Merge pull request #162 from openvax/change-fm-index-path

Using an environment variable to set where the reference peptide index lives.

.travis.yml

@@ -42,6 +42,8 @@ before_install:
   - mkdir tmp
   - export NETMHC_BUNDLE_TMPDIR=$PWD/tmp
   - export PATH=$PATH:$NETMHC_BUNDLE_HOME/bin
+  # tells vaxrank where to install the reference peptide cache
+  - export VAXRANK_REF_PEPTIDES_DIR=$HOME/.cache/vaxrank
 env:
   global:
     # MHC_BUNDLE_PASS

requirements.txt

@@ -14,3 +14,4 @@ xlrd
 xvfbwrapper
 future>=0.16.0  # needed by pylint
 astropy
+datacache

vaxrank/__init__.py

@@ -1 +1 @@
-__version__ = "0.7.11"
+__version__ = "0.7.12"

vaxrank/epitope_prediction.py

@@ -18,11 +18,11 @@
 import logging
 import os
 
-from appdirs import user_cache_dir
 import numpy as np
 import shellinford
 import six
 
+from datacache import get_data_dir
 
 logger = logging.getLogger(__name__)
 
@@ -76,7 +76,8 @@ def fm_index_path(genome):
     """
     Returns a path for cached reference peptides, for the given genome.
     """
-    cache_dir = user_cache_dir('vaxrank')
+    # if $VAXRANK_REF_PEPTIDES_DIR is set, that'll be the location of the cache
+    cache_dir = get_data_dir(envkey='VAXRANK_REF_PEPTIDES_DIR')
     if not os.path.exists(cache_dir):
         os.makedirs(cache_dir)