Merge pull request #783 from deemalone/master

Adding Raven v 1.8.3

README.md

@@ -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 |

raven/1.8.3/Dockerfile

@@ -0,0 +1,64 @@
+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

raven/1.8.3/README.md

@@ -0,0 +1,13 @@
+# 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.