Installing Bio-Tradis Fail about bio-tradis HOT 6 CLOSED

No problem! I assume it worked?

from bio-tradis.

That's a bit mysterious. Adding a -v to the cpanm command should provide more info, particularly if any tests fail, e.g.:

sudo cpanm -f -v Bio::Tradis

Can you post the output from this?

from bio-tradis.

Error summary:

Looks like you failed 9 tests of 45.
Failed test 'smalt in PATH'
at t/requires_external.t line 8.
Failed test 'tabix in PATH'
at t/requires_external.t line 8.
Looks like you failed 2 tests of 6.
Failed 6/15 test programs. 17/218 subtests failed.
make: *** [test_dynamic] Error 2
! Testing Bio-Tradis-1.3.3 failed but installing it anyway.

Here is the complete output: install.log

from bio-tradis.

So, to me it looks like these are path issues with smalt and samtools (tabix comes from samtools).

I'm assuming smalt and tabix are in your path with your user account? I.e. you can run 'smalt' and 'tabix' at the command line and get the help screens?

If this is the case, then I suspect this an issue with your sudo not preserving the environment and/or running the root profile -- this is the case with some Linux distributions (see here: https://unix.stackexchange.com/questions/83191/how-to-make-sudo-preserve-path). You can test if this is the case by comparing the output of:

echo 'echo $PATH' | sh

and

echo 'echo $PATH' | sudo sh

If these are different, then I think this solution from that stackoverflow thread I linked to should fix your problem, though I haven't been able to test this:

sudo env "PATH=$PATH" cpanm -f -v Bio::Tradis

Any luck with that? I'm guessing Bio::Tradis should be installed properly now anyway as these errors shouldn't affect the installation (can you run 'bacteria_tradis' from the commandline?), but it'd be comforting to have all the tests succeeding....

from bio-tradis.

Thank you so much, @lbarquist!!

from bio-tradis.

Great, hope it's useful to you!

@andrewjpage mind closing this issue when you've got a chance? I don't have permissions. Thanks!

from bio-tradis.