diff --git a/Program_Licenses.md b/Program_Licenses.md index 7ef078c9f..173ea984a 100644 --- a/Program_Licenses.md +++ b/Program_Licenses.md @@ -100,6 +100,7 @@ The licenses of the open-source software that is contained in these Docker image | liftoff | GNU GPLv3 | https://github.com/agshumate/Liftoff/blob/master/LICENSE.md | | lima | BSD-3 | https://github.com/PacificBiosciences/barcoding/blob/master/LICENSE | | longshot | MIT | https://github.com/pjedge/longshot/blob/master/LICENSE | +| lrge | MIT | https://github.com/mbhall88/lrge?tab=MIT-1-ov-file#readme | | Lyve-SET | MIT | https://github.com/lskatz/lyve-SET/blob/master/LICENSE | | Mafft | BSD | https://mafft.cbrc.jp/alignment/software/license.txt | | Mash | non-standard license (see link) | https://github.com/marbl/Mash/blob/master/LICENSE.txt | diff --git a/README.md b/README.md index bdc66221c..056e130f0 100644 --- a/README.md +++ b/README.md @@ -209,6 +209,7 @@ To learn more about the docker pull rate limits and the open source software pro | [liftoff](https://hub.docker.com/r/staphb/liftoff/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/liftoff)](https://hub.docker.com/r/staphb/liftoff)| | https://github.com/agshumate/Liftoff | | [lima](https://hub.docker.com/r/staphb/lima/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/lima)](https://hub.docker.com/r/staphb/lima)| | https://github.com/PacificBiosciences/barcoding | | [longshot](https://hub.docker.com/r/staphb/longshot/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/longshot)](https://hub.docker.com/r/staphb/longshot)| | https://github.com/pjedge/longshot | +| [lrge](https://hub.docker.com/r/staphb/lrge/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/lrge)](https://hub.docker.com/r/staphb/lrge)| | https://github.com/mbhall88/lrge | | [Lyve-SET (includes CG-Pipeline scripts and raxml)](https://hub.docker.com/r/staphb/lyveset/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/lyveset)](https://hub.docker.com/r/staphb/lyveset) | | https://github.com/lskatz/lyve-SET https://github.com/lskatz/CG-Pipeline | | [MAFFT](https://hub.docker.com/r/staphb/mafft/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mafft)](https://hub.docker.com/r/staphb/mafft) | | https://mafft.cbrc.jp/alignment/software/ | | [Mash](https://hub.docker.com/r/staphb/mash/)
[![docker pulls](https://badgen.net/docker/pulls/staphb/mash)](https://hub.docker.com/r/staphb/mash) | | https://github.com/marbl/Mash | diff --git a/lrge/0.1.3/Dockerfile b/lrge/0.1.3/Dockerfile new file mode 100644 index 000000000..f911cafd5 --- /dev/null +++ b/lrge/0.1.3/Dockerfile @@ -0,0 +1,45 @@ +ARG LRGE_VER="0.1.3" + +FROM ubuntu:jammy AS app + +ARG LRGE_VER + +# 'LABEL' instructions tag the image with metadata that might be important to the user +LABEL base.image="ubuntu:jammy" +LABEL dockerfile.version="1" +LABEL software="lrge" +LABEL software.version="${LRGE_VER}" +LABEL description="Long Read-based Genome size Estimation from overlaps" +LABEL website="https://github.com/mbhall88/lrge" +LABEL license="https://github.com/mbhall88/lrge/blob/main/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +# 'RUN' executes code during the build +# Install dependencies via apt-get or yum if using a centos or fedora base +RUN apt-get update && apt-get install -y --no-install-recommends \ + wget \ + ca-certificates && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +RUN wget -q https://github.com/mbhall88/lrge/releases/download/lrge-${LRGE_VER}/lrge-${LRGE_VER}-x86_64-unknown-linux-gnu.tar.gz && \ + tar -xvf lrge-${LRGE_VER}-x86_64-unknown-linux-gnu.tar.gz && \ + mv lrge-${LRGE_VER}-x86_64-unknown-linux-gnu/lrge /usr/local/bin && \ + rm -rf lrge-${LRGE_VER}-x86_64-unknown-linux-gnu.tar.gz lrge-0.1.3-x86_64-unknown-linux-gnu + +# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' +CMD [ "lrge", "--help" ] + +WORKDIR /data + +FROM app AS test + +# set working directory so that all test inputs & outputs are kept in /test +WORKDIR /test + +RUN lrge --help && lrge --version + +# stolen from https://github.com/mbhall88/lrge +RUN wget -q -O reads.fq.gz "ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR283/049/SRR28370649/SRR28370649_1.fastq.gz" && \ + lrge -t 8 reads.fq.gz -o results.txt && \ + head results.txt diff --git a/lrge/0.1.3/README.md b/lrge/0.1.3/README.md new file mode 100644 index 000000000..874d11b3c --- /dev/null +++ b/lrge/0.1.3/README.md @@ -0,0 +1,20 @@ +# lrge container + +Main tool: [lrge](https://github.com/mbhall88/lrge) + +Code repository: https://github.com/mbhall88/lrge + +Basic information on how to use this tool: +- executable: lrge +- help: -h +- version: -v +- description: | +> Long Read-based Genome size Estimation from overlaps for nanopore/ONT reads + +Full documentation: https://github.com/mbhall88/lrge + +## Example Usage + +```bash +lrge -t 8 reads.fq.gz -o size.txt +```