I've encountered what appears to be a subtle bug with release 18.05, which breaks the installation of tools from the toolshed, and appears to be a result of not having mercurial (hg) available in /usr/bin on the system that Galaxy is installed on (in this case Scientific Linux 6.5).
When attempting to install a tool (e.g. devteam/fastqc) from the main toolshed via the admin interface, after clicking "install" the tool installation status goes immediately to "Error". The tool repository isn't cloned to "shed_tools" and no dependencies are installed.
I've been unable to find any error messages in the logs. However, attempting to install via the API does return the message:
Error cloning repository: [Errno 2] No such file or directory
which comes from the "clone_repository" function in lib/tool_shed/util/hg_util.py (when something goes wrong with the "hg clone ..." command).
Installing Mercurial 1.3 via yum on the server and attempting tool installation again gives a slightly different error via the API:
Error cloning repository: Command '['hg', 'clone', '-r', u'17', u'https://toolshed.g2.bx.psu.edu/repos/devteam/fastqc', u'/XXXXXXXXXXXXXX/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/c15237684a01/fastqc']' returned non-zero exit status 255 Output was: abort: No such file or directory: /XXXXXXXXXXXXXXXXXX/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/fastqc/c15237684a01/fastqc
Uninstalling the system Mercurial and instead installing version 3.7.3 and making a link from /usr/bin/hg seems to fix the problem, and tools can be installed without problems.
I couldn't find any evidence of this being reported before, and I don't know if I've missed some configuration detail which means that Galaxy isn't picking up hg from its virtualenv instead of /usr/bin.
Has anyone else encountered this problem? and is there a fix/workaround for it (other than horrible links to /usr/bin/hg)?
Any advice gratefully received!
-- Peter Briggs email@example.com Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482