From 27f2190cfb2021be83e1949274a8b20c51a4fa58 Mon Sep 17 00:00:00 2001 From: Erin Young Date: Tue, 29 Oct 2024 19:58:57 +0000 Subject: [PATCH] adding genomad version 1.8.1 --- README.md | 2 +- genomad/1.8.1/Dockerfile | 84 ++++++++++++++++++++++++++++++++++++++++ genomad/1.8.1/README.md | 40 +++++++++++++++++++ 3 files changed, 125 insertions(+), 1 deletion(-) create mode 100644 genomad/1.8.1/Dockerfile create mode 100644 genomad/1.8.1/README.md diff --git a/README.md b/README.md index 66943bd3b..234d5f023 100644 --- a/README.md +++ b/README.md @@ -174,7 +174,7 @@ To learn more about the docker pull rate limits and the open source software pro | [GAMBIT](https://hub.docker.com/r/staphb/gambit)
[![docker pulls](https://badgen.net/docker/pulls/staphb/gambit)](https://hub.docker.com/r/staphb/gambit) | | https://github.com/jlumpe/gambit | | [GAMMA](https://hub.docker.com/r/staphb/gamma)
[![docker pulls](https://badgen.net/docker/pulls/staphb/gamma)](https://hub.docker.com/r/staphb/gamma) | | https://github.com/rastanton/GAMMA/ | | [GenoFLU](https://hub.docker.com/r/staphb/genoflu)
[![docker pulls](https://badgen.net/docker/pulls/staphb/genoflu)]() | | https://github.com/USDA-VS/GenoFLU | -| [geNomad](https://hub.docker.com/r/staphb/genomad)
[![docker pulls](https://badgen.net/docker/pulls/staphb/genomad)](https://hub.docker.com/r/staphb/genomad) | | https://github.com/apcamargo/genomad | +| [geNomad](https://hub.docker.com/r/staphb/genomad)
[![docker pulls](https://badgen.net/docker/pulls/staphb/genomad)](https://hub.docker.com/r/staphb/genomad) | | https://github.com/apcamargo/genomad | | [GenoVi](https://hub.docker.com/r/staphb/genovi)
[![docker pulls](https://badgen.net/docker/pulls/staphb/genovi)](https://hub.docker.com/r/staphb/genovi) | | https://github.com/robotoD/GenoVi | | [gfastats](https://hub.docker.com/r/staphb/gfastats)
[![docker pulls](https://badgen.net/docker/pulls/staphb/gfastats)](https://hub.docker.com/r/staphb/gfastats) | | https://github.com/vgl-hub/gfastats | | [Gubbins](https://hub.docker.com/r/staphb/gubbins)
[![docker pulls](https://badgen.net/docker/pulls/staphb/gubbins)](https://hub.docker.com/r/staphb/gubbins) | | https://github.com/nickjcroucher/gubbins | diff --git a/genomad/1.8.1/Dockerfile b/genomad/1.8.1/Dockerfile new file mode 100644 index 000000000..b765aedbb --- /dev/null +++ b/genomad/1.8.1/Dockerfile @@ -0,0 +1,84 @@ + +ARG GENOMAD_VER="1.8.1" +ARG ARAGORN_VER="1.2.41" +ARG MMSEQS2_VER="15-6f452" + +FROM ubuntu:jammy as builder + +ARG ARAGORN_VER + +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates \ + libc6-dev \ + make \ + gcc \ + wget + +# get ARAGORN +RUN wget -q https://www.trna.se/ARAGORN/Downloads/aragorn${ARAGORN_VER}.c && \ + gcc -O3 -ffast-math -finline-functions -o aragorn aragorn${ARAGORN_VER}.c && \ + /aragorn -h + +FROM ubuntu:jammy as app + +ARG GENOMAD_VER +ARG MMSEQS2_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="geNomad" +LABEL software.version="${GENOMAD_VER}" +LABEL description="Identification of mobile genetic elements" +LABEL website="https://github.com/apcamargo/genomad" +LABEL license="https://github.com/apcamargo/genomad/blob/main/LICENSE" +LABEL maintainer="Erin Young" +LABEL maintainer.email="eriny@utah.gov" + +COPY --from=builder /aragorn /usr/local/bin/ + +RUN apt-get update && apt-get install -y --no-install-recommends \ + ca-certificates \ + procps \ + python3 \ + python3-pip \ + wget && \ + apt-get autoclean && rm -rf /var/lib/apt/lists/* + +# get MMSEQS2 +RUN wget -q https://github.com/soedinglab/MMseqs2/releases/download/${MMSEQS2_VER}/mmseqs-linux-avx2.tar.gz && \ + tar -xvf mmseqs-linux-avx2.tar.gz && \ + rm mmseqs-linux-avx2.tar.gz + +# get genomad +RUN wget -q https://github.com/apcamargo/genomad/archive/refs/tags/v${GENOMAD_VER}.tar.gz && \ + python3 -m pip install --no-cache-dir v${GENOMAD_VER}.tar.gz && \ + rm -rf v${GENOMAD_VER}.tar.gz && \ + mkdir /data + +ENV PATH="/mmseqs/bin:$PATH" LC_ALL=C + +# downloads latest database, which is version 1.7 and about ~1.6 G in size +RUN genomad download-database . + +# 'CMD' instructions set a default command when the container is run. This is typically 'tool --help.' +CMD genomad --help + +# 'WORKDIR' sets working directory +WORKDIR /data + +FROM app as test + +# set working directory so that all test inputs & outputs are kept in /test +WORKDIR /test + +RUN genomad --help && \ + genomad --version && \ + aragorn -h && \ + mmseqs -h + +# downloads genome from NCBI and runs end-to-end (which looks like all steps) on the downloaded fasta +RUN pip list && \ + wget -q https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/025/259/185/GCA_025259185.1_ASM2525918v1/GCA_025259185.1_ASM2525918v1_genomic.fna.gz && \ + gunzip GCA_025259185.1_ASM2525918v1_genomic.fna.gz && \ + genomad end-to-end GCA_025259185.1_ASM2525918v1_genomic.fna test /genomad_db --splits 16 diff --git a/genomad/1.8.1/README.md b/genomad/1.8.1/README.md new file mode 100644 index 000000000..06ba24758 --- /dev/null +++ b/genomad/1.8.1/README.md @@ -0,0 +1,40 @@ +g# geNomad container + +Main tool: [geNomad](https://github.com/apcamargo/genomad/) + +Code repository: https://github.com/apcamargo/genomad/ + +Additional tools: +- aragorn: 1.2.41 +- mmseq2: 15-6f452 + +Basic information on how to use this tool: +- executable: genomad +- help: --help +- version: --version +- description: Identification of mobile genetic elements + +Additional information: + +The geNomad database version 1.7 is downloaded in /genomad_db. + +Full documentation: https://portal.nersc.gov/genomad/ + +## Example Usage + +```bash +# to download the database (database is already downloaded at /genomad_db) +genomad download-database . + +# recommended usage +genomad end-to-end input.fna output /genomad_db + +# subsections of genomad +genomad annotate metagenome.fna genomad_output /genomad_db +genomad find-proviruses metagenome.fna genomad_output /genomad_db +genomad marker-classification metagenome.fna genomad_output /genomad_db +genomad nn-classification metagenome.fna /genomad_output +genomad aggregated-classification metagenome.fna /genomad_output +genomad score-calibration metagenome.fna /genomad_output +genomad summary metagenome.fna /genomad_output +```