Issues and Troubleshooting

Old Issues

Here we collect some old troubleshooting tips for reference purposes. This is based on previous versions of the software and no longer apply.

Running the GUI in a Mac (a.k.a running in pyenv)

Unfortunately, Apple is infamous for installing a broken sqlite3 library in Mac OS, that has caused me unmeasurable grief in several past occasions.

While on a Mac, you might experience that hitting "Run" on the GUI will output: "INFO - Loading weight model" and then an error message, or nothing happens. This is a symptom of Apple's sqlite3 failings.

The solution is to use Python with a custom, decent and sane sqlite3 version.

Here I present one outset to get it fixed, and getting MetaXcan's UI to run as a collateral. The gist of it is to install sqlite3 with homebrew, and then use pyenv. Extensive use of the command line is required.

###Step 1: Install homebrew

$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

###Step 2: Install sqlite3 lib with Homebrew

$ brew install sqlite3

###Step 3: Install pyenv, and have it use custom sqlite3

$ PYTHON_CONFIGURE_OPTS="LD_RUN_PATH=/usr/local/opt/sqlite/lib LDFLAGS=-L/usr/local/opt/sqlite/lib CPPFLAGS=-I/usr/local/opt/sqlite/include" pyenv install 2.7.10

You will need to set MetaXcan's folder to use this version of python, as in:

$ cd MetaXcan # or whatever
$ pyenv local 2.7.10

###Step 4: install MetaXcan prerequisites

$ pip install numpy
$ pip install scipy
$ pip install pandas

###That's it!