Skip to content

Source redundant environment variables from single script #375

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
thalassemia wants to merge 4 commits into
base: master
Choose a base branch
from
+19 −18
Open

Source redundant environment variables from single script #375

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
a0b1d9a
Source redundant environment variables from single script
thalassemia Jan 27, 2026
b18ea47
Remove unused cache dir variable
thalassemia Jan 27, 2026
adc54eb
Merge branch 'master' into singularity-dry
thalassemia Jan 30, 2026
4a8a4e5
Sporadic build issue should be fixed now
thalassemia Jan 30, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
24 changes: 6 additions & 18 deletions runscripts/container/Singularity
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,15 +9,8 @@ From: ghcr.io/astral-sh/uv@sha256:cda8422643a3d47dd5d457639dce8f5fbd130ef158ff4a
export IMAGE_GIT_HASH="{{ git_hash }}"
export IMAGE_GIT_BRANCH="{{ git_branch }}"
export IMAGE_TIMESTAMP="{{ timestamp }}"
export UV_CACHE_DIR="/vEcoli/.uv_cache"
# Silence warning about cache and sync targets being on different filesystems
export UV_LINK_MODE="copy"
# Prevent uv dirs from being created in any locations that may overlap with
# host filesystems that Apptainer may automount
export UV_TOOL_DIR="/vEcoli/.uv_tools"
export UV_TOOL_BIN_DIR="/vEcoli/.uv_tools/bin"
export UV_PYTHON_INSTALL_DIR="/vEcoli/.uv_python"
export UV_PYTHON_BIN_DIR="/vEcoli/.uv_python/bin"
# Source shared uv environment variables
. /vEcoli/singularity-env.sh
# runscripts/container/build-image.sh has some custom logic to replace this
# with the environment variables that are set in .env
{{ dot_env_vars }}
Expand All @@ -31,6 +24,7 @@ From: ghcr.io/astral-sh/uv@sha256:cda8422643a3d47dd5d457639dce8f5fbd130ef158ff4a

%files
repo.tar /repo.tar
runscripts/container/singularity-env.sh /vEcoli/singularity-env.sh

%post
mkdir -p /vEcoli
Expand All @@ -40,12 +34,6 @@ From: ghcr.io/astral-sh/uv@sha256:cda8422643a3d47dd5d457639dce8f5fbd130ef158ff4a
fi
apt-get update && apt-get install -y gcc procps nano curl
cd /vEcoli
# Silence warning about cache and sync targets being on different filesystems
export UV_LINK_MODE="copy"
# Prevent uv dirs from being created in any locations that may overlap with
# host filesystems that Apptainer may automount
export UV_TOOL_DIR="/vEcoli/.uv_tools"
export UV_TOOL_BIN_DIR="/vEcoli/.uv_tools/bin"
export UV_PYTHON_INSTALL_DIR="/vEcoli/.uv_python"
export UV_PYTHON_BIN_DIR="/vEcoli/.uv_python/bin"
UV_CACHE_DIR="/vEcoli/.uv_cache" UV_COMPILE_BYTECODE=1 uv sync --frozen
# Source shared uv environment variables
. /vEcoli/singularity-env.sh
UV_COMPILE_BYTECODE=1 uv sync --frozen
Copy link
Contributor Author

@thalassemia thalassemia Jan 27, 2026 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Compiling bytecode is recommended at image build time to improve container startup time. Once the container is started, Nextflow does not modify the code or install additional packages, so there is no point in leaving it on. If end users choose to modify code or install additional packages inside an interactive container, the latency added by bytecode recompilation is probably negligible.

13 changes: 13 additions & 0 deletions runscripts/container/singularity-env.sh
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,13 @@
#!/bin/bash
# Shared environment variables for Singularity build and runtime

# Silence warning about cache and sync targets being on different filesystems
export UV_LINK_MODE="copy"

# Prevent uv dirs from being created in any locations that may overlap with
# host filesystems that Apptainer may automount
export UV_TOOL_DIR="/vEcoli/.uv_tools"
export UV_TOOL_BIN_DIR="/vEcoli/.uv_tools/bin"
export UV_PYTHON_INSTALL_DIR="/vEcoli/.uv_python"
export UV_PYTHON_BIN_DIR="/vEcoli/.uv_python/bin"
export UV_CACHE_DIR="/vEcoli/.uv_cache"