Commit 5b517800 authored by Glenn Hickey's avatar Glenn Hickey
Browse files

dont spec. minior python version - too specific to ubuntu release

parent e949890b
Pipeline #1738 failed with stage
in 10 minutes and 1 second
......@@ -14,7 +14,7 @@ cd "cactus-bin-${REL_TAG}"
To build a python virtualenv and activate, do the following steps:
```
virtualenv -p python3.8 cactus_env
virtualenv -p python3 cactus_env
echo "export PATH=$(pwd)/bin:\$PATH" >> cactus_env/bin/activate
echo "export PYTHONPATH=$(pwd)/lib:\$PYTHONPATH" >> cactus_env/bin/activate
source cactus_env/bin/activate
......
FROM quay.io/comparative-genomics-toolkit/ubuntu:22.04 AS builder
# apt dependencies for build
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential git python3.8 python3.8-dev python3-pip zlib1g-dev wget libbz2-dev pkg-config libhdf5-dev liblzo2-dev libtokyocabinet-dev wget liblzma-dev libxml2-dev libssl-dev libpng-dev uuid-dev libcurl4-gnutls-dev libffi-dev python python3-virtualenv rsync
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential git python3 python3-dev python3-pip zlib1g-dev wget libbz2-dev pkg-config libhdf5-dev liblzo2-dev libtokyocabinet-dev wget liblzma-dev libxml2-dev libssl-dev libpng-dev uuid-dev libcurl4-gnutls-dev libffi-dev python2 python3-virtualenv rsync
# build cactus binaries
RUN mkdir -p /home/cactus
......@@ -48,7 +48,7 @@ RUN for i in /usr/local/bin/* ; do if [ -f ${i} ] && [ $(ldd ${i} | grep "not fo
# build cactus python3
RUN cd /home/cactus && rm -rf cactus_env && \
python3.8 -m virtualenv -p python3.8 cactus_env && \
python3 -m virtualenv -p python3 cactus_env && \
. cactus_env/bin/activate && \
python3 -m pip install -U setuptools pip==21.3.1 && \
python3 -m pip install -U -r ./toil-requirement.txt && \
......@@ -62,7 +62,7 @@ RUN rm -rf /home/cactus/hal_lib && \
FROM quay.io/comparative-genomics-toolkit/ubuntu:22.04
# apt dependencies for runtime
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends git python3.8 python3-pip python3.8-distutils zlib1g libbz2-1.0 net-tools libhdf5-100 liblzo2-2 libtokyocabinet9 libkrb5-3 libk5crypto3 time liblzma5 libcurl4 libcurl4-gnutls-dev libxml2 libgomp1 libffi6
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends git python3 python3-pip python3-distutils zlib1g libbz2-1.0 net-tools libhdf5-100 liblzo2-2 libtokyocabinet9 libkrb5-3 libk5crypto3 time liblzma5 libcurl4 libcurl4-gnutls-dev libxml2 libgomp1 libffi6
# copy cactus runtime essentials (note: important cactus_env keeps its path)
RUN mkdir /home/cactus
......
......@@ -6,7 +6,7 @@
FROM quay.io/vgteam/dind
# apt dependencies for build
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential git python3.8 python3.8-dev python3-pip zlib1g-dev wget libbz2-dev pkg-config libhdf5-dev liblzo2-dev libtokyocabinet-dev wget liblzma-dev libxml2-dev libssl-dev libpng-dev uuid-dev libcurl4-gnutls-dev libffi-dev python
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get install -y build-essential git python3 python3-dev python3-pip zlib1g-dev wget libbz2-dev pkg-config libhdf5-dev liblzo2-dev libtokyocabinet-dev wget liblzma-dev libxml2-dev libssl-dev libpng-dev uuid-dev libcurl4-gnutls-dev libffi-dev python2
# apt dependencies for ci
RUN DEBIAN_FRONTEND=noninteractive apt-get install -y default-jre wget docker.io python3-virtualenv libcurl4-gnutls-dev libgnutls28-dev
......@@ -64,7 +64,7 @@ python3 -m pip install virtualenv
To set up a virtual environment in the directory `cactus_env`, run:
```
python3 -m virtualenv -p python3.8 cactus_env
python3 -m virtualenv -p python3 cactus_env
```
Then, to enter the virtualenv, run:
......
9079018b65a1c1bfb6ec521e2584f53bc739cf38
94ff9b5438cc4b34d0a19e99f1a6d8ea263b7b6c
......@@ -17,7 +17,7 @@ Follow the steps in the README, making sure to install toil with its extra AWS s
```
git clone https://github.com/comparativegenomicstoolkit/cactus.git
cd cactus
virtualenv -p python 3.8 venv
virtualenv -p python3 venv
source venv/bin/activate
pip install -r toil-requirement.txt
```
......
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