cannot install cgat-apps as a CGAT developer

[kevinrue]

The installation as a cgat-developer is currently failing for me due to the curl commands in install.sh trying download conda environment files cgat-*.yml taht do not exist (yet?).

In short, there seem to be some YAML files of environment specifications missing from GitHub.

Specifically, in this else block https://github.com/cgat-developers/cgat-apps/blob/597cb47f2196df978c75dd8e3493eb22d163551b/install.sh#L103 all the CONDA_INSTALL_TYPE_APPS= and CONDA_INSTALL_TYPE_CORE= instances seem to point to files (e.g., *-production/yml, *-devel.yml) that are not available yet when resolving the commands here (https://github.com/cgat-developers/cgat-apps/blob/597cb47f2196df978c75dd8e3493eb22d163551b/install.sh#L328)

For instance for cgