diff --git a/shiver/ccbr_shiver_1.7.3/Dockerfile.v2 b/shiver/ccbr_shiver_1.7.3/Dockerfile.v2 new file mode 100644 index 00000000..1ec7d698 --- /dev/null +++ b/shiver/ccbr_shiver_1.7.3/Dockerfile.v2 @@ -0,0 +1,65 @@ +FROM nciccbr/ccbr_ubuntu_22.04:v4 + +ARG BUILD_DATE="000000" +ENV BUILD_DATE=${BUILD_DATE} +ARG BUILD_TAG="000000" +ENV BUILD_TAG=${BUILD_TAG} +ARG REPONAME="000000" +ENV REPONAME=${REPONAME} +ARG DOCKERFILE="Dockerfile" +ENV DOCKERFILE=${DOCKERFILE} + +ENV DEBIAN_FRONTEND=noninteractive + +# Install Miniforge/conda/mamba into /opt2/conda +RUN wget --quiet "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh" -O /tmp/miniforge.sh && \ + /bin/bash /tmp/miniforge.sh -b -p /opt2/conda && \ + rm -f /tmp/miniforge.sh && \ + chmod -R a+rx /opt2/conda + +ENV PATH="/opt2/conda/bin:$PATH" + +RUN conda config --add channels bioconda && \ + conda config --add channels conda-forge && \ + conda config --add channels defaults && \ + conda config --set channel_priority strict && \ + conda install -n base -y mamba && \ + conda clean -afy + +COPY environment.yml /data2/ + +RUN mamba env create -n shiver -f /data2/environment.yml && \ + mamba clean -a -y + +ENV PATH="/opt2/conda/envs/shiver/bin:/opt2/conda/bin:$PATH" + +RUN cd /data2 && \ + git clone https://github.com/ChrisHIV/shiver.git && \ + cp -r shiver/data/example_input test_data && \ + rm -rf shiver + +RUN cd /data2 && \ + wget -O hxb2_ref.fasta "https://www.ncbi.nlm.nih.gov/sviewer/viewer.fcgi?id=K03455&db=nuccore&report=fasta" + +RUN cd /data2 && \ + echo "Running shiver test..." && \ + shiver_init.sh my_init_dir /opt2/conda/envs/shiver/bin/config.sh \ + hxb2_ref.fasta \ + test_data/adapters_Illumina.fasta \ + test_data/primers_GallEtAl2012.fasta && \ + shiver_align_contigs.sh my_init_dir /opt2/conda/envs/shiver/bin/config.sh \ + test_data/MysteryHIV_contigs.fasta my_output_id && \ + shiver_map_reads.sh my_init_dir /opt2/conda/envs/shiver/bin/config.sh \ + test_data/MysteryHIV_contigs.fasta my_output_id \ + my_output_id.blast my_output_id_cut_wRefs.fasta \ + test_data/MysteryHIV_1.fastq \ + test_data/MysteryHIV_2.fastq && \ + echo "Shiver test completed successfully!" && \ + ls -la my_output_id* + +COPY test_shiver.sh /data2/ +RUN chmod +x /data2/test_shiver.sh + +COPY ${DOCKERFILE} /opt2/Dockerfile_${REPONAME}.${BUILD_TAG} + +WORKDIR /data2 \ No newline at end of file diff --git a/shiver/ccbr_shiver_1.7.3/environment.yml b/shiver/ccbr_shiver_1.7.3/environment.yml index 1d962185..40141ba4 100644 --- a/shiver/ccbr_shiver_1.7.3/environment.yml +++ b/shiver/ccbr_shiver_1.7.3/environment.yml @@ -4,12 +4,18 @@ channels: - conda-forge - defaults dependencies: - - python=3.13 + - python=3.10 - shiver=1.7.3 - biopython=1.85 - - numpy=2.3.0 - - pandas=2.3.0 + - numpy + - pandas + - matplotlib + - pysam - samtools=1.22 + - bcftools + - htslib + - gatk4=4.6.2.0 + - openjdk=17 - blast=2.16.0 - mafft=7.526 - trimmomatic=0.39 @@ -19,9 +25,8 @@ dependencies: - entrez-direct=22.4 - wget=1.21.4 - curl=8.14.1 - - openjdk=23.0.2 - pip=25.1.1 - pip: - - pyfastaq==3.17.0 - - aiofiles==24.1.0 - - setuptools==80.9.0 + - pyfastaq==3.17.0 + - aiofiles==24.1.0 + - setuptools==80.9.0 \ No newline at end of file diff --git a/shiver/ccbr_shiver_1.7.3/v2-dev.README.md b/shiver/ccbr_shiver_1.7.3/v2-dev.README.md new file mode 100644 index 00000000..e278cf8e --- /dev/null +++ b/shiver/ccbr_shiver_1.7.3/v2-dev.README.md @@ -0,0 +1,32 @@ +## CCBR/Dockers2 nciccbr/ccbr_shiver_1.7.3:v2-dev + +Dockerfile source: https://github.com/CCBR/Dockers2/blob/a06b97d223ffd982149eb1cd7469209a2006c35a/shiver/ccbr_shiver_1.7.3/Dockerfile.v2 + + +Built on: 2026-03-19_18:14:38 + +Build tag: v2-dev + +Base image: nciccbr/ccbr_ubuntu_22.04:v4 + +Dockerfile path in repo: shiver/ccbr_shiver_1.7.3/Dockerfile.v2 + + +| Tool | Version | +|---------|---------| +| bcftools | NOTINDOCKER | +| bedops | 2.4.40 typical | +| bedtools | v2.30.0 | +| bowtie | 1.3.1 | +| bowtie2 | 2.4.4 | +| bwa | NOTINDOCKER | +| cutadapt | NOTINDOCKER | +| git | 2.34.1 | +| java | 2026-01-20 | +| multiqc | 1.25.1 | +| parallel | 20210822 | +| pigz | 2.6 | +| python2 | 2.7.18 | +| python3 | 3.10.20 | +| samtools | 1.22.1 | +| vcftools | 0.1.16 | \ No newline at end of file