Closed j-berg closed 5 years ago
Since there is no way for pypi to reliably take into account all the intricacies of the package installation process and determine what they are, our preferred installation is through conda conda install -c bioconda cgat-apps
.
Got it, thanks for the quick response -- unfortunately I was having issues with that too that I'm still trying to work through (I'll attach below incase you're familiar with how to work through it, if not we can close the issue.
jordan-berg:tests jordan$ conda install -c bioconda cgatcore
Collecting package metadata: done
Solving environment: failed
UnsatisfiableError: The following specifications were found to be in conflict:
- clangxx
Use "conda search <package> --info" to see the dependencies for each package
Hmm, this error relates to an incomparable version of the clang compiler.
I would install in a clean environment:
conda create -n cgat-env
conda activate cgat-env
conda install -c bioconda cgat-apps
conda install -c bioconda cgatcore
Trying this I get:
jordan-berg:tests jordan$ conda list
# packages in environment at /Users/jordan/miniconda3/envs/cgat_test:
#
# Name Version Build Channel
jordan-berg:tests jordan$ conda install -c bioconda cgat-apps
Collecting package metadata: done
Solving environment: failed
UnsatisfiableError: The following specifications were found to be in conflict:
- cgat-apps
Use "conda search <package> --info" to see the dependencies for each package.
I tried installing cgatcore
first, which works, but then shows the same error when trying to install cgat-apps
:/
That’s very strange, Cgat-apps is in conflict with Cgat-apps. This indicates that you already have Cgat-apps installed?
I think your pip install Cgat-apps may be in conflict with the conda, can you pip uninstall Cgat-apps first?
I tried, but with the same result unfortunately. I uninstalled any mention of a cgat app from pip and conda, tried running the previous install commands and its still citing a conflict. Also tried hunting through directories where a pip or conda install may have deposited something but not properly disposed of during uninstall and still nothing.
Any suggestions @sebastian-luna-valero.
There is something very strange with your environment. What system are you installing into?
How about manually installing by:
git clone https://github.com/cgat-developers/cgat-apps.git
cd cgat-apps
python setup install
cgat --help
Then you will have to install the missing dependancies as an when you require them through conda conda install <package>
.
Alternatively, we have an installation script detailed on the README page of cgat-apps.
Actually, looking at your error trace, I assume this is OSX? what version are you running?
It might be worth checking again for previous installations if you used python setup install
in the past as files need to be removed manually. You may want to use python setup.py install --record files.txt
to keep track of what got installed. See this stackoverflow question for example.
Thanks, All.
@j-berg could you please try this instead:
conda create -n cgat-env -c conda-forge -c bioconda -c defaults --override-channels cgat-apps
If that went well, then the following should work:
conda activate cgat-env
cgat --help
Best regards, Sebastian
@sebastian-luna-valero I ran the commands you suggested and it looks like everything is working, thanks!
It appears the pypi hosted version is not automatically checking for missing dependencies
Here is an example:
There are several other cases too, such as with
cgatcore
,cython
, andparamiko
to name a few