Error when installing CGAT

[Rozita1]

Hi,

I am trying to install CGAT and I'm getting the following error. Can you please help?

My previous code was: qrshx cd ~ wget https://github.com/cgat-developers/cgat-apps/archive/master.zip mkdir /data/$USER/cgat_install unzip master.zip cd cgat-apps-master ./install.sh --production --location #########################################################

An error occurred in:

• line number: 879
• exit status: 1

• command: shift 2

  The script will abort now. User input was:

  ./install.sh --production --location

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

  Debugging: CFLAGS: CPATH: C_INCLUDE_PATH: CPLUS_INCLUDE_PATH: LIBRARY_PATH: LD_LIBRARY_PATH: CGAT_HOME: CONDA_INSTALL_DIR: CONDA_INSTALL_TYPE_APPS: CONDA_INSTALL_TYPE_CORE: CONDA_INSTALL_ENV: PYTHONPATH: INSTALL_BRANCH: master CORE_BRANCH: master RELEASE: CODE_DOWNLOAD_TYPE: 0

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

[Acribbs]

Hi,

Our preferred method of installing cgat-apps is to use conda:

conda install -c conda-forge -c bioconda cgat-apps

If you would like to install a developmental version onto your local environment then I would suggest:

git clone https://github.com/cgat-developers/cgat-apps.git cd cgat-apps python setup.py develop

However, if you would like to use the install script then the reason for your error in this instance is not specifying the path for installation after the --location flag.

[Rozita1]

Thank you, just got it installed, finally.