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cannot install pybedtools as part of requirements.txt #116
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Hmm, I should probably include the C++ source files and only run Cython if the user has it installed.
Cython has more options available now than it did when pybedtools' setup.py was first written; this may be a more streamlined approach: I will look into this more as I get time. Thanks for reporting this. |
Thanks for looking into it! I think it has to do with pip's 2-step walkover of the setup.py when running with -r. The first time it's just gathering requirement info by running setup.py and examing the installation_requires field. (or something along those lines, I have only a very vague and possibly incorrect understanding of what's going on) In this case, the setup script crashes because of the cython check. If the cython check is moved to be an annotated installation requirement instead of being run any time setup.py is, then the problem could probably be avoided. |
One of the bcbio-nextgen requirements is pybedtools and this library cannot be part of a requirements.txt file. More information can be found on the following links: - pypa/pip#2083 - daler/pybedtools#116
One of the bcbio-nextgen requirements is pybedtools and this library cannot be part of a requirements.txt file. More information can be found on the following links: - pypa/pip#2083 - daler/pybedtools#116
This should be working after the big refactor (which included setup.py) in v0.7.0. |
If I have pybedtools specified in my requirements.txt I get an error.
here is an example requirements.txt
running
results in
If I install each line individually it succeeds. This seems to be a result of a malformed setup.py. See pypa/pip#25 for more information on the root cause. I've filed an issue with pip about this as well, pypa/pip#2083, but I suspect the response their is going to be "it's a pybedtools issue"
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