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Update README.md and Dockerfile
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- remove blosc for pypy3, does not affect the current workflow
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chaklim committed Dec 30, 2019
1 parent 90dc1a9 commit 833515c
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2 changes: 1 addition & 1 deletion Dockerfile
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Expand Up @@ -30,4 +30,4 @@ RUN echo "source activate clair-env" > ~/.bashrc
ENV PATH /opt/conda/envs/clair-env/bin:$PATH
RUN /bin/bash -c ". activate clair-env && \
pypy3 -m ensurepip && \
pypy3 -m pip install --no-cache-dir intervaltree blosc"
pypy3 -m pip install --no-cache-dir intervaltree"
6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -32,7 +32,7 @@ conda activate clair
# install pypy and packages on clair environemnt
conda install -c conda-forge pypy3.6
pypy3 -m ensurepip
pypy3 -m pip install blosc intervaltree
pypy3 -m pip install intervaltree

# install python packages on clair environment
pip install numpy blosc intervaltree tensorflow==1.13.2 pysam matplotlib
Expand Down Expand Up @@ -82,11 +82,11 @@ CLAIR=`which clair.py`
python $CLAIR --help
```

The conda environment has the Pypy intepreter installed, but two Pypy libraries `intervaltree` and `blosc` are still missing. The reason why the two packages are not installed by default is because they are not yet available in any conda repositories. To install the two libraries for Pypy, after activating the conda environment, please run the follow commands:
The conda environment has the Pypy intepreter installed, but one Pypy package `intervaltree` is still missing. The reason why this is not installed by default is because this is not yet available in any conda repositories. To install the package for Pypy, after activating the conda environment, please run the follow commands:

```bash
pypy3 -m ensurepip
pypy3 -m pip install --no-cache-dir intervaltree blosc
pypy3 -m pip install --no-cache-dir intervaltree
```

Download the models to a folder and continue the process
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