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Adding Raven v 1.8.3 #783

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2 changes: 1 addition & 1 deletion README.md
Original file line number Diff line number Diff line change
Expand Up @@ -213,7 +213,7 @@ To learn more about the docker pull rate limits and the open source software pro
| [QuickSNP](https://hub.docker.com/r/staphb/quicksnp/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | <ul><li>1.0.1</li></ul> | https://github.com/k-florek/QuickSNP |
| [racon](https://hub.docker.com/r/staphb/racon) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| <ul><li>1.4.3</li><li>1.4.20</li></ul> | https://github.com/lbcb-sci/racon <br/> https://github.com/isovic/racon (ARCHIVED) |
| [rasusa](https://hub.docker.com/r/staphb/rasusa/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | <ul><li>0.1.0</li><li>0.2.0</li><li>0.3.0</li><li>0.6.0</li><li>0.7.0</li></ul> | https://github.com/mbhall88/rasusa |
| [raven](https://hub.docker.com/r/staphb/raven/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | <ul><li>1.5.1</li><li>1.8.1</li></ul> | https://github.com/lbcb-sci/raven |
| [raven](https://hub.docker.com/r/staphb/raven/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | <ul><li>1.5.1</li><li>1.8.1</li><li>[1.8.3](./raven/1.8.3)</li></ul> | https://github.com/lbcb-sci/raven |
| [RAxML](https://hub.docker.com/r/staphb/raxml/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/raxml)](https://hub.docker.com/r/staphb/raxml) | <ul><li>8.2.12 (RAxML) and 0.9.0 (RAxML Next Generation)</li></ul> | https://github.com/stamatak/standard-RAxML <br/> https://github.com/amkozlov/raxml-ng |
| [ResFinder](https://hub.docker.com/r/staphb/resfinder/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) | <ul><li>4.1.1</li></ul> | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ |
| [Roary](https://hub.docker.com/r/staphb/roary/) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | <ul><li>3.12.0</li><li>3.13.0</li></ul> | https://github.com/sanger-pathogens/Roary |
Expand Down
64 changes: 64 additions & 0 deletions raven/1.8.3/Dockerfile
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ARG RAVEN_VERSION=1.8.3

# base image
FROM ubuntu:jammy as app

ARG RAVEN_VERSION

# metadata
LABEL base.image="ubuntu:jammy"
LABEL dockerfile.version="1"
LABEL software="raven"
LABEL software.version="${RAVEN_VERSION}"
LABEL description="Raven is a de novo genome assembler for long uncorrected reads."
LABEL website="https://github.com/lbcb-sci/raven"
LABEL license="https://github.com/lbcb-sci/raven/blob/master/LICENSE"
LABEL maintainer="Erin Young"
LABEL maintainer.email="[email protected]"

# otherwise tzdata won't install
ARG DEBIAN_FRONTEND=noninteractive

# install dependencies via apt-get or yum if using a centos or fedora base
RUN apt-get update && apt-get install -y \
wget \
clang \
git \
gcc \
zlib1g-dev \
build-essential \
cmake \
libboost-all-dev \
doxygen \
&& apt-get autoclean \
&& rm -rf /var/lib/apt/lists/*

# install raven
RUN wget https://github.com/lbcb-sci/raven/archive/refs/tags/${RAVEN_VERSION}.tar.gz && \
tar -xvf ${RAVEN_VERSION}.tar.gz && \
rm ${RAVEN_VERSION}.tar.gz

WORKDIR raven-${RAVEN_VERSION}


RUN cmake -S ./ -B ./build -DRAVEN_BUILD_EXE=1 -DCMAKE_BUILD_TYPE=Release -Wno-dev && \
cmake --build build && \
cmake --install ./build

# set environmental variables e.g. $PATH and locale settings for singularity compatibility
ENV PATH="/raven-${RAVEN_VERSION}/:$PATH" \
LC_ALL=C

# set working directory
WORKDIR /data

CMD raven --help

FROM app as test

WORKDIR /test

ARG RAVEN_VERSION

RUN raven --graphical-fragment-assembly ERA476754.gfa /raven-${RAVEN_VERSION}/RavenTest/data/ERA476754.fastq.gz > ERA476754.fasta && \
test -f ERA476754.gfa && test -f ERA476754.fasta
13 changes: 13 additions & 0 deletions raven/1.8.3/README.md
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# raven container

Main tool : [raven](https://github.com/lbcb-sci/raven)

> Raven is a de novo genome assembler for long uncorrected reads.

## Example Usage

```
raven --polishing-rounds 2 --threads 4 --graphical-fragment-assembly sample.gfa sample.fastq > sample.fasta
```

Note : This version is built to work with CPUs. Does not support NVIDIA CUDA support.