error message during installation of CGAT-core

[amayer21]

Hello,

I'm trying to install CGAT-core at my new place and got the following error message (I've included a few lines before the error message):

running develop
running egg_info
creating cgatcore.egg-info
writing cgatcore.egg-info/PKG-INFO
writing dependency_links to cgatcore.egg-info/dependency_links.txt
writing top-level names to cgatcore.egg-info/top_level.txt
writing manifest file 'cgatcore.egg-info/SOURCES.txt'
reading manifest file 'cgatcore.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'requires.txt'
writing manifest file 'cgatcore.egg-info/SOURCES.txt'
running build_ext
Creating /home/mass/ifilesets/ULG/u230707/cgat-install/conda-install/envs/cgat-c/lib/python3.6/site-packages/cgatcore.egg-link (link to .)
Adding cgatcore 0.5.4 to easy-install.pth file

Installed /home/mass/ifilesets/ULG/u230707/cgat-install/cgat-core
Processing dependencies for cgatcore==0.5.4
Finished processing dependencies for cgatcore==0.5.4
Traceback (most recent call last):
  File "scripts/conda.py", line 47, in <module>
    (out, err) = run_command(statement)
  File "scripts/conda.py", line 41, in run_command
    raise Exception(issue)
Exception:  Problem running command: conda info --json
 Stderr was: b'manpath: warning: $MANPATH set, ignoring /etc/man_db.conf\n'

 ########################################################## 

 An error occurred in:

 - line number: 336
 - exit status: 1
 - command: python scripts/conda.py

 The script will abort now. User input was: 

 ./install-CGAT-tools.sh --devel

 Please copy and paste this error and report it via Git Hub: 
 https://github.com/cgat-developers/cgat-core/issues 

 Debugging: 
 CFLAGS:  -I/home/u/u230707/cgat-install/conda-install/envs/cgat-c/include -L/home/u/u230707/cgat-install/conda-install/envs/cgat-c/lib
 CPATH: /cm/shared/apps/slurm/14.11.11/include -I/home/u/u230707/cgat-install/conda-install/envs/cgat-c/include -L/home/u/u230707/cgat-install/conda-install/envs/cgat-c/lib
 C_INCLUDE_PATH: :/home/u/u230707/cgat-install/conda-install/envs/cgat-c/include
 CPLUS_INCLUDE_PATH: :/home/u/u230707/cgat-install/conda-install/envs/cgat-c/include
 LIBRARY_PATH: /cm/shared/apps/slurm/14.11.11/lib64/slurm:/cm/shared/apps/slurm/14.11.11/lib64:/home/u/u230707/cgat-install/conda-install/envs/cgat-c/lib
 LD_LIBRARY_PATH: /cm/shared/apps/slurm/14.11.11/lib64/slurm:/cm/shared/apps/slurm/14.11.11/lib64:/cm/local/apps/gcc/5.1.0/lib:/cm/local/apps/gcc/5.1.0/lib64:/home/u/u230707/cgat-install/conda-install/envs/cgat-c/lib:/home/u/u230707/cgat-install/conda-install/envs/cgat-c/lib/R/lib
 CGAT_HOME: /home/u/u230707/cgat-install
 CONDA_INSTALL_DIR: /home/u/u230707/cgat-install/conda-install
 CONDA_INSTALL_TYPE: core-devel.yml
 CONDA_INSTALL_ENV: cgat-c
 PYTHONPATH: 
 INSTALL_BRANCH: master
 RELEASE: 
 CODE_DOWNLOAD_TYPE: 0

 ########################################################## 

I had a look to the scripts involved in the error (conda.py) and it says:

It assumes that a conda environment is active, and will run conda commands to 
    * Get the install folder for conda
    * Get a list of the existing environment
    * Pin all packages in all conda environments

I didn't have any conda environment active before to start the installation... Not sure what to do...

PS: I've also noticed a warning message earlier in the installation process but I guess that's not an important one... Here it is, just in case:

WARNING: could not import _license.show_info
# try:
# $ conda install -n root _license

Thanks for your help! (and Happy New Year!!!)

[Acribbs]

Hi,

Unfortunately the installation script is broken at the moment. For the minute I would use the txt file that charlie provided here: https://github.com/cgat-developers/cgat-flow/issues/81#issuecomment-447334834

Then run:

conda create --name <env> --file <file>

[Acribbs]

Happy new year, hope your enjoying your new job!

[amayer21]

Thanks Adam!

I realised I did a mistake by posting this issue in the cgat-flow repository while I was trying to install cgat-core. Not sure if there is a way to move this issue afterwards? I guess Charlie's txt file will install the CGAT-flow environment (ie a lot more than what's in cgat-core environment)? Not sure the problem

When looking at the std out and the script, I had the impression the cgat-core environment had been set up correctly, so I decided to ignore the error message and give a try at sourcing and activating the environment without using Charlie's file. It seems to work... but of course, there may be things missing that I haven't noticed yet... (this is of course very naive and maybe a bit stupid as I don't really understand the error message but I couldn't help giving a try)

I'm currently trying the cgat-showcase pipeline to test if everything is ok... I'm having an error message but can't say if it's a problem linked to this one (ie environment not set up properly) or specific to cgat-showcase. Will post it in the cgat-showcase repository.

New job is great :-) I enjoy bioinformatic so much!!! Missing my Oxford friends and colleagues though!

[Acribbs]

Ah ok, installing cgatcore is now very easy using conda.

conda install -c bioconda cgatcore

Then you should be able to import cgatcore into your pipeline using

import cgatcore

Im currently working on the cgat showcase as we speak so please feel free to raise and issue on the showcase.

BW, Adam

[Acribbs]

Please reopen if you feel