Illumina / hap.py

Haplotype VCF comparison tools
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Docker fails to build for both bases #180

Open rickymagner opened 10 months ago

rickymagner commented 10 months ago

Hi,

Both the provided Dockerfile and Dockerfile.centos6 fail to build for me. The first results in the following error:

 => [ 9/15] RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.7-bin.tar.gz &&     tar xzf apache-ant-1.9.7-bin.tar.gz &&     rm apache-ant-1.9.7-bin.tar.gz                                                                                                                                            3.1s
 => [10/15] WORKDIR /opt/hap.py-source                                                                                                                                                                                                                                                                                   0.0s
 => ERROR [11/15] RUN python install.py /opt/hap.py --with-rtgtools --no-tests                                                                                                                                                                                                                                           0.4s
------
 > [11/15] RUN python install.py /opt/hap.py --with-rtgtools --no-tests:
#15 0.411 Traceback (most recent call last):
#15 0.411   File "install.py", line 27, in <module>
#15 0.411     from urllib.request import urlopen
#15 0.411 ImportError: No module named request
------
executor failed running [/bin/sh -c python install.py /opt/hap.py --with-rtgtools --no-tests]: exit code: 1

and the second fails with

 => => extracting sha256:cbddbc0189a05ef8d3ac344a82cb5cf43279e80004433782cc7874b487f4a9a7                                                                                                                                                                                                                                3.4s
 => ERROR [ 2/12] RUN yum install -y     bzip2     bzip2-devel     centos-release-scl     cmake     curl     devtoolset-8-gcc     devtoolset-3-binutils     devtoolset-8-gcc-c++     devtoolset-8-gcc-gfortran     git     gzip     java-1.8.0-openjdk     ncurses-devel     perl     tar     wget     which     zlib-d  1.0s
------
 > [ 2/12] RUN yum install -y     bzip2     bzip2-devel     centos-release-scl     cmake     curl     devtoolset-8-gcc     devtoolset-3-binutils     devtoolset-8-gcc-c++     devtoolset-8-gcc-gfortran     git     gzip     java-1.8.0-openjdk     ncurses-devel     perl     tar     wget     which     zlib-devel RUN yum upgrade -y && yum update -y && yum clean all:
#5 0.321 Loaded plugins: fastestmirror
#5 0.351 Setting up Install Process
#5 0.602 Error: Cannot retrieve repository metadata (repomd.xml) for repository: base. Please verify its path and try again
#5 0.602 YumRepo Error: All mirror URLs are not using ftp, http[s] or file.
#5 0.602  Eg. Invalid release/repo/arch combination/
#5 0.602 removing mirrorlist with no valid mirrors: /var/cache/yum/x86_64/6/base/mirrorlist.txt
------
executor failed running [/bin/sh -c yum install -y     bzip2     bzip2-devel     centos-release-scl     cmake     curl     devtoolset-8-gcc     devtoolset-3-binutils     devtoolset-8-gcc-c++     devtoolset-8-gcc-gfortran     git     gzip     java-1.8.0-openjdk     ncurses-devel     perl     tar     wget     which     zlib-devel RUN yum upgrade -y && yum update -y && yum clean all]: exit code: 1

It'd be great to be able to build the image with the files provided, since I've had some trouble installing them myself locally. I imagine updating the install script to python3 might solve some of the 2 vs 3 issues with the urllib library.