phantompeakqualtools missing from install_dependencies
jloupe opened this issue · 3 comments
When installing dependencies, it reports an error on line 63 for cloning phantompeakqualtools.
When attempting to run the pipeline, it errors at xcor with an stderr message of no run_spp.R in directories.
I tested git clone https://github.com/kundajelab/phantompeakqualtools but it works now.
I think this should be a temporary problem of github server?
Please uninstall dependencies and install them again.
Thank you for the quick response.
We tried it a couple of times across different days, including this morning. I am not sure how it could be the server.
Since the error states run_spp.R is not in any directory, I manually added it to the chipseq_pipeline-master directory. I did a quick run starting with tagAligns and stopping at xcor, and it appears to have run that pipeline correctly. I am repeating the experiment through IDR currently to see if this fixes it.
Pipeline is not guaranteed to run correctly if the dependency installer fails. Please don't use any hacky way to install dependencies. All dependencies must be installed by install_dependencies.sh.