diff --git a/install.sh b/install.sh
index 1b06765e..82c83e3d 100755
--- a/install.sh
+++ b/install.sh
@@ -7,6 +7,7 @@ set -e
 PYTHON_VERSION='3.6.0'
 PYTHON_INTERPRETER='python3.6'
 ROOT=$(readlink -f $(dirname ${BASH_SOURCE}))
+mkdir -p ${ROOT}/tmpdata
 export TMPDIR=${ROOT}/tmpdata # Write temporary files to tmpdata
 export CPIPE_ROOT=$ROOT
 TEMP_SUBDIR=`mktemp -d`
diff --git a/tasks/common.py b/tasks/common.py
index cf2f9b81..d37b2b07 100644
--- a/tasks/common.py
+++ b/tasks/common.py
@@ -163,7 +163,7 @@ def unzip_todir(input, directory, type):
         tar = tarfile.open(fileobj=input, mode='r:bz2')
         tar.extractall(tempdir)
     else:
-        raise ValueError('Can only download .tar.gz, .tar.bz2, or .zip file')
+        raise ValueError('Type: {0} given. Can only download .tar.gz, .tar.bz2, or .zip file'.format(type))
 
     # If there is only one subdirectory, take the files inside that
     files = [os.path.join(tempdir, f) for f in os.listdir(tempdir)]
@@ -207,7 +207,7 @@ def download_zip(url_str, directory, type=None):
     input = BytesIO(url.read())
 
     # Try to deduce the type from the URL
-    if not type:
+    if type is None:
         [name, ext2] = os.path.splitext(url_str)
         [name, ext1] = os.path.splitext(name)
 
@@ -217,6 +217,9 @@ def download_zip(url_str, directory, type=None):
             type = 'tgz'
         elif (ext1 == '.tar' and ext2 == '.bz2') or ext2 == '.tbz2':
             type = 'tbz2'
+        else:
+            raise ValueError ("Unknow filetype: ext1: {}, ext2: {}\nurl_str: {}".format(ext1, ext2,
+                                                                                        url_str))
 
     unzip_todir(input, directory, type)
 
diff --git a/tasks/download/download_reference_files.py b/tasks/download/download_reference_files.py
index 2e3a175f..8c7f0fac 100644
--- a/tasks/download/download_reference_files.py
+++ b/tasks/download/download_reference_files.py
@@ -130,7 +130,15 @@ def task_download_ucsc():
                     ["ucsc.hg19.dict.gz", "ucsc.hg19.fasta.gz", "ucsc.hg19.fasta.fai.gz"],
                     UCSC_ROOT,
                     'bundle/hg19/'
-                )
+                ),
+                cmd('''
+                mkdir -p ucsc\
+                && pushd {data_dir}/ucsc\
+                    && gunzip -c ucsc.hg19.dict.gz >ucsc.hg19.dict\
+                    && gunzip -c ucsc.hg19.fasta.fai.gz >ucsc.hg19.fasta.fai\
+                    && gunzip -c ucsc.hg19.fasta.gz >ucsc.hg19.fasta
+                '''.format(data_dir=DATA_ROOT), cwd=DATA_ROOT, executable='bash')
+
             ],
             'uptodate': [run_once],
         }
@@ -311,7 +319,7 @@ def task_bwa_index_ucsc_reference():
     return {
         'targets': [UCSC_BWA_INDEX],
         'actions': [
-            '{tools}/bwa/bwa index -a bwtsw {data}/ucsc/ucsc.hg19.fasta'.format(tools=TOOLS_ROOT, data=DATA_ROOT)
+            '{tools}/bin/bwa index -a bwtsw {data}/ucsc/ucsc.hg19.fasta'.format(tools=TOOLS_ROOT, data=DATA_ROOT)
         ],
         'task_dep': [
             'install_bwa',
diff --git a/tasks/download/download_tools.py b/tasks/download/download_tools.py
index 7deff6ec..9f2cb6cb 100644
--- a/tasks/download/download_tools.py
+++ b/tasks/download/download_tools.py
@@ -67,6 +67,9 @@ def action():
                     curl -L https://cpanmin.us/ -o cpanm
                     chmod +x cpanm
             ''', cwd=temp_dir)
+            return {
+                'dir': temp_dir
+            }
 
         return {
             'actions': [action],
@@ -99,7 +102,7 @@ def task_download_bwa():
     if swift_install():
         return nectar_download('bwa')
     else:
-        return download_task("https://codeload.github.com/lh3/bwa/tar.gz/v{0}".format(BWA_VERSION))
+        return download_task("https://codeload.github.com/lh3/bwa/tar.gz/v{0}".format(BWA_VERSION), type='tgz')
 
 
 def task_download_htslib():
@@ -130,7 +133,7 @@ def task_download_bedtools():
     if swift_install():
         return nectar_download('bedtools')
     else:
-        return download_task("https://codeload.github.com/arq5x/bedtools2/tar.gz/v{0}".format(BEDTOOLS_VERSION))
+        return download_task("https://codeload.github.com/arq5x/bedtools2/tar.gz/v{0}".format(BEDTOOLS_VERSION), type='tgz')
 
 def task_download_vep():
     if swift_install():
@@ -331,7 +334,7 @@ def task_download_zlib():
         return nectar_download('zlib')
     else:
         return download_task(
-            'https://codeload.github.com/madler/zlib/tar.gz/v{}'.format(ZLIB_VERSION))
+            'https://codeload.github.com/madler/zlib/tar.gz/v{}'.format(ZLIB_VERSION), type='tgz')
 
 def task_download_vcfanno():
     if has_swift_auth():