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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
61 stars 22 forks source link

conda env create #85

Open mlovci opened 7 years ago

mlovci commented 7 years ago

Automates local conda build before installation.

Solves this problem:

$ conda create --name outrigger-env_ outrigger
Fetching package metadata .............

PackageNotFoundError: Package missing in current osx-64 channels:
  - outrigger
olgabot commented 7 years ago

Thank you! Makefiles use exactly tabs and no spaces for the directions, so double-check that the makefile is valid

olgabot commented 7 years ago

Is this something you wanted to add to the .travis.yml file as well? Or for installation? I ask because if it's for installation, it should also be documented in the README.rst

mlovci commented 7 years ago

Thanks for the tabs reminder. The dash is intentional before the environment directive, it will allow steps that require it to pass if that fails (for example, if the environment exists). I'm submitting another PR with code to do the conda env activation before install. Re-submitting with more changes to instructions and .travis.yml

mlovci commented 7 years ago

Nevermind about re-submitting, the new commits are already here.

olgabot commented 7 years ago

Can you check on the failing builds? Here's an excerpt:

source activate `cat environment.yml |grep name | cut -f2 -d " "` && python setup.py install
/bin/sh: 1: source: not found
make: *** [install] Error 127
The command "make install" failed and exited with 2 during .
Your build has been stopped.