malariagen / agam-report-base Goto Github PK

#7 simple switch of function name

Pyfaidx is apparently the new thing. Need version 0.5.4 or later for numpy array support.

The install scripts have been migrated to the malariagen/binder repo, so can be removed from this repo.

Could either:

• check for system and download appropriate script.
• warn mac not supported.

@alimanfoo We occasionally need to query MySQL databases in the vector-ops production notebooks. This requires the MySQLdb python package, which can be installed like so:

conda install -c bioconda mysqlclient

(as per https://stackoverflow.com/questions/34140472/how-can-i-use-conda-to-install-mysqldb)

Should we create a separate vector-ops production conda environment? Or simply add packages as necessary to the agam-report-base/install/conda.txt environment package list?

Many of the production vector-ops notebooks query mysql databases such as FITS (File Tracking system) to retrieve sample data. They rely on the mysqlclient conda package. We need to add this to the conda install.txt. See #16

Installing conda with agam-report-base/install/conda_install.sh installs python 3.6.6 on my laptop, but python 3.6.5 on my desktop