Open olgabot opened 7 years ago
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
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)
Description
I installed
outrigger
using theenvironment.yml
file and didn't get the command line entry points, so I installed viapip
and then got errors with the C libraries ofpysam
.Steps to Reproduce
conda env create --file environment.yml --name outrigger_v1.0.0rc1_v2
source activate outrigger_v1.0.0rc1_v2
which outrigger
doesn't point to the environment (~/anaconda/envs/outrigger_v1.0.0rc1_v2/bin
) but instead to the base environment (~/anaconda/bin
)pip install .
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.What actually works:
Installing the old way, i.e. via:
And this does properly install
outrigger
: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.