Update Genomad to 1.11.2

README.md

@@ -183,7 +183,7 @@ To learn more about the docker pull rate limits and the open source software pro
 | [GAMBIT](https://hub.docker.com/r/staphb/gambit) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gambit)](https://hub.docker.com/r/staphb/gambit) | <details><summary>Click to see all versions</summary> <ul><li>[0.3.0](./build-files/gambit/0.3.0/)</li><li>[0.4.0](./build-files/gambit/0.4.0/)</li><li>[0.5.0](./build-files/gambit/0.5.0/)</li><li>[1.0.0](./build-files/gambit/1.0.0/)</li></ul> </details> | https://github.com/jlumpe/gambit |
 | [GAMMA](https://hub.docker.com/r/staphb/gamma) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gamma)](https://hub.docker.com/r/staphb/gamma) | <details><summary>Click to see all versions</summary> <ul><li>[1.4](./build-files/gamma/1.4/)</li><li>[2.1](./build-files/gamma/2.1/)</li><li>[2.2](./build-files/gamma/2.2/)</li></ul> </details> | https://github.com/rastanton/GAMMA/ |
 | [GenoFLU](https://hub.docker.com/r/staphb/genoflu) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genoflu)]() | <details><summary>Click to see all versions</summary> <ul><li>[1.03](./build-files/genoflu/1.03/)</li><li>[1.05](./build-files/genoflu/1.05/)</li><li>[1.06](./build-files/genoflu/1.06/)</li></ul> </details> | https://github.com/USDA-VS/GenoFLU |
-| [geNomad](https://hub.docker.com/r/staphb/genomad) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genomad)](https://hub.docker.com/r/staphb/genomad) | <details><summary>Click to see all versions</summary> <ul><li>[1.7.4](./build-files/genomad/1.7.4/)</li><li>[1.8.0](./build-files/genomad/1.8.0/)</li><li>[1.8.1](./build-files/genomad/1.8.1/)</li><li>[1.11.0](./build-files/genomad/1.11.0/)</li><li>[1.11.1](./build-files/genomad/1.11.1/)</li></ul> </details> | https://github.com/apcamargo/genomad |
+| [geNomad](https://hub.docker.com/r/staphb/genomad) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genomad)](https://hub.docker.com/r/staphb/genomad) | <details><summary>Click to see all versions</summary> <ul><li>[1.7.4](./build-files/genomad/1.7.4/)</li><li>[1.8.0](./build-files/genomad/1.8.0/)</li><li>[1.8.1](./build-files/genomad/1.8.1/)</li><li>[1.11.0](./build-files/genomad/1.11.0/)</li><li>[1.11.1](./build-files/genomad/1.11.1/)</li><li>[1.11.2](./build-files/genomad/1.11.2/)</li></ul> </details> | https://github.com/apcamargo/genomad |
 | [GenoVi](https://hub.docker.com/r/staphb/genovi) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/genovi)](https://hub.docker.com/r/staphb/genovi) | <details><summary>Click to see all versions</summary> <ul><li>[0.2.16](./build-files/genovi/0.2.16/)</li></ul> </details> | https://github.com/robotoD/GenoVi |
 | [gfastats](https://hub.docker.com/r/staphb/gfastats) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/gfastats)](https://hub.docker.com/r/staphb/gfastats) | <details><summary>Click to see all versions</summary> <ul><li>[1.3.6](./build-files/gfastats/1.3.6/)</li><li>[1.3.7](./build-files/gfastats/1.3.7/)</li><li>[1.3.10](./build-files/gfastats/1.3.10/)</li><li>[1.3.11](./build-files/gfastats/1.3.11/)</li></ul> </details> | https://github.com/vgl-hub/gfastats |
 | [grandeur_ref](https://hub.docker.com/r/staphb/grandeur_ref) <br/> [![docker pulls](https://badgen.net/docker/pulls/staphb/grandeur_ref)](https://hub.docker.com/r/staphb/grandeur_ref) | <details><summary>Click to see all versions</summary> <ul><li>[4.5](./build-files/grandeur_ref/4.5/)</li><li>[4.6](./build-files/grandeur_ref/4.6/)</li></ul> </details> | Part of https://github.com/UPHL-BioNGS/Grandeur |

build-files/genomad/1.11.2/Dockerfile

@@ -0,0 +1,91 @@
+ARG GENOMAD_VER="1.11.2"
+ARG ARAGORN_VER="1.2.41"
+ARG MMSEQS2_VER="17-b804f"
+
+FROM ubuntu:noble 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:noble 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:noble"
+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 add (with tensorflow cpu and tensorflow)
+RUN wget -q https://github.com/apcamargo/genomad/archive/refs/tags/v${GENOMAD_VER}.tar.gz && \
+    python3 -m pip install --no-cache-dir --break-system-packages v${GENOMAD_VER}.tar.gz && \
+    python3 -m pip install --no-cache-dir --break-system-packages tensorflow-cpu && \
+    rm -rf v${GENOMAD_VER}.tar.gz && \
+    mkdir /data
+
+# get genomad (without tensorflow CPU) (Intitially was throwing an error)
+# RUN wget -q https://github.com/apcamargo/genomad/archive/refs/tags/v${GENOMAD_VER}.tar.gz && \
+#     python3 -m pip install --no-cache-dir --break-system-packages v${GENOMAD_VER}.tar.gz && \
+#     rm -rf v${GENOMAD_VER}.tar.gz && \
+#     mkdir /data
+
+#ENV PATH="/mmseqs/bin:$PATH" LC_ALL=C 
+ENV PATH="/mmseqs/bin:$PATH" LC_ALL=C CUDA_VISIBLE_DEVICES=""
+
+# 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

build-files/genomad/1.11.2/README.md

@@ -0,0 +1,40 @@
+# geNomad container
+
+Main tool: [geNomad](https://github.com/apcamargo/genomad/)
+
+Code repository: https://github.com/apcamargo/genomad/
+
+Additional tools:
+- aragorn: 1.2.41
+- mmseq2: 17-b804f
+
+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
+```