feat: create ichorcna docker

ichorCNA/ccbr_ichorcna_0.3.2/Dockerfile.v1

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+FROM nciccbr/ccbr_ubuntu_base_20.04:v7
+
+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}
+
+COPY environment.yml /data2/
+ENV CONDA_ENV=ichorcna
+RUN mamba env create -n ${CONDA_ENV} -f /data2/environment.yml && \
+    /opt2/conda/bin/conda init bash && \
+    echo "conda activate ${CONDA_ENV}" >> ~/.bashrc && \
+    chmod -R a+rx /opt2
+
+ENV PATH="/opt2/conda/envs/${CONDA_ENV}/bin:/opt2/conda/bin:$PATH"
+
+# Install HMMcopy utilities
+RUN cd /data2 && \
+    git clone https://github.com/shahcompbio/hmmcopy_utils.git && \
+    cd hmmcopy_utils && \
+    cmake . && \
+    make && \
+    cp bin/* /opt2/conda/envs/${CONDA_ENV}/bin/
+
+# Clone ichorCNA v0.3.2 for scripts
+RUN cd /data2 && \
+    git clone https://github.com/broadinstitute/ichorCNA.git && \
+    ln -s /data2/ichorCNA/scripts /opt2/conda/envs/${CONDA_ENV}/lib/R/library/ichorCNA/scripts
+
+# Copy and run test
+COPY test_ichorcna.sh /data2/
+RUN chmod +x /data2/test_ichorcna.sh && \
+    /bin/bash -c "source activate ${CONDA_ENV} && /data2/test_ichorcna.sh"
+
+COPY ${DOCKERFILE} /opt2/Dockerfile_${REPONAME}.${BUILD_TAG}
+
+WORKDIR /data2

ichorCNA/ccbr_ichorcna_0.3.2/environment.yml

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+name: ichorcna
+channels:
+  - bioconda
+  - conda-forge
+  - defaults
+dependencies:
+  - python=3.9
+  - seqtk=1.5
+  - fastp=0.24.0
+  - r-base=4.2
+  - r-devtools=2.4.5
+  - r-plyr=1.8.9
+  - r-stringi
+  - icu=70
+  - bioconductor-hmmcopy
+  - bioconductor-genomeinfodb
+  - bioconductor-genomicranges
+  - r-ichorcna=0.3.2
+  - cmake=3.26
+  - make
+  - cxx-compiler
+  - pip=25.1.1
+  - pip:
+    - atari==0.1.4
+    - igv-reports==1.16.1

