installation on Ubuntu 14.04 about checkqc HOT 18 CLOSED

Hi @avilella!

Thank you for reporting this issue. I've been able to reproduce it in a virtual machine. The problem seems to be that checkqc requires a python version greater than 3.5. I'll make sure that this information is added to the README.

I followed this guide to install python3.5. And then I created a virtual environment with python3.5 to install checkqc into.

I then installed pip and created a virtual environment using python 3.5 to run checkqc, and this appears to work:

sudo apt-get install python3-pip
sudo pip3 install virtualenv
virtualenv --python=python3.5 venv-py3.5
source venv-py3.5/bin/activate
pip install -f https://github.com/Illumina/interop/releases/tag/v1.1.1 interop
pip install checkqc
checkqc --version

Does this work for you? I'll make sure to update the documentation accordingly.

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I'm not familiar with the DNA Nexus Make files, but looking at the log above it looks like it is still trying to use python 3.4.

Could you try using this guide to make sure you have python 3.5 installed first?https://askubuntu.com/questions/682869/how-do-i-install-a-different-python-version-using-apt-get

If that does not work perhaps you could try starting by trying to update pip? I'm not sure exactly which version would be required, but this is what it looks like in the Ubuntu 14.04 virtual machine that I'm running:

(venv-py3.5) vagrant@vagrant-ubuntu-trusty-64:~$ pip --version
pip 9.0.1 from /home/vagrant/venv-py3.5/lib/python3.5/site-packages (python 3.5)

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Hey @avilella. If you have Python2 and Python3 installed along each other then running pip will often still refer to the version 2 ecosystem, whereas pip3 should use the version 3.

I.e. in your list of commands above try running pip3 --version, pip3 install -f https://github.com/Illumina/interop/releases/tag/v1.1.1 interop, pip3 install checkqc instead.

Sometimes when environments have been mixed up incorrectly it can also work to call the Python binary and load the pip module manually (instead of going through the pip wrapper). I.e. a pip3 install foo would become python3 -m pip install foo.

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Hi @avilella!
Did you manage to resolve this issue, or is there something we can do to help?

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It seems that it is still using python 3.4 which is unsupported. Here is an idea which might force the correct binaries to be used throughout:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo rm -f /etc/apt/apt.conf.d/99dnanexus

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install -y python3.5

sudo apt-get install -y python3-pip
sudo pip3 install virtualenv
virtualenv --python=python3.5 venv-py3.5

/home/dnanexus/venv-py3.5/bin/pip3.5 install --upgrade pip
/home/dnanexus/venv-py3.5/bin/pip3.5 --version
/home/dnanexus/venv-py3.5/bin/pip3.5 install -f https://github.com/Illumina/interop/releases/tag/v1.1.1 interop
/home/dnanexus/venv-py3.5/bin/pip3.5 install checkqc
/home/dnanexus/venv-py3.5/bin/checkqc --version

Not very pretty, but explicitly pointing to the correct version binaries should hopefully make sure the correct once are used all the way through.

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Hi @avilella !

The interop libraries are now available to install via PyPI. This might make it easier for you to install. We still require a python 3.5 as the minimum supported python version, though.

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Yes. But you can skip the /home/dnanexus/venv-py3.5/bin/pip3.5 install -f https://github.com/Illumina/interop/releases/tag/v1.1.1 interop part. The updated recipe should be something like this:

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo rm -f /etc/apt/apt.conf.d/99dnanexus

sudo add-apt-repository ppa:deadsnakes/ppa
sudo apt-get update
sudo apt-get install -y python3.5

sudo apt-get install -y python3-pip
sudo pip3 install virtualenv
virtualenv --python=python3.5 venv-py3.5

/home/dnanexus/venv-py3.5/bin/pip3.5 install --upgrade pip
/home/dnanexus/venv-py3.5/bin/pip3.5 --version
/home/dnanexus/venv-py3.5/bin/pip3.5 install checkqc
/home/dnanexus/venv-py3.5/bin/checkqc --version

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Hi @avilella !
I'm just curious to hear if you got CheckQC working following the instructions above?

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I think it should be available from here /home/dnanexus/venv-py3.5/bin/checkqc. So if you point directly at that binary it should run.

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I tested the pip install method on 16.04, which is now supported in DNAnexus, and it worked. The 14.04 still an issue, but less so with the 16.04 option.

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I'm happy to hear that this worked out.

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