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verified publisher icon bioinformed

Cleaning up setup script to make it more universal

Open ghost opened this issue 10 years ago • 5 comments

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

ghost avatar May 20 '15 20:05 ghost

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.

bioinformed avatar May 21 '15 12:05 bioinformed

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 [email protected] 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.

ghost avatar May 21 '15 13:05 ghost

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.

bioinformed avatar May 21 '15 21:05 bioinformed

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):'

ghost avatar May 21 '15 21:05 ghost

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

bioinformed avatar May 21 '15 22:05 bioinformed