ichorCNA/ccbr_ichorcna_0.3.2/test_ichorcna.sh

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+#!/bin/bash
+set -e
+
+echo "Testing ichorCNA v0.3.2 installation..."
+
+# Create test directories
+mkdir -p /data2/ichorcna_test/output
+
+# Set ichorCNA path (should be set by Dockerfile, but fallback if needed)
+if [ -z "${ICHORCNA_PATH}" ]; then
+    ICHORCNA_PATH="/data2/ichorCNA"
+fi
+
+echo "Using ichorCNA at: ${ICHORCNA_PATH}"
+
+# Test 1: Verify readCounter exists (from HMMcopy)
+echo "Testing readCounter..."
+readCounter --help > /dev/null 2>&1 || echo "Warning: readCounter not found (optional)"
+
+# Test 2: Verify ichorCNA R package loads and check version
+echo "Testing ichorCNA R package..."
+Rscript -e "library(ichorCNA); v <- packageVersion('ichorCNA'); cat('ichorCNA version:', as.character(v), '\n'); stopifnot(as.character(v) == '0.3.2')"
+
+# Test 3: Check required script exists
+echo "Checking runIchorCNA.R script..."
+if [ ! -f "${ICHORCNA_PATH}/scripts/runIchorCNA.R" ]; then
+    echo "ERROR: runIchorCNA.R script not found"
+    exit 1
+fi
+
+# Test 4: Check required extdata files exist (hg19 for test data)
+echo "Checking extdata files..."
+ls -lh ${ICHORCNA_PATH}/inst/extdata/gc_hg19_1000kb.wig
+ls -lh ${ICHORCNA_PATH}/inst/extdata/map_hg19_1000kb.wig
+ls -lh ${ICHORCNA_PATH}/inst/extdata/MBC_315.ctDNA.reads.wig
+
+# Test 5: Run ichorCNA on test data (using hg19 references to match test data)
+echo "Running ichorCNA on test sample..."
+Rscript ${ICHORCNA_PATH}/scripts/runIchorCNA.R \
+    --libdir "${ICHORCNA_PATH}" \
+    --id test_sample \
+    --WIG ${ICHORCNA_PATH}/inst/extdata/MBC_315.ctDNA.reads.wig \
+    --gcWig ${ICHORCNA_PATH}/inst/extdata/gc_hg19_1000kb.wig \
+    --mapWig ${ICHORCNA_PATH}/inst/extdata/map_hg19_1000kb.wig \
+    --ploidy "c(2,3)" \
+    --normal "c(0.5,0.6,0.7,0.8,0.9)" \
+    --maxCN 5 \
+    --includeHOMD False \
+    --chrs "c(1:22, \"X\")" \
+    --chrTrain "c(1:22)" \
+    --estimateNormal True \
+    --estimatePloidy True \
+    --estimateScPrevalence False \
+    --txnE 0.9999 \
+    --txnStrength 10000 \
+    --outDir /data2/ichorcna_test/output
+
+# Test 6: Verify output files were created
+echo "Verifying output files..."
+if [ ! -f "/data2/ichorcna_test/output/test_sample.cna.seg" ]; then
+    echo "ERROR: Expected output file test_sample.cna.seg not created"
+    exit 1
+fi
+
+if [ ! -f "/data2/ichorcna_test/output/test_sample.seg.txt" ]; then
+    echo "ERROR: Expected output file test_sample.seg.txt not created"
+    exit 1
+fi
+
+# Test 7: Check output contains data
+SEG_LINES=$(wc -l < /data2/ichorcna_test/output/test_sample.seg.txt)
+if [ ${SEG_LINES} -lt 2 ]; then
+    echo "ERROR: Output segmentation file is empty or too small"
+    exit 1
+fi
+
+echo "✓ All ichorCNA v0.3.2 tests passed!"
+echo ""
+echo "Output files:"
+ls -lh /data2/ichorcna_test/output/
+
+# Clean up test directory
+rm -rf /data2/ichorcna_test

ichorCNA/ccbr_ichorcna_0.3.2/v1-dev.README.md

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+## CCBR/Dockers2 nciccbr/ccbr_ichorcna_0.3.2:v1-dev
+
+Dockerfile source: https://github.com/CCBR/Dockers2/blob/a0ac517d963fbeddfb01c810fbd06d9365c02f22/ichorCNA/ccbr_ichorcna_0.3.2/Dockerfile.v1
+
+
+Built on: 2025-11-11_19:09:31 
+
+Build tag: v1-dev 
+
+Base image: nciccbr/ccbr_ubuntu_base_20.04:v7 
+
+Dockerfile path in repo: ichorCNA/ccbr_ichorcna_0.3.2/Dockerfile.v1 
+
+
+| Tool | Version |
+|---------|---------|
+| bbtools | NOTINDOCKER |
+| bcftools | 1.10.2 using htslib 1.10.2-3ubuntu0.1 |
+| bedops | 2.4.37 typical |
+| bedtools | v2.27.1 |
+| bowtie | 1.2.3 |
+| bowtie2 | 2.3.5.1 |
+| bwa | 0.7.17-r1188 |
+| cutadapt | NOTINDOCKER |
+| fastqc | NOTINDOCKER |
+| fastQValidator | NOTINDOCKER |
+| fastqscreen | NOTINDOCKER |
+| git | 2.25.1 |
+| java | 1.8.0_422 |
+| kraken2 | NOTINDOCKER |
+| kronatools | NOTINDOCKER |
+| multiqc | NOTINDOCKER |
+| parallel | 20161222 |
+| picard | NOTINDOCKER |
+| pigz | 2.4 |
+| preseq | NOTINDOCKER |
+| python2 | 2.7.18 |
+| python3 | 3.9.23 |
+| qualimap | NOTINDOCKER |
+| rsem | NOTINDOCKER |
+| rseqc | NOTINDOCKER |
+| samtools | 1.10 |
+| ucsc_tools | NOTINDOCKER |
+| vcftools | 0.1.16 |
+