | ||
|
|
||
| Main tool : [racon](https://github.com/lbcb-sci/racon) | ||
|
|
||
| Code repository: https://github.com/lbcb-sci/racon | ||
|
|
||
| Basic information on how to use this tool: | ||
| - executable: racon | ||
| - help: -h | ||
| - version: -v | ||
| - description: Polishes long read assemblies | ||
|
|
||
| > Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step. | ||
| # Example Usage | ||
|
|
||
| ```bash | ||
| # general | ||
| racon <sequences> <overlaps> <target sequences> | ||
|
|
||
| # more specific | ||
| racon --match 8 --mismatch -6 --gap -8 --window-length 500 --threads {threads} {input.reads} {input.alignment} {input.assembly} | ||
| ``` |