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bioinformed / vgraph

vgraph is a command line application and Python library to compare genetic variants using variant graphs. ``vgraph`` utilizes a graph representation of genomic variants in to precisely compare complex variants that are refractory to comparison by conventional comparison methods.
Apache License 2.0
42 stars 10 forks source link

Cleaning up setup script to make it more universal #1

Open ghost opened 9 years ago

ghost commented 9 years ago

Hi Kevin,

Thanks so much for creating this tool! I made a few trivial changes that makes the setup more universal (hopefully) and lets it work on my mac, for one thing. The original version was not working for simple reasons.

Best -Kaushik

bioinformed commented 9 years ago

Thanks for your contribution! Are these changes needed to support Windows? I ask because the current method appears to work on both OS X and Linux.

ghost commented 9 years ago

Hi Kevin,

I'm on Mac OS. When I followed the instructions in the readme the tool installed fine but did not run. I use virtual environments to isolate my testing. I think the script forces you to use the system python. It is safer to use Python's entry points mechanism which takes care of all this and on Windows I think it creates an .exe that you can click/call.

Best -Kaushik

On Thu, May 21, 2015 at 8:58 AM, Kevin Jacobs notifications@github.com wrote:

Thanks for your contribution! Are these changes needed to support Windows? I ask because the current method appears to work on both OS X and Linux.

— Reply to this email directly or view it on GitHub https://github.com/bioinformed/vgraph/pull/1#issuecomment-104264527.

bioinformed commented 9 years ago

Thanks for the information. I also use virtualenvs and didn't have a problem. Your point is still valid and I'll test on Windows and make sure we cover all platforms.

ghost commented 9 years ago

Hi Kevin,

Thanks for looking into this. here is my stack trace, in case it helps.

Best -Kaushik

Successfully installed nose vgraph
Cleaning up...
(vgraph-test)sbg-kg:Sandbox kghose$ vgraph
from: can't read /var/mail/__future__
from: can't read /var/mail/os.path
from: can't read /var/mail/argparse
from: can't read /var/mail/collections
from: can't read /var/mail/operator
from: can't read /var/mail/pysam
from: can't read /var/mail/vgraph.bed
from: can't read /var/mail/vgraph.norm
from: can't read /var/mail/vgraph.intervals
from: can't read /var/mail/vgraph.iterstuff
from: can't read /var/mail/vgraph.vargraph
/Users/kghose/.venvs/vgraph-test/bin/vgraph: line 17: syntax error near unexpected token `('
/Users/kghose/.venvs/vgraph-test/bin/vgraph: line 17: `def records_to_loci(ref, records):'
bioinformed commented 9 years ago

Ah! That is very helpful. I wonder how it works at all on my OS X box without a shebang line.