Dear devs 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! Best wishes Peter -- Peter Briggs [email protected] Bioinformatics Core Facility University of Manchester B.1083 Michael Smith Bldg Tel: (0161) 2751482 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/
