Skip to content
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

python3: add missing packages #274

Merged
merged 4 commits into from
Aug 23, 2024
+17 −1
Merged

python3: add missing packages #274

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
4e4badd
`python3`: add missing packages
espenhgn Aug 23, 2024
cd1c193
pip install pysurvival, add tests
espenhgn Aug 23, 2024
cb68e51
drop pysurvival
espenhgn Aug 23, 2024
67fe0c4
pin versions
espenhgn Aug 23, 2024
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
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ If MD5 sum is not listed for a certain release then it means that the container

### Added

* Add Python packages `imbalanced-learn, lightgbm, openpyxl` + PRSice_linux binary to `python3.sif` container
* Add Conda environment file for project dependencies
* Add Python packages `scikit-survival, pandas-plink, numba, xmltodict, pyliftover, configparser, intervaltree` to `python3.sif` container
* Add `Haplin`, `WSpiller/MVMR`, `noahlorinczcomi/MRBEE` R packages to `r.sif` container
Expand Down
10 changes: 9 additions & 1 deletion docker/dockerfiles/python3/Dockerfile
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -22,14 +22,17 @@ RUN mamba install python=3.10.6 \
configparser=7.0.0 \
"h5py=3.7.0=nompi*" \
jupyterlab=3.4.8 \
lightgbm=4.5.0 \
lifelines=0.27.0 \
imbalanced-learn=0.12.3 \
intervaltree=3.1.0 \
matplotlib-venn=0.11.5 \
matplotlib=3.6.0 \
more-itertools=9.0.0 \
numdifftools=0.9.39 \
numba=0.60.0 \
numpy=1.23.3 \
openpyxl=3.1.5 \
pandas=1.5.0 \
pandas-plink=2.2.9 \
psutil=5.9.3 \
Expand All @@ -46,7 +49,6 @@ RUN mamba install python=3.10.6 \
--yes && \
mamba clean -a -y


# pip install stuff in env.
RUN pip install --no-cache-dir cbgen==1.0.2 && \
pip install --no-cache-dir bgen-reader==4.0.8 && \
Expand Down Expand Up @@ -75,6 +77,12 @@ WORKDIR /tools/ukb
RUN git clone https://github.com/precimed/ukb.git . && \
git reset --hard dc57e0d8380cd9b2eca479dc6f181d76ca5a429a

# PRSice_linux binary (useful)
WORKDIR /tmp/prsice
COPY /scripts/install_prsice.sh /tmp/prsice/
RUN bash /tmp/prsice/install_prsice.sh && \
rm -rf /tmp/prsice

WORKDIR /tools

# https://github.com/comorment/containers/issues/267:
Expand Down
7 changes: 7 additions & 0 deletions tests/test_python3.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,10 @@ def test_python3_plink():
out = subprocess.run(call.split(' '))
assert out.returncode == 0

def test_python3_prsice():
call = f'singularity run {pth} PRSice_linux --version'
out = subprocess.run(call.split(' '))
assert out.returncode == 0

def test_python3_python():
call = f'singularity run {pth} python --version'
Expand Down Expand Up @@ -51,14 +55,17 @@ def test_python3_packages():
packages = [
'configparser',
'h5py',
'imblearn',
'intervaltree',
'ldpred',
'lifelines',
'lightgbm',
'matplotlib',
'matplotlib_venn',
'numba',
'numdifftools',
'numpy',
'openpyxl',
'pandas',
'pandas_plink',
'plinkio',
Expand Down
Loading