Installing via environment.yml doesn't add command line entry points

[olgabot]

Description

I installed outrigger using the environment.yml file and didn't get the command line entry points, so I installed via pip and then got errors with the C libraries of pysam.

Steps to Reproduce

1. conda env create --file environment.yml --name outrigger_v1.0.0rc1_v2
2. source activate outrigger_v1.0.0rc1_v2
3. which outrigger doesn't point to the environment (~/anaconda/envs/outrigger_v1.0.0rc1_v2/bin) but instead to the base environment (~/anaconda/bin)
4. pip install .
5. outrigger -h

Expected behavior: I expected to see the help message for how to use outrigger.

Actual behavior: Instead I saw this error message with pysam that I think has to do with how it was installed.

$ outrigger index -h
Traceback (most recent call last):
  File "/home/obotvinnik/anaconda/envs/outrigger_v1.0.0rc1_v2/bin/outrigger", line 11, in <module>
    load_entry_point('outrigger==1.0.0rc1', 'console_scripts', 'outrigger')()
  File "/home/obotvinnik/anaconda/envs/outrigger_v1.0.0rc1_v2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 561, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/obotvinnik/anaconda/envs/outrigger_v1.0.0rc1_v2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2631, in load_entry_point
    return ep.load()
  File "/home/obotvinnik/anaconda/envs/outrigger_v1.0.0rc1_v2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2291, in load
    return self.resolve()
  File "/home/obotvinnik/anaconda/envs/outrigger_v1.0.0rc1_v2/lib/python3.5/site-packages/pkg_resources/__init__.py", line 2297, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/obotvinnik/workspace-git/outrigger/outrigger/commandline.py", line 19, in <module>
    from outrigger.io import star, gtf, bam
  File "/home/obotvinnik/workspace-git/outrigger/outrigger/io/bam.py", line 7, in <module>
    import pysam
  File "/home/obotvinnik/anaconda/envs/outrigger_v1.0.0rc1_v2/lib/python3.5/site-packages/pysam/__init__.py", line 6, in <module>
    from pysam.cutils import *
ImportError: /home/obotvinnik/anaconda/envs/outrigger_v1.0.0rc1_v2/lib/python3.5/site-packages/pysam/cutils.cpython-35m-x86_64-linux-gnu.so: undefined symbol: cram_container_get_landmarks

What actually works:

Installing the old way, i.e. via:

conda create -n outrigger_v1.0.0rc1_v3 --file conda_requirements.txt  --yes
source activate outrigger_v1.0.0rc1_v3
pip install -r requirements.txt 
pip install .

And this does properly install outrigger:

$ which outrigger
~/anaconda/envs/outrigger_v1.0.0rc1_v3/bin/outrigger
$ outrigger -h
usage: outrigger [-h] [--version] {index,validate,psi} ...

outrigger (1.0.0rc1). Calculate "percent-spliced in" (Psi) scores of
alternative splicing on a *de novo*, custom-built splicing index -- just for
you!

positional arguments:
  {index,validate,psi}  Sub-commands
    index               Build an index of splicing events using a graph
                        database on your junction reads and an annotation
    validate            Ensure that the splicing events found all have the
                        correct splice sites
    psi                 Calculate "percent spliced-in" (Psi) values using the
                        splicing event index built with "outrigger index"

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

Versions

You can get this information from executing outrigger --version at the
command line. Please include the OS (Operating System) and what version of
the OS you're running.

$ outrigger --version
outrigger 1.0.0rc1
$ uname -a
Linux tscc-login2.sdsc.edu 2.6.32-642.6.1.el6.x86_64 #1 SMP Wed Oct 5 00:36:12 UTC 2016 x86_64 x86_64 x86_64 GNU/Linux

[olgabot]

This particular part of the stack trace:

  File "/home/obotvinnik/workspace-git/outrigger/outrigger/commandline.py", line 19, in <module>
    from outrigger.io import star, gtf, bam
  File "/home/obotvinnik/workspace-git/outrigger/outrigger/io/bam.py", line 7, in <module>
    import pysam

Shouldn't be happening because this should be calling the outrigger/commandline.py from /home/obotvinnik/anaconda/envs/outrigger_v1.0.0rc1_v2/lib/python3.5/site-package, not /home/obotvinnik/workspace-git/outrigger/outrigger/commandline.py

[ghost]

Description

I encountered this issue but was eventually able to resolve it. I first tried environment creation from the environment.yml file and can confirm that outrigger was not by default installed to ~/anaconda2/envs/outrigger-env/bin, nor anywhere that I could easily find, including in /usr/lib/python* (system site packages). Consequently, outrigger -h was not recognized at the command line.

What worked

Changing directory into the cloned repo after activating the new environment, followed by pip install ./, which correctly installed outrigger to ~/anaconda2/envs/outrigger-env/bin and lead to expected output with outrigger -h, outrigger index -h, etc...

Steps to replicate successful environment install from source on Ubuntu 14.04

(as root)

1. cd /var/git/
2. git clone /~https://github.com/YeoLab/outrigger.git
3. cd outrigger
4. conda env create --file environment.yml
5. source activate outrigger-env
6. pip install ./
7. outrigger -h (returns expected output)