How to Execute 'X86_64-Conda_Cos6-Linux-Gnu-Gcc': No Such File or Directory (Pysam Installation)

unable to execute 'x86_64-conda_cos6-linux-gnu-gcc': No such file or directory (pysam installation)

It looks like Anaconda had a new release (4.3.27) that sets the C compiler path to a non-existing executable (quite an embarrassing bug; I'm sure they'll fix it soon). I had a similar issue with pip installing using the latest Miniconda, which I fixed by using the 4.3.21 version and ensuring I was not doing something like conda update conda.

See https://repo.continuum.io/miniconda/ which has release dates and versions.

setup script exited with error: command 'x86_64-linux-gnu-gcc' failed with exit status 1

Try installing these packages.

sudo apt-get install build-essential autoconf libtool pkg-config python-opengl python-pil python-pyrex python-pyside.qtopengl idle-python2.7 qt4-dev-tools qt4-designer libqtgui4 libqtcore4 libqt4-xml libqt4-test libqt4-script libqt4-network libqt4-dbus python-qt4 python-qt4-gl libgle3 python-dev libssl-dev

sudo easy_install greenlet

sudo easy_install gevent

Anaconda failed building wheel for faulthandler on TravisCI for python 2.7

After additional searching I found this related post, following which I replaced the miniconda version in .travis.yml to Miniconda2-4.3.21-Linux-x86_64.sh for Python 2 and Miniconda3-4.3.21-Linux-x86_64.sh for Python 3, and prevented conda from updating by commenting out - conda update -q conda. This time my environment built correctly for all python versions, problem fixed.

As noted in the linked post, this seems like a bug in the installation script for Anaconda (and miniconda) 4.3.27, and the solution is to use an earlier version (e.g. 4.3.21) and prevent conda from updating.

manually installing pysam error: ImportError: No module named version

version.py is in path/to/pysam-master/pysam. The script uses the os-module to add the pysam directory to the working directory of the environment before importing:

sys.path.insert(0, "pysam")

So, this specific problem should be solved by replacing the "pysam" in

sys.path.insert(0, "pysam")

with the full path to the pysam-directory.

error: command 'x86_64-linux-gnu-gcc' failed with exit status 1 and ERROR: Failed building wheel for mysqlclient

Based on the two first lines, you're missing the libssl-dev system package; try apt-get install -y libssl-dev in your dockerfile.

You'll also need libmysqlclient-dev, if you haven't added that already.