From 833515c5e88a9a53c18513bec2f357268b486320 Mon Sep 17 00:00:00 2001 From: chaklim Date: Mon, 30 Dec 2019 15:15:00 +0800 Subject: [PATCH] Update README.md and Dockerfile - remove blosc for pypy3, does not affect the current workflow --- Dockerfile | 2 +- README.md | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/Dockerfile b/Dockerfile index 2ddfa88..829e996 100644 --- a/Dockerfile +++ b/Dockerfile @@ -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" diff --git a/README.md b/README.md index 88ec430..82063d4 100644 --- a/README.md +++ b/README.md @@ -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 @@ -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