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(a)manchester.ac.uk>
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
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',
devteam/fastqc/c15237684a01/fastqc']' returned non-zero exit status 255
abort: No such file or directory: /XXXXXXXXXXXXXXXXXX/shed_tools/
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 peter.briggs(a)manchester.ac.uk
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:
To search Galaxy mailing lists use the unified search at: