From 18636393552f3c4fe6a64e46cdb2bbca7574c7c6 Mon Sep 17 00:00:00 2001 From: Curtis Kapsak Date: Sat, 9 Nov 2024 17:19:41 +0000 Subject: [PATCH] minor changes to medaka dockerfile and readme; also updated run-singularity.yml to use a different runner and more importantly apptainer github action to see if it will appropriately test singularity/apptainer functionality --- .github/workflows/run-singularity.yml | 10 +++++----- medaka/2.0.1/Dockerfile | 14 +++++++------- medaka/2.0.1/README.md | 6 +++--- 3 files changed, 15 insertions(+), 15 deletions(-) diff --git a/.github/workflows/run-singularity.yml b/.github/workflows/run-singularity.yml index 79ff5401f..fe3a5bad9 100644 --- a/.github/workflows/run-singularity.yml +++ b/.github/workflows/run-singularity.yml @@ -20,15 +20,15 @@ on: jobs: build_singularity: - runs-on: ubuntu-20.04 + runs-on: ubuntu-24.04 steps: - name: Check out Repo uses: actions/checkout@v4 - name: Set up Singularity - uses: eWaterCycle/setup-singularity@v7 + uses: eWaterCycle/setup-apptainer@v2 with: - singularity-version: 3.8.3 + apptainer-version: 1.3.5 - - name: Run a singularity container - run: singularity run docker://${{ inputs.repository_name }}/${{ inputs.image_name }} ${{ inputs.command }} + - name: Run a singularity/apptainer container + run: apptainer run docker://${{ inputs.repository_name }}/${{ inputs.image_name }} ${{ inputs.command }} diff --git a/medaka/2.0.1/Dockerfile b/medaka/2.0.1/Dockerfile index 6a99edf7c..dfd81d91a 100644 --- a/medaka/2.0.1/Dockerfile +++ b/medaka/2.0.1/Dockerfile @@ -5,7 +5,7 @@ ARG BCFTOOLS_VER=${SAMTOOLS_VER} ARG HTSLIB_VER=${SAMTOOLS_VER} ARG MINIMAP2_VER="2.28" -FROM ubuntu:jammy as builder +FROM ubuntu:jammy AS builder ARG SAMTOOLS_VER ARG BCFTOOLS_VER @@ -66,7 +66,7 @@ RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VE make install RUN wget -q https://github.com/samtools/htslib/releases/download/${HTSLIB_VER}/htslib-${HTSLIB_VER}.tar.bz2 && \ - tar -vxjf htslib-${HTSLIB_VER}.tar.bz2 && \ + tar -xjf htslib-${HTSLIB_VER}.tar.bz2 && \ rm -v htslib-${HTSLIB_VER}.tar.bz2 && \ cd htslib-${HTSLIB_VER} && \ ./configure && \ @@ -74,10 +74,10 @@ RUN wget -q https://github.com/samtools/htslib/releases/download/${HTSLIB_VER}/h make install RUN curl -L https://github.com/lh3/minimap2/releases/download/v${MINIMAP2_VER}/minimap2-${MINIMAP2_VER}_x64-linux.tar.bz2 | tar -jxvf - --no-same-owner && \ - mv minimap2-${MINIMAP2_VER}_x64-linux/minimap2 /usr/local/bin + mv -v minimap2-${MINIMAP2_VER}_x64-linux/minimap2 /usr/local/bin ### start of app stage ### -FROM ubuntu:jammy as app +FROM ubuntu:jammy AS app ARG MEDAKA_VER ARG PYABPOA_VER @@ -91,7 +91,7 @@ LABEL description="Consensus sequence correction provided by ONT Research" LABEL website="https://github.com/nanoporetech/medaka" LABEL license="https://github.com/nanoporetech/medaka/blob/master/LICENSE.md" LABEL maintainer="Curtis Kapsak" -LABEL maintainer.email="pjx8@cdc.gov" +LABEL maintainer.email="kapsakcj@gmail.com" LABEL maintainer1="Erin Young" LABEL maintainer1.email="eriny@utah.gov" @@ -132,10 +132,10 @@ ENV LC_ALL=C WORKDIR /data # default command is to pull up help options -CMD medaka --help +CMD [ "medaka", "--help" ] ### start of test stage ### -FROM app as test +FROM app AS test RUN apt-get update && apt-get install --no-install-recommends -y wget diff --git a/medaka/2.0.1/README.md b/medaka/2.0.1/README.md index 78b25c98c..c1cf4e82f 100644 --- a/medaka/2.0.1/README.md +++ b/medaka/2.0.1/README.md @@ -1,8 +1,9 @@ -# medaka container +# Medaka container Main tool : [medaka](https://github.com/nanoporetech/medaka) Additional tools: + - bcftools version 1.21 - samtools version 1.21 - htslib version 1.21 @@ -16,18 +17,17 @@ Full documentation: [https://github.com/nanoporetech/medaka](https://github.com/ ## Example Usage ```bash - # listing models medaka tools list\_models # polishing medaka_consensus -i sample.fastq.gz -d sample.fasta -o medaka/sample -t 4 - ``` ## Medaka models Medaka updates frequently. These are the medaka models in this image: + ``` Available: r103_fast_g507, r103_fast_snp_g507, r103_fast_variant_g507, r103_hac_g507, r103_hac_snp_g507, r103_hac_variant_g507, r103_sup_g507, r103_sup_snp_g507, r103_sup_variant_g507, r1041_e82_260bps_fast_g632, r1041_e82_260bps_fast_variant_g632, r1041_e82_260bps_hac_g632, r1041_e82_260bps_hac_v4.0.0, r1041_e82_260bps_hac_v4.1.0, r1041_e82_260bps_hac_variant_g632, r1041_e82_260bps_hac_variant_v4.1.0, r1041_e82_260bps_joint_apk_ulk_v5.0.0, r1041_e82_260bps_sup_g632, r1041_e82_260bps_sup_v4.0.0, r1041_e82_260bps_sup_v4.1.0, r1041_e82_260bps_sup_variant_g632, r1041_e82_260bps_sup_variant_v4.1.0, r1041_e82_400bps_bacterial_methylation, r1041_e82_400bps_fast_g615, r1041_e82_400bps_fast_g632, r1041_e82_400bps_fast_variant_g615, r1041_e82_400bps_fast_variant_g632, r1041_e82_400bps_hac_g615, r1041_e82_400bps_hac_g632, r1041_e82_400bps_hac_v4.0.0, r1041_e82_400bps_hac_v4.1.0, r1041_e82_400bps_hac_v4.2.0, r1041_e82_400bps_hac_v4.3.0, r1041_e82_400bps_hac_v5.0.0, r1041_e82_400bps_hac_variant_g615, r1041_e82_400bps_hac_variant_g632, r1041_e82_400bps_hac_variant_v4.1.0, r1041_e82_400bps_hac_variant_v4.2.0, r1041_e82_400bps_hac_variant_v4.3.0, r1041_e82_400bps_hac_variant_v5.0.0, r1041_e82_400bps_sup_g615, r1041_e82_400bps_sup_v4.0.0, r1041_e82_400bps_sup_v4.1.0, r1041_e82_400bps_sup_v4.2.0, r1041_e82_400bps_sup_v4.3.0, r1041_e82_400bps_sup_v5.0.0, r1041_e82_400bps_sup_variant_g615, r1041_e82_400bps_sup_variant_v4.1.0, r1041_e82_400bps_sup_variant_v4.2.0, r1041_e82_400bps_sup_variant_v4.3.0, r1041_e82_400bps_sup_variant_v5.0.0, r104_e81_fast_g5015, r104_e81_fast_variant_g5015, r104_e81_hac_g5015, r104_e81_hac_variant_g5015, r104_e81_sup_g5015, r104_e81_sup_g610, r104_e81_sup_variant_g610, r941_e81_fast_g514, r941_e81_fast_variant_g514, r941_e81_hac_g514, r941_e81_hac_variant_g514, r941_e81_sup_g514, r941_e81_sup_variant_g514, r941_min_fast_g507, r941_min_fast_snp_g507, r941_min_fast_variant_g507, r941_min_hac_g507, r941_min_hac_snp_g507, r941_min_hac_variant_g507, r941_min_sup_g507, r941_min_sup_snp_g507, r941_min_sup_variant_g507, r941_prom_fast_g507, r941_prom_fast_snp_g507, r941_prom_fast_variant_g507, r941_prom_hac_g507, r941_prom_hac_snp_g507, r941_prom_hac_variant_g507, r941_prom_sup_g507, r941_prom_sup_snp_g507, r941_prom_sup_variant_g507, r941_sup_plant_g610, r941_sup_plant_variant_g610 Default consensus: r1041_e82_400bps_sup_v5.0.0