Workaround for pypa/pip#3165 (#21)

Author: kislyuk

site/datasets/census/hca-download-census

@@ -18,9 +18,9 @@ function initialize() {
 function install_hca_tool() {
     echo "Installing hca tool (see ${LOGFILE} for errors)..."
 
-    if ! pip install --upgrade hca >> ${LOGFILE} 2>&1 ; then
+    if ! pip install hca --upgrade --ignore-installed six >> ${LOGFILE} 2>&1 ; then
         echo -e "\n\nThat failed, trying again as superuser.  You may be prompted for your password..."
-        sudo pip install --upgrade hca 2>&1 >> ${LOGFILE}
+        sudo pip install hca --upgrade --ignore-installed six 2>&1 >> ${LOGFILE}
     fi
 
     HCA=hca

site/datasets/ischaemic-sensitivity/hca-download-ischaemic-sensitivity

@@ -18,9 +18,9 @@ function initialize() {
 function install_hca_tool() {
     echo "Installing hca tool (see ${LOGFILE} for errors)..."
 
-    if ! pip install --upgrade hca >> ${LOGFILE} 2>&1 ; then
+    if ! pip install hca --upgrade --ignore-installed six >> ${LOGFILE} 2>&1 ; then
         echo -e "\n\nThat failed, trying again as superuser.  You may be prompted for your password..."
-        sudo pip install --upgrade hca 2>&1 >> ${LOGFILE}
+        sudo pip install hca --upgrade --ignore-installed six 2>&1 >> ${LOGFILE}
     fi
 
     HCA=hca

site/datasets/melanoma/hca-download-melanoma

@@ -18,9 +18,9 @@ function initialize() {
 function install_hca_tool() {
     echo "Installing hca tool (see ${LOGFILE} for errors)..."
 
-    if ! pip install --upgrade hca >> ${LOGFILE} 2>&1 ; then
+    if ! pip install hca --upgrade --ignore-installed six >> ${LOGFILE} 2>&1 ; then
         echo -e "\n\nThat failed, trying again as superuser.  You may be prompted for your password..."
-        sudo pip install --upgrade hca 2>&1 >> ${LOGFILE}
+        sudo pip install hca --upgrade --ignore-installed six 2>&1 >> ${LOGFILE}
     fi
 
     HCA=hca