genepattern / single_cell_clustering_notebook

Single-cell RNA-seq Clustering Analysis Notebook

Try out the notebook by launching the binder above. It may be slow to launch while it installs package dependencies.

Local Installation

This notebook uses Python 3.6.

1. Install required python packages with:

pip install -r requirements.txt

2. Run the post install script.

bash postBuild

3. Launch Jupyter Notebook to open the notebook titled Single Cell RNA-seq Clustering Analysis.ipynb

single_cell_clustering_notebook's Issues

Binder no longer starts

This notebook no longer runs in Binder. When you click the "launch binder" badge, it results in the following error:

Click for Binder error message

Waiting for build to start...
Picked Git content provider.
Cloning into '/tmp/repo2docker2roswvck'...
HEAD is now at 133cea6 Merge pull request #27 from genepattern/develop
Building conda environment for python=3.7Using PythonBuildPack builder
Building conda environment for python=3.7Building conda environment for python=3.7Step 1/53 : FROM buildpack-deps:bionic
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Step 2/53 : ENV DEBIAN_FRONTEND=noninteractive
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Step 3/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends locales > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
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Step 4/53 : RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen &&     locale-gen
 ---> Using cache
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Step 5/53 : ENV LC_ALL en_US.UTF-8
 ---> Using cache
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Step 6/53 : ENV LANG en_US.UTF-8
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Step 7/53 : ENV LANGUAGE en_US.UTF-8
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Step 8/53 : ENV SHELL /bin/bash
 ---> Using cache
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Step 9/53 : ARG NB_USER
 ---> Using cache
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Step 10/53 : ARG NB_UID
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Step 11/53 : ENV USER ${NB_USER}
 ---> Using cache
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Step 12/53 : ENV HOME /home/${NB_USER}
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Step 13/53 : RUN groupadd         --gid ${NB_UID}         ${NB_USER} &&     useradd         --comment "Default user"         --create-home         --gid ${NB_UID}         --no-log-init         --shell /bin/bash         --uid ${NB_UID}         ${NB_USER}
 ---> Using cache
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Step 14/53 : RUN wget --quiet -O - https://deb.nodesource.com/gpgkey/nodesource.gpg.key |  apt-key add - &&     DISTRO="bionic" &&     echo "deb https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list &&     echo "deb-src https://deb.nodesource.com/node_10.x $DISTRO main" >> /etc/apt/sources.list.d/nodesource.list
 ---> Using cache
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Step 15/53 : RUN apt-get -qq update &&     apt-get -qq install --yes --no-install-recommends        less        nodejs        unzip        > /dev/null &&     apt-get -qq purge &&     apt-get -qq clean &&     rm -rf /var/lib/apt/lists/*
 ---> Using cache
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Step 16/53 : EXPOSE 8888
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Step 17/53 : ENV APP_BASE /srv
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Step 18/53 : ENV NPM_DIR ${APP_BASE}/npm
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Step 19/53 : ENV NPM_CONFIG_GLOBALCONFIG ${NPM_DIR}/npmrc
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Step 20/53 : ENV CONDA_DIR ${APP_BASE}/conda
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Step 21/53 : ENV NB_PYTHON_PREFIX ${CONDA_DIR}/envs/notebook
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Step 22/53 : ENV KERNEL_PYTHON_PREFIX ${NB_PYTHON_PREFIX}
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Step 23/53 : ENV PATH ${NB_PYTHON_PREFIX}/bin:${CONDA_DIR}/bin:${NPM_DIR}/bin:${PATH}
 ---> Using cache
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Step 24/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2factivate-2dconda-2esh-2747be /etc/profile.d/activate-conda.sh
 ---> Using cache
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Step 25/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2fenvironment-2epy-2d3-2e7-2efrozen-2eyml-b3d5bc /tmp/environment.yml
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Step 26/53 : COPY build_script_files/-2fusr-2flib-2fpython3-2e6-2fsite-2dpackages-2frepo2docker-2fbuildpacks-2fconda-2finstall-2dminiconda-2ebash-12d101 /tmp/install-miniconda.bash
 ---> Using cache
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Step 27/53 : RUN mkdir -p ${NPM_DIR} && chown -R ${NB_USER}:${NB_USER} ${NPM_DIR}
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Step 28/53 : USER ${NB_USER}
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Step 29/53 : RUN npm config --global set prefix ${NPM_DIR}
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Step 30/53 : USER root
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Step 31/53 : RUN bash /tmp/install-miniconda.bash && rm /tmp/install-miniconda.bash /tmp/environment.yml
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Step 32/53 : ARG REPO_DIR=${HOME}
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Step 33/53 : ENV REPO_DIR ${REPO_DIR}
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Step 34/53 : WORKDIR ${REPO_DIR}
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Step 35/53 : ENV PATH ${HOME}/.local/bin:${REPO_DIR}/.local/bin:${PATH}
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Step 36/53 : ENV CONDA_DEFAULT_ENV ${KERNEL_PYTHON_PREFIX}
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Step 37/53 : COPY src/requirements.txt ${REPO_DIR}/requirements.txt
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Step 38/53 : USER root
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Removing intermediate container cb79fb0d91d9
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Step 39/53 : RUN chown -R ${NB_USER}:${NB_USER} ${REPO_DIR}
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Step 40/53 : USER ${NB_USER}
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Step 41/53 : RUN ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"
 ---> Running in 598fa56b5cf2
Collecting cmake==0.9.0 (from -r requirements.txt (line 1))
  Downloading https://files.pythonhosted.org/packages/b4/f1/7e9fa0a5ea7004b97cc8f5365fce25462af6e0da0b9f955f629e4655f1af/cmake-0.9.0.tar.gz (34.9MB)
    ERROR: Command errored out with exit status 1:
     command: /srv/conda/envs/notebook/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-dpe75ski/cmake/setup.py'"'"'; __file__='"'"'/tmp/pip-install-dpe75ski/cmake/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' egg_info --egg-base pip-egg-info
         cwd: /tmp/pip-install-dpe75ski/cmake/
    Complete output (5 lines):
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-install-dpe75ski/cmake/setup.py", line 6, in <module>
        from pip.req import parse_requirements
    ModuleNotFoundError: No module named 'pip.req'
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.
Removing intermediate container 598fa56b5cf2
The command '/bin/sh -c ${KERNEL_PYTHON_PREFIX}/bin/pip install --no-cache-dir -r "requirements.txt"' returned a non-zero code: 1

The root issue is due to a change introduced in pip when going from version 9 to version 10, which makes cmake uninstallable. This happened a while ago, so this has been broken for some time.

Solution is to bump the dependencies in requirements.txt, but the notebook may also need updating if any APIs have changed.

error with binder

hi, I am trying to launch the binder but I get
Error loading genepattern/single_cell_clustering_notebook/master!
See logs below for details.

ModuleNotFoundError: No module named 'beakerx'

I think this would be fixed by adding beakerx to the list of requirements. I encountered this issue today trying to rerun the notebook on binder.

error in scanpy setup command

Hi,
I tried to install the required packages on a freshly set up conda environment with Python 3.6.9 and pip 19.2.3. After the command pip install -r requirements.txt I ran into a problem with scanpy:

Complete output (1 lines):
    error in scanpy setup command: "values of 'package_data' dict" must be a list of strings (got '*.txt')
    ----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

I am now trying to use the latest version of scanpy (1.4.4) and hope that the notebook will run.
Any ideas?