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brielin / Popcorn

Software for estimating correlation of trait effect sizes across populations
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Can't install 'bed-reader>=0.1.2' issue #20

Open zhangchuyi opened 3 years ago

zhangchuyi commented 3 years ago

Dear Brielin, I met a problem when installing POPCORN under Python=2.7.15 and Ubuntu 18.04.2 LTS After I installed all packages in "requirement.txt" by "mamba install xxx", I use "python setup.py install" to setup the software and then I got the following error:

Installed /home/lilab/zhangchuyi/anaconda3/envs/POPCORN/lib/python2.7/site-packages/popcorn-0.9.9-py2.7.egg Processing dependencies for popcorn==0.9.9 Searching for bed-reader>=0.1.2 Reading https://pypi.org/simple/bed-reader/ No local packages or working download links found for bed-reader>=0.1.2 error: Could not find suitable distribution for Requirement.parse('bed-reader>=0.1.2')

I went check the information in the provided website "https://pypi.org/simple/bed-reader/" and found that there are two versions of bed-reader, the old version bed-reader 0.0.5a0 and the new version bed-reader=0.1.2, however both two versions require python>3 which is inconsistent with the requirement (python < 3) for POPCORN. I failed to install any version by using either "pip install" or "mamba install". I have no idea how to deal with it. I'd appreciate it if you could help me.

brielin commented 3 years ago

Do you know where the bed-reader dependency is coming from? That isn't in the requirements.txt file here. It is possible that another package now depends on that and you might need an older version.

ofrei commented 1 year ago

@zhangchuyi @brielin here is a singularity container with popcorn installed. This comes with all dependencies pre-installed, including the bed-reader.