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Revert "add new tools" #322

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Merged
pantherman594 merged 2 commits into from
Feb 17, 2026
Merged

Revert "add new tools" #322

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964db9f
Revert "add new tools (#309)"
pantherman594 Feb 17, 2026
32f2c6f
Merge remote-tracking branch 'origin/master' into revert-309-yuhuyoyo…
pantherman594 Feb 17, 2026
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19 changes: 0 additions & 19 deletions features/src/workbench-tools/install.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -89,19 +89,6 @@ CONDA_PACKAGES_2=(
"plink2"
"regenie"
"vcftools"
"conda-forge::google-cloud-storage"
"conda-forge::ipykernel"
"conda-forge::ipywidgets"
"conda-forge::jupyter"
"conda-forge::openai"
"conda-forge::matplotlib"
"conda-forge::numpy"
"conda-forge::plotly"
"conda-forge::pandas"
"conda-forge::seaborn"
"conda-forge::scikit-learn"
"conda-forge::scipy"
"conda-forge::tqdm"
)

mkdir -p "${WORKBENCH_TOOLS_DIR}"
Expand Down Expand Up @@ -130,12 +117,6 @@ chown -R "${USERNAME}:" "${WORKBENCH_TOOLS_DIR}"
# Set CROMWELL_JAR environment variable
printf 'export CROMWELL_JAR="%s"\n' "${WORKBENCH_TOOLS_DIR}/2/share/cromwell/cromwell.jar"

# Prepend workbench-tools Python site-packages to PYTHONPATH to prevent conflicts
# with base image Python environments (e.g., NeMo's Python 3.12). This ensures
# workbench-tools packages and their dependencies are found first.
# shellcheck disable=SC2016 # we want $PYTHONPATH to be evaluated at runtime
printf 'export PYTHONPATH="%s/2/lib/python3.9/site-packages:${PYTHONPATH:-}"\n' "${WORKBENCH_TOOLS_DIR}"

# Make dsub a function that includes the correct PYTHONPATH. NeMo sets
# PYTHONPATH so we need to override it here. We use a function instead of an
# alias because aliases are not expanded in non-interactive shells.
Expand Down
14 changes: 0 additions & 14 deletions test/test.sh
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Expand Up @@ -44,20 +44,6 @@ if [[ "$HAS_WORKBENCH_TOOLS" == "true" ]]; then
check "vep: filter_vep" "filter_vep --help > /dev/null"
check "vep: variant_recoder" "variant_recoder --help | head -n10"
check "vep: haplo" "haplo --help | head -n10"
# Python packages (use conda python directly)
check "python: google-cloud-storage" '/opt/workbench-tools/2/bin/python3 -c "import google.cloud.storage"'
check "python: ipykernel" '/opt/workbench-tools/2/bin/python3 -c "import ipykernel"'
check "python: ipywidgets" '/opt/workbench-tools/2/bin/python3 -c "import ipywidgets"'
check "python: jupyter" '/opt/workbench-tools/2/bin/python3 -c "import jupyter"'
check "python: openai" '/opt/workbench-tools/2/bin/python3 -c "import openai"'
check "python: matplotlib" '/opt/workbench-tools/2/bin/python3 -c "import matplotlib"'
check "python: numpy" '/opt/workbench-tools/2/bin/python3 -c "import numpy"'
check "python: plotly" '/opt/workbench-tools/2/bin/python3 -c "import plotly"'
check "python: pandas" '/opt/workbench-tools/2/bin/python3 -c "import pandas"'
check "python: seaborn" '/opt/workbench-tools/2/bin/python3 -c "import seaborn"'
check "python: scikit-learn" '/opt/workbench-tools/2/bin/python3 -c "import sklearn"'
check "python: scipy" '/opt/workbench-tools/2/bin/python3 -c "import scipy"'
check "python: tqdm" '/opt/workbench-tools/2/bin/python3 -c "import tqdm"'
fi

# The postgres-client feature should install these
Expand Down