pysam version 0.9.1.4 causes an error on install.

owainkenwayucl commented 8 years ago

I've been updating various packages on our cluster and it looks like the latest version of pysam causes an error when you pip install pysamstats:

Collecting pysamstats
  Downloading pysamstats-0.24.3.tar.gz (265kB)
    100% |████████████████████████████████| 266kB 3.8MB/s
    Complete output from command python setup.py egg_info:
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
      File "/tmp/pip-build-347ta_gj/pysamstats/setup.py", line 12, in <module>
        if StrictVersion(pysam.__version__) < StrictVersion(required_pysam_version):
      File "/shared/ucl/apps/python/3.4.3/gnu-4.9.2/lib/python3.4/distutils/version.py", line 40, in __init__
        self.parse(vstring)
      File "/shared/ucl/apps/python/3.4.3/gnu-4.9.2/lib/python3.4/distutils/version.py", line 143, in parse
        raise ValueError("invalid version number '%s'" % vstring)
    ValueError: invalid version number '0.9.1.4'

    ----------------------------------------
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-build-347ta_gj/pysamstats/

If I had to guess this is caused by the version number being w.x.y.z instead of x.y.z, as installing against pysam 0.9.0 works fine.

alimanfoo commented 8 years ago

Thanks @owainkenwayucl, sorry for the slow response. I need to update pysamstats anyway to check compatibility with recent pysam versions, have been waiting for the pysam install issues to settle down. Hopefully can schedule some time on this in the next few weeks.

podpearson commented 8 years ago

If anyone wants a quick workaround to get pysamstats to install with pysam 0.9.1.4, clone from github, change the string StrictVersion to LooseVersion in setup.py (3 places), then run python setup.py install

alimanfoo commented 8 years ago

Thanks Richard.

On Friday, October 7, 2016, Richard Pearson notifications@github.com wrote:

If anyone wants a quick workaround to get pysamstats to install with pysam 0.9.1.4, clone from github, change the string StrictVersion to LooseVersion in setup.py (3 places), then run python setup.py install

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/alimanfoo/pysamstats/issues/56#issuecomment-252268980, or mute the thread https://github.com/notifications/unsubscribe-auth/AAq8QuH1ooPY3bIbo663GlbHoY-PtKxqks5qxlibgaJpZM4JrEzC .

Alistair Miles Head of Epidemiological Informatics Centre for Genomics and Global Health http://cggh.org The Wellcome Trust Centre for Human Genetics Roosevelt Drive Oxford OX3 7BN United Kingdom Email: alimanfoo@googlemail.com Web: http://purl.org/net/aliman Twitter: https://twitter.com/alimanfoo Tel: +44 (0)1865 287721

alimanfoo / pysamstats

pysam version 0.9.1.4 causes an error on install. #56