From dba11c58448eead03eb56c6061655619f588759f Mon Sep 17 00:00:00 2001 From: deemalone <104962534+deemalone@users.noreply.github.com> Date: Mon, 6 Nov 2023 10:25:59 -0700 Subject: [PATCH 1/5] Create Dockerfile updated to 1.8.3 --- raven/1.8.3/Dockerfile | 62 ++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 raven/1.8.3/Dockerfile diff --git a/raven/1.8.3/Dockerfile b/raven/1.8.3/Dockerfile new file mode 100644 index 000000000..ad2102742 --- /dev/null +++ b/raven/1.8.3/Dockerfile @@ -0,0 +1,62 @@ +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="${RAVEN_VERSION}" +LABEL description="Raven is a de novo genome assembler for long uncorrected reads." +LABEL website="https://github.com/lbcb-sci/raven" +LABEL license="https://github.com/lbcb-sci/raven/blob/master/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +# otherwise tzdata won't install +ARG DEBIAN_FRONTEND=noninteractive + +# install dependencies via apt-get or yum if using a centos or fedora base +RUN apt-get update && apt-get install -y \ + wget \ + clang \ + git \ + gcc \ + zlib1g-dev \ + build-essential \ + cmake \ + libboost-all-dev \ + doxygen \ + && apt-get autoclean \ + && rm -rf /var/lib/apt/lists/* + +# install raven +RUN wget https://github.com/lbcb-sci/raven/archive/refs/tags/${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}/:$PATH" \ + LC_ALL=C + +# set working directory +WORKDIR /data + +FROM app as test + +WORKDIR /test + +ARG RAVEN_VERSION + +RUN raven --graphical-fragment-assembly ERA476754.gfa /raven-${RAVEN_VERSION}/RavenTest/data/ERA476754.fastq.gz > ERA476754.fasta && \ + test -f ERA476754.gfa && test -f ERA476754.fasta From 38142140a2062d7ecf46e25674bee652415fd9c3 Mon Sep 17 00:00:00 2001 From: deemalone <104962534+deemalone@users.noreply.github.com> Date: Mon, 6 Nov 2023 10:42:44 -0700 Subject: [PATCH 2/5] Create README.md --- raven/1.8.3/README.md | 13 +++++++++++++ 1 file changed, 13 insertions(+) create mode 100644 raven/1.8.3/README.md diff --git a/raven/1.8.3/README.md b/raven/1.8.3/README.md new file mode 100644 index 000000000..740211049 --- /dev/null +++ b/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. From 9f5062d049d856439fa2e90eede16c843fa08b96 Mon Sep 17 00:00:00 2001 From: deemalone <104962534+deemalone@users.noreply.github.com> Date: Mon, 6 Nov 2023 11:13:23 -0700 Subject: [PATCH 3/5] Update README.md to include 1.8.3 to the list of raven versions available --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f6498cd5a..96268f44f 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | | https://github.com/k-florek/QuickSNP | | [racon](https://hub.docker.com/r/staphb/racon)
[![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| | https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED) | | [rasusa](https://hub.docker.com/r/staphb/rasusa/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | | https://github.com/mbhall88/rasusa | -| [raven](https://hub.docker.com/r/staphb/raven/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | | https://github.com/lbcb-sci/raven | +| [raven](https://hub.docker.com/r/staphb/raven/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | | https://github.com/lbcb-sci/raven | | [RAxML](https://hub.docker.com/r/staphb/raxml/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/raxml)](https://hub.docker.com/r/staphb/raxml) | | https://github.com/stamatak/standard-RAxML
https://github.com/amkozlov/raxml-ng | | [ResFinder](https://hub.docker.com/r/staphb/resfinder/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) | | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ | | [Roary](https://hub.docker.com/r/staphb/roary/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | | https://github.com/sanger-pathogens/Roary | From 965f95e74bd9e7fe5cd3a8fe104940de7c01bb60 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 7 Nov 2023 11:20:08 -0700 Subject: [PATCH 4/5] Added hyperlink --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 96268f44f..c295dac13 100644 --- a/README.md +++ b/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/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/quicksnp)](https://hub.docker.com/r/staphb/quicksnp) | | https://github.com/k-florek/QuickSNP | | [racon](https://hub.docker.com/r/staphb/racon)
[![docker pulls](https://badgen.net/docker/pulls/staphb/racon)](https://hub.docker.com/r/staphb/racon)| | https://github.com/lbcb-sci/racon
https://github.com/isovic/racon (ARCHIVED) | | [rasusa](https://hub.docker.com/r/staphb/rasusa/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/rasusa)](https://hub.docker.com/r/staphb/rasusa) | | https://github.com/mbhall88/rasusa | -| [raven](https://hub.docker.com/r/staphb/raven/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | | https://github.com/lbcb-sci/raven | +| [raven](https://hub.docker.com/r/staphb/raven/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/raven)](https://hub.docker.com/r/staphb/raven) | | https://github.com/lbcb-sci/raven | | [RAxML](https://hub.docker.com/r/staphb/raxml/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/raxml)](https://hub.docker.com/r/staphb/raxml) | | https://github.com/stamatak/standard-RAxML
https://github.com/amkozlov/raxml-ng | | [ResFinder](https://hub.docker.com/r/staphb/resfinder/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/resfinder)](https://hub.docker.com/r/staphb/resfinder) | | https://bitbucket.org/genomicepidemiology/resfinder/src/master/ | | [Roary](https://hub.docker.com/r/staphb/roary/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/roary)](https://hub.docker.com/r/staphb/roary) | | https://github.com/sanger-pathogens/Roary | From 948cd3512286f8e473667b1c5778a1b8bd9231b2 Mon Sep 17 00:00:00 2001 From: Young Date: Tue, 7 Nov 2023 11:22:05 -0700 Subject: [PATCH 5/5] Added CMD --- raven/1.8.3/Dockerfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/raven/1.8.3/Dockerfile b/raven/1.8.3/Dockerfile index ad2102742..36bc0ec85 100644 --- a/raven/1.8.3/Dockerfile +++ b/raven/1.8.3/Dockerfile @@ -52,6 +52,8 @@ ENV PATH="/raven-${RAVEN_VERSION}/:$PATH" \ # set working directory WORKDIR /data +CMD raven --help + FROM app as test WORKDIR /test