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mdozmorov / genome_runner

Academic Free License v3.0
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Installation presupposes bioconductor is loaded #69

Closed gilesc closed 9 years ago

gilesc commented 9 years ago

I have done the following: git clone repo cd repo python2 setup.py develop --user python2 -m grsnp.dbcreator -g hg19 -d ~/data/genome_runner

I get the following error: use 'source("http://bioconductor.org/biocLite.R")' to update 'BiocInstaller' after 'utils' package is attached Error: could not find function "biocLite" /sbin/python2: No module named singledispatch

This implies two things. GenomeRunner requires some python dependencies I don't have (singledispatch). The python dependencies should be in a requirements.txt and this should be loaded into the setup.py, so that it installs dependencies when you run setup.py.

It also implies that the code assumes that I have bioconductor installed and loaded. Whatever R script is being run probably needs to have as its first line: source("http://bioconductor.org/biocLite.R")

mdozmorov commented 9 years ago

Should be fixed in the 'parallel' branch