search

seandavi / GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor
http://seandavi.github.io/GEOquery/
Other
88 stars 36 forks source link

GEOQuery inside of docker #77

Closed jlevy44 closed 5 years ago

jlevy44 commented 5 years ago

Hey there, I'm running GEOquery (using rpy2) inside of docker, wrapped using CWL. I'm trying to create a workflow that will let me download GEO files then analyze them. However, when running this script, I keep getting the following error after running it a few times:

geo.getGEOSuppFiles(query)

/opt/conda/lib/python3.6/site-packages/rpy2/rinterface/init.py:145: RRuntimeWarning: No supplemental files found.

warnings.warn(x, RRuntimeWarning) /opt/conda/lib/python3.6/site-packages/rpy2/rinterface/init.py:145: RRuntimeWarning: Check URL manually if in doubt

warnings.warn(x, RRuntimeWarning) /opt/conda/lib/python3.6/site-packages/rpy2/rinterface/init.py:145: RRuntimeWarning: https://ftp.ncbi.nlm.nih.gov/geo/series/GSE107nnn/GSE107038/suppl/

warnings.warn(x, RRuntimeWarning) /opt/conda/lib/python3.6/site-packages/rpy2/rinterface/init.py:145: RRuntimeWarning: Error in file(con, "rb") : cannot open the connection

If you check the url, you can clearly see that there are supplemental files. What are your thoughts? I'm not sure what to do?

jlevy44 commented 5 years ago

Could it be possible that #38 is at play here?

seandavi commented 5 years ago

Interesting use case. A couple of questions to start:

jlevy44 commented 5 years ago

Oh, thanks!

Just reinstalled curl with conda inside the docker container and now it seems to work. I'll let you know if something like this happens again. Much appreciated!

Just so everyone knows, GEOquery works outside of the container on an hpc and wget was already installed. Here was the error I was getting before reinstalling curl: curl: error while loading shared libraries: libssl.so.1.0.0: cannot open shared object file: No such file or directory

Closing this issue! Thanks for the help.

seandavi commented 5 years ago

Love it when problems correct themselves....