Merge pull request #1 from YogiOnBioinformatics/python

Python Image

README.md

@@ -1,2 +1,6 @@
-# Comp-Bio-Containers
-Containers that I use in my work. 
+# Comp-Bio-Images
+
+Code to create images that I use for my daily work. 
+
+📂 `python`: 
+- Image for analyses done in `Python 3` using `Jupyter Lab`

python/Dockerfile

@@ -0,0 +1,18 @@
+# Python 3.10.5
+FROM python:3.10.5
+
+# add user 
+RUN useradd -ms /bin/bash yraghav
+USER yraghav
+
+# change working directory
+WORKDIR /home/yraghav/
+
+# Make directory and copy files
+RUN mkdir -p /home/yraghav/comp-bio-containers/python/
+COPY ./* /home/yraghav/comp-bio-containers/python/
+
+# ugprade pip and install requirements 
+RUN pip3 install --upgrade pip
+RUN pip install -r /home/yraghav/comp-bio-containers/python/requirements.txt
+

python/README.md

@@ -0,0 +1,29 @@
+# Python Image
+
+Image with tons of useful Python packages that can be used in Jupyter Lab. 
+
+[Docker Hub URL](https://hub.docker.com/repository/docker/yraghav97/python-image)
+<br>
+<br>
+
+📄 `requirements.txt`: 
+
+Python packages with versions that are installed in the image. 
+
+📄 `Dockerfile`: 
+
+Instructions for how to create the image. 
+
+📄 `build_and_publish.sh`: 
+
+Script to build and publish the image. 
+Need to replace `{insert tag}` with version. 
+
+
+📂 `rivanna/`📄`cluster_init.sh`: 
+
+Script to add to `iPython Kernel` so it can load the container. 
+
+📂 `rivanna/`📄`kernel.json`:
+
+File specifying the `Jupyter Lab` kernel settings in `Rivanna`. 

python/build_and_publish.sh

@@ -0,0 +1,6 @@
+# build docker image
+docker build -t python-image:{insert tag} . 
+
+# tag and push to docker hub
+docker tag python-image:{insert tag} yraghav97/python-image:{insert tag}
+docker push yraghav97/python-image:{insert tag}

python/kernel.json

@@ -0,0 +1,9 @@
+{
+ "argv": [
+  "/home/jve4pt/.local/share/jupyter/kernels/python/rivanna/cluster_init_singularity.sh",
+  "-f",
+  "{connection_file}"
+ ],
+ "display_name": "Yogi's Python Container",
+ "language": "python"
+}

python/requirements.txt

@@ -0,0 +1,121 @@
+anyio==3.6.1
+argon2-cffi==21.3.0
+argon2-cffi-bindings==21.2.0
+asttokens==2.0.5
+async-generator==1.10
+attrs==21.4.0
+Babel==2.10.3
+backcall==0.2.0
+beautifulsoup4==4.11.1
+bleach==5.0.1
+bokeh==2.4.3
+certifi==2022.6.15
+cffi==1.15.1
+charset-normalizer==2.1.0
+click==8.1.3
+cloudpickle==2.1.0
+cryptography==37.0.4
+cycler==0.11.0
+dask==2022.7.1
+debugpy==1.6.2
+decorator==5.1.1
+defusedxml==0.7.1
+entrypoints==0.4
+executing==0.9.0
+fastjsonschema==2.16.1
+Flask==2.1.3
+fonttools==4.34.4
+fsspec==2022.5.0
+h11==0.13.0
+idna==3.3
+iniconfig==1.1.1
+ipykernel==6.15.1
+ipython==8.4.0
+ipython-genutils==0.2.0
+itsdangerous==2.1.2
+jedi==0.18.1
+Jinja2==3.1.2
+joblib==1.1.0
+json5==0.9.8
+jsonschema==4.7.2
+jupyter-client==7.3.4
+jupyter-core==4.11.1
+jupyter-server==1.18.1
+jupyterlab==3.4.4
+jupyterlab-pygments==0.2.2
+jupyterlab-server==2.15.0
+kiwisolver==1.4.4
+locket==1.0.0
+MarkupSafe==2.1.1
+matplotlib==3.5.2
+matplotlib-inline==0.1.3
+mistune==0.8.4
+nbclassic==0.4.3
+nbclient==0.6.6
+nbconvert==6.5.0
+nbformat==5.4.0
+nest-asyncio==1.5.5
+networkx==2.8.5
+notebook==6.4.12
+notebook-shim==0.1.0
+numpy==1.23.1
+outcome==1.2.0
+packaging==21.3
+pandas==1.4.3
+pandocfilters==1.5.0
+parso==0.8.3
+partd==1.2.0
+patsy==0.5.2
+pexpect==4.8.0
+pickleshare==0.7.5
+Pillow==9.2.0
+plotly==5.9.0
+pluggy==1.0.0
+prometheus-client==0.14.1
+prompt-toolkit==3.0.30
+psutil==5.9.1
+ptyprocess==0.7.0
+pure-eval==0.2.2
+py==1.11.0
+pycparser==2.21
+Pygments==2.12.0
+pyOpenSSL==22.0.0
+pyparsing==3.0.9
+pyrsistent==0.18.1
+PySocks==1.7.1
+pytest==7.1.2
+python-dateutil==2.8.2
+pytz==2022.1
+PyYAML==6.0
+pyzmq==23.2.0
+requests==2.28.1
+scikit-learn==1.1.1
+scipy==1.8.1
+seaborn==0.11.2
+selenium==4.3.0
+Send2Trash==1.8.0
+six==1.16.0
+sklearn==0.0
+sniffio==1.2.0
+sortedcontainers==2.4.0
+soupsieve==2.3.2.post1
+stack-data==0.3.0
+statsmodels==0.13.2
+tenacity==8.0.1
+terminado==0.15.0
+threadpoolctl==3.1.0
+tinycss2==1.1.1
+tomli==2.0.1
+toolz==0.12.0
+tornado==6.2
+tqdm==4.64.0
+traitlets==5.3.0
+trio==0.21.0
+trio-websocket==0.9.2
+typing_extensions==4.3.0
+urllib3==1.26.11
+wcwidth==0.2.5
+webencodings==0.5.1
+websocket-client==1.3.3
+Werkzeug==2.2.0
+wsproto==1.1.0

python/rivanna/cluster_init_singularity.sh

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+#!/bin/bash
+
+module load singularity
+singularity exec $HOME/.local/share/jupyter/kernels/python/python-image.sif python -m ipykernel $@