dependency_script: cp rather than symlink to $DOWNLOAD_CACHE

When the downloaded file is an archive which gets unpacked in
the working directory, this is harmless. However, when the
download file is moved directly to $INSTALL_DIR (e.g. JAR files)
this leaves the installation with a symlink pointing at the
cache - which might get deleted.

Also, some tools will look for their own dependencies relative
to the real file (and not the symlink) which will point them
at $DOWNLOAD_CACHE rather than $INSTALL_DIR.

planemo/shed2tap/base.py

@@ -516,11 +516,11 @@ def _commands_and_downloaded_file(url, target_filename=None, sha256sum=None):
         'elif [[ -f "$DOWNLOAD_CACHE/%s" ]]' % downloaded_filename,
         'then',
         '    echo "Reusing cached %s"' % downloaded_filename,
-        '    ln -s "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, target_filename),
+        '    cp "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, target_filename),
         'else',
         '    echo "Downloading %s"' % downloaded_filename,
         '    curl -L -o "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, url),
-        '    ln -s "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, target_filename),
+        '    cp "$DOWNLOAD_CACHE/%s" "%s"' % (downloaded_filename, target_filename),
         ]
     if sha256sum:
         # This is inserted into the if-else for a fresh download only.