kbessonov1984
commented
4 years ago Hello,
We are glad to help. I developed Galaxy wrapper for the tool. The error code is not very detailed so it is difficult to tell what went wrong with MOB-Suite 3.0.0 installation. Could you also post relevant excerpt from the galaxy.log file? Is bioconda channel added to your conda install?
I propose to have it installed manually instead installing the tool via the Galaxy Admin interface.
#login to the server where galaxy is installed
#install mob-suite in a separate conda environment like so (note double underscore in the environment name)
conda create -n __mob_suite@3.0.0 -y
#add conda channels (optional)
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
#activate environment and install MOB-Suite and initialize it
conda activate __mob_suite@3.0.0
conda install mob_suite=3.0.0 -y
#initialize all MOB-Suite databases to make 1st run faster (optional)
mob_initAfter successful MOB-Suite install manually install the tool wrapper and modify tool_ file so that tool shows in the list
The wrapper xml files are available from here
#create new folder in tools directory
cd tools && mkdir mob_suite && cd mob_suite
#download the 2 xml wrapper files to this new directory
wget https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/mob_recon.xml
wget wget https://raw.githubusercontent.com/phac-nml/galaxy_tools/master/tools/mob_suite/mob_typer.xmlFinally modify tool_conf.xml file in config folder by adding this new xml code. Start galaxy server daemon via run.sh --daemon start and see if the tool appears in the list. If not renamed, the tools config file can be tool_conf.xml.sample.
<section id="mobsuite" name="Plasmid typing and reconstruction">
<tool file="mob_suite/mob_recon.xml"/>
<tool file="mob_suite/mob_typer.xml"/>
</section>Here is a snapshot of a successful install
PHemarajata
Hi, I was trying to install the mob-suite via Galaxy toolshed into my own Galaxy instance but I kept getting this error while conda is running.
ERROR conda.core.link:_execute(568): An error occurred while installing package 'bioconda::mob_suite-3.0.0-py_1'. LinkError: post-link script failed for package bioconda::mob_suite-3.0.0-py_1 running your command again with
-vwill provide additional information location of failed script: /home/phemarajata/galaxy/database/dependencies/_conda/envs/__mob_suite@3.0.0/bin/.mob_suite-post-link.shI tried to resolve the dependencies using conda a few times, but was never successful. Is there anything I should do differently? Thank you and stay safe.