[Bioperl-l] environment variables (et al.) for bioperl-run tests

Amir Karger akarger at CGR.Harvard.edu
Tue Jan 6 17:44:32 UTC 2009

> Amir Karger wrote:
> > We just installed Bioperl-run on a cluster with very limited
> environment
> > variables. So a huge number of tests failed.
> None of the tests should fail. It's a bug if they do, so please let
> us
> know the details. When an environment variable isn't set or a
> program
> not installed, the test should skip, not fail.

Oops! I lied. I should have more clearly stated that most of the tests
nicely skipped, and some even told me that a certain environment
variable should be set. The only things that actually broke are:

t/AnalysisFactory_soap....10/12 proxy: transport protocol not specified
# Looks like you planned 12 tests but only ran 11.
# Looks like your test died just after 11.
t/AnalysisFactory_soap.... Dubious, test returned 255 (wstat 65280,
 Failed 1/12 subtests

Also, I got an error from RepeatMasker and Vista, which should probably
be more graceful when things aren't in the PATH:

t/RepeatMasker............Use of uninitialized value in concatenation
(.) or string at
ker.pm line 175.
RepeatMasker program not found as  or not executable.
RepeatMasker program not found. Skipping tests 1 to 10.

t/Vista...................readline() on closed filehandle PIPE at
t/Vista.t line 39.
Use of uninitialized value in numeric lt (<) at t/Vista.t line 53.
You need at least version 1.2 of JDK to run vista

It looks like the bug Chris referred me to is a bug to fix the above
errors, which is great. But if all the tests pass and I haven't actually
tested any of my bio binaries, I'm going to be kind of bummed when I
actually try to use them. I'm not sure how flexible the testing
mechanism is: is there an easy way to give the user a one-line feedback
when they run the test that says "The following binaries weren't found
or did not have relevant environment variables set, so their subtests
were skipped: blastall, clustalw, primer3, ...". That would be awesome.
Even better would be if it referenced a file to look at or a wiki page
listing how to set up PATH and other environment variables for each

Sorry for the mis-type. 


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