[Debian-med-packaging] Bug#818584: ImportError: No module named pyyaml2

[Afif Elghraoui]

Package: spades
Version: 3.7.1+dfsg-1
Severity: important
Control: block 818575 by -1

Tests for the circlator package in progress failed while runnining spades:

~~~
  0:00:47.008    92M / 484M  INFO    General                 (path_extend_launch.hpp    : 247)   Traversing tandem repeats
  0:00:47.008    92M / 484M  INFO   PathExtendIO             (pe_io.hpp                 : 190)   Writing contigs to /tmp/adt-run.gG5zgN/build.2PK/circlator-1.2.0/test/test-dir/OUT/03.assemble.tmp.spades.107.c0mblm8f//K107/scaffolds
  0:00:47.061    92M / 484M  INFO    General                 (launch.hpp                : 114)   SPAdes finished
  0:00:47.068    84M / 484M  INFO    General                 (main.cpp                  : 169)   Assembling time: 0 hours 0 minutes 47 seconds

===== Assembling finished. 


===== Mismatch correction started.

== Processing of contigs

No module named pyyaml2
Traceback (most recent call last):
  File "/usr/lib/spades/bin/spades.py", line 844, in main
    ext_python_modules_home, log, assembled, result_corrected_filename)
  File "/usr/share/spades/spades_pipeline/corrector_logic.py", line 43, in run_corrector
    import pyyaml2 as pyyaml
ImportError: No module named pyyaml2


== Error ==  exception caught: <type 'exceptions.ImportError'>

In case you have troubles running SPAdes, you can write to spades.support at bioinf.spbau.ru
Please provide us with params.txt and spades.log files from the output directory.
~~~

Although spades declares a dependency on python-yaml, either the import statement needs to be patched to say "import yaml" (if the interface is the same), or this other python yaml library may need to be packaged.