fixes bowtie2-build TypeError in PyPy

[nellore]

This is a band-aid for an error encountered when at least one version of PyPy is the default version of Python:

bowtie2-build --version
Traceback (most recent call last):
  File "/home/travis/build/nellore/rail/src/bowtie2/bowtie2-build", line 86, in <module>
    main()
  File "/home/travis/build/nellore/rail/src/bowtie2/bowtie2-build", line 83, in main
    subprocess.call(argv)
  File "/opt/python/pypy2.7-5.8.0/lib-python/2.7/subprocess.py", line 168, in call
    return Popen(*popenargs, **kwargs).wait()
  File "/opt/python/pypy2.7-5.8.0/lib-python/2.7/subprocess.py", line 340, in __init__
    if args[1:] in (
TypeError: deque[:] is not supported

[junaruga]

In my opinion, the challenge of this repository is this repository can need test cases on at least Python3, and optionally PyPy3, and PyPy. Currently used Python is Python 2.7 as a default setting of Travis CI.

I prepared the example in my bowtie2 repository. The Travis results: https://travis-ci.org/junaruga/bowtie2/builds/429289751 My repository's "feature/ci-pyhon" branch: https://github.com/junaruga/bowtie2/tree/feature/ci-pyhon The modification: https://github.com/junaruga/bowtie2/commit/2827319

This modification can be after the PR: https://github.com/BenLangmead/bowtie2/issues/207 , because I changed .travis.yml to use matrix/include for that.

In the case there are 5 test cases. Maybe we can prepare very light weight test to only check validation of python script such as make python-test, because make allall && make simple-test is very heavy.

References https://docs.travis-ci.com/user/languages/python/#pypy-support https://github.com/pypa/pip/blob/18.0/.travis.yml#L31-L40

[junaruga]

@nellore It seems the pull-request was merged at https://github.com/BenLangmead/bowtie2/commit/57b609196e511a80a55e7b9f089bb431c52eddcb .

[junaruga]

I think this issue was fixed at this commit. https://github.com/BenLangmead/bowtie2/commit/57b609196e511a80a55e7b9f089bb431c52eddcb We can close this PR.