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cgat-developers / cgat-flow

cgat-flow repository
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pysam error #152

Closed jscaber closed 2 years ago

jscaber commented 2 years ago

Hi all,

very basic question, sorry: to make the rnaseqqc pipeline work I had to delete an old cgat (leftover from ) which I found in conda site-packages. Since then I have the following pysam error

'''File "cgat/BamTools/geneprofile.pyx", line 1, in init cgat.BamTools.geneprofile ValueError: pysam.libcalignedsegment.PileupColumn size changed, may indicate binary incompatibility. Expected 88 from C header, got 72 from PyObject'''

I have done python setup.py develop which generates the cython headers. and more recently in desperation python setup.py install.

Anything else I need to do? pysam is the correct pinned version 0.15.2 (i may have forgotten some dots)

Jakub

Acribbs commented 2 years ago

Ah this is because I made changes to cgat for the new versions of pysam. Pysam has gone through a lot of changes and we initially pinned the pysam because it was going to be a big task to modify cgat code. However, you should now use latest pysam version and the error should go away

jscaber commented 2 years ago

It did! Should we unpin pysam in cgatflow?

Acribbs commented 2 years ago

Yeh good idea, see #153.