Move dependencies to ${HOME}/dependencies

ant builds copy everything in the pwd into ant_build and then try to
build all of the java files copied, including those of the dependencies
which are built separately.  This does not end well.

.travis.yml

@@ -6,7 +6,7 @@ jdk:
 sudo: false
 cache:
   directories:
-  - "build"
+  - "${HOME}/dependencies"
 before_install:
   - "export CASHER_TIME_OUT=300"
   - "export DISPLAY=:99.0"

install_dependencies.sh

@@ -10,10 +10,10 @@ EMBOSS_VERSION="6.6.0"
 EMBOSS_DOWNLOAD_URL="ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-${EMBOSS_VERSION}.tar.gz"
 
 # Make an install location
-if [ ! -d 'build' ]; then
-  mkdir build
+if [ ! -d "${HOME}/dependencies" ]; then
+  mkdir ${HOME}/dependencies
 fi
-cd build
+cd ${HOME}/dependencies
 build_dir=$(pwd)
 
 # DOWNLOAD ALL THE THINGS