Clipper installation fails

[ekfiagbedzi]

All the installation instructions work till I run
pip install .
where I get the below error

ERROR: Command errored out with exit status 1: /home/biopython/anaconda3/envs/clipper3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-req-build-xzdp502n/setup.py'"'"'; file='"'"'/tmp/pip-req-build-xzdp502n/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(file);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' install --record /tmp/pip-record-ippyc680/install-record.txt --single-version-externally-managed --compile --install-headers /home/biopython/anaconda3/envs/clipper3/include/python3.7m/clipper Check the logs for full command output.

[IrisWEI-1996]

Hi I met the same problem before when installing the other software. I'm not entirely sure if this is caused by the conflict between the different virtual environments and I would suggest if you could try conda install instead.

conda install -c bioconda bioconductor-clipper 
conda install -c bioconda/label/gcc7 bioconductor-clipper

[algaebrown]

Hi @ekfiagbedzi and @IrisWEI-1996 sorry for the late reply.

@ekfiagbedzi can you provide the log file as suggested in the error message?
@IrisWEI-1996 biocondutor-clipper is a different package

we are working on making clipper available on PyPI and conda, hopefully can make installation easier.

🙏 Thanks

[sj-hao]

Hi @ekfiagbedzi, I have the same question now. Have you solved this problem successfully?