Difficulty in installing manually

[conchoecia]

I'm working on making a Docker image for the latest FALCON unzip, but am running into some errors early on in which there are some unrecognized python packages. Here is my Dockerfile so far:

FROM ubuntu:16.04

RUN apt-get update && apt-get install -y gcc g++ perl python automake make \
                                       wget curl libdb-dev \
                                       zlib1g-dev bzip2 \
                                       python-pip python-dev \
                   && apt-get clean

## set up tool config and deployment area:

ENV SRC /usr/local/src
ENV BIN /usr/local/bin

RUN pip install --upgrade pip
RUN pip install virtualenv

## Set up falcon-unzip
ENV PREFIX=/usr/local/lib/python2.7
ENV download='https://downloads.pacbcloud.com/public/falcon/falcon-2018.08.08-21.41-py2.7-ucs4-beta.tar.gz'

RUN cd ${PREFIX} && \
         curl ${download} \
         -o /temp/fuz.tar.gz
RUN tar xvzf /temp/fuz.tar.gz -C ${PREFIX}
ENV LD_LIBRARY_PATH=${PREFIX}/lib:${LD_LIBRARY_PATH}
ENV PATH=${PREFIX}/bin:${PATH}

These are the instructions for the Standard install, or at least my interpretation of the instructions. When I test this initial install with pbalign --help inside the docker, I get the following error. Any idea about what is going on?

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/bin/pbalign", line 7, in <module>
    from pbalign.pbalignrunner import main
ImportError: No module named pbalign.pbalignrunner

Thanks! I am confused if I have attempted to install this incorrectly or need to install something else.

[conchoecia]

It seems to be working now. I was able to get it to work using PYTHONUSERBASE:

FROM ubuntu:16.04
MAINTAINER dts@ucsc.edu

RUN apt-get update && apt-get install -y gcc g++ perl python automake make \
                                       wget curl libdb-dev \
                                       zlib1g-dev bzip2 \
                                       python-pip python-dev \
                   && apt-get clean

## set up tool config and deployment area:

ENV SRC /usr/local/src
ENV BIN /usr/local/bin

RUN pip install --upgrade pip
RUN pip install virtualenv

## Set up falcon-unzip
ENV PREFIX=/usr/local
ENV PYTHONUSERBASE=${PREFIX}
ENV download='https://downloads.pacbcloud.com/public/falcon/falcon-2018.08.08-21.41-py2.7-ucs4-beta.tar.gz'

RUN mkdir /temp
RUN cd ${PREFIX} && \
         curl ${download} \
         -o /temp/fuz.tar.gz
RUN tar xvzf /temp/fuz.tar.gz -C ${PREFIX}
ENV LD_LIBRARY_PATH=${PREFIX}/lib:${LD_LIBRARY_PATH}
ENV PATH=${PREFIX}/bin:${PATH}

[pb-cdunn]

Glad you got it working. People tell me that nobody knows how to use PYTHONUSERBASE, but it's a standard part of python, way simpler than virtualenv.

Anyway, you might find the new bioconda package simpler to use. It's not yet stable, but you can experiment with it: conda install pb-assembly