Hi Peter,

Recent galaxy releases are using the `hg` command that should be automatically installed along with other galaxy dependencies.
If you're running galaxy in a virtualenv then that virtualenv should have the `hg` script in the bin folder.
Depending on how you start galaxy you may need to add the virtualenv's `bin` folder to the `PATH`.

Hope that helps,

On 25 June 2018 at 07:51, Peter Briggs <peter.briggs@manchester.ac.uk> wrote:
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 Briggs peter.briggs@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482

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