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assemble_pairs error when pandaseq not installed #39

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 
Bug in error message from bp_test for assemble_pairs.
When pandaseq is not installed, an undefined method RunTimeError causes an 
inappropriate
error message instead of the intended "Error: command failed"

What steps will reproduce the problem?
1. pandaseq is NOT installed
2. run assemble_pairs test (exact test as run by bp_test):
$ assemble_pairs -I $BP_DIR/bp_test/in/assemble_pairs.in -O 
$BP_TMP/user.assemble_pairs.out

expected output
*nothing*

instead see
/usr/local/bin/biopieces/bp_bin/assemble_pairs:104:in `block in <main>': 
undefined method `RunTimeError' for main:Object (NoMethodError)
    from /usr/local/bin/biopieces/code_ruby/lib/maasha/biopieces.rb:87:in `open'
    from /usr/local/bin/biopieces/bp_bin/assemble_pairs:53:in `<main>'

What version of the product are you using? On what operating system?
Biopieces Feb 9, 2013
Ubuntu 12.04 or Fedora 15, doesn't seem to be OS dependent

Please provide any additional information below.
After install of pandaseq, no error is generated

Original issue reported on code.google.com by dsena...@facstaff.wisc.edu on 10 Feb 2013 at 4:22

GoogleCodeExporter commented 9 years ago 
Pandaseq is no longer the engine for paired sequence assembly.

Original comment by martinah...@gmail.com on 26 Apr 2013 at 7:10