From c2204b32081ce6def2ed271f31ccc3ad2f695f7d Mon Sep 17 00:00:00 2001 From: peterjc Date: Tue, 23 Aug 2016 11:43:27 +0100 Subject: [PATCH] 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 $INSTALL_DIR. --- planemo/shed2tap/base.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/planemo/shed2tap/base.py b/planemo/shed2tap/base.py index e3d6eb407..9d096d2d4 100644 --- a/planemo/shed2tap/base.py +++ b/planemo/shed2tap/base.py @@ -516,11 +516,11 @@ def _commands_and_downloaded_file(url, target_filename=None, sha256sum=None): 'elif [[ -f "$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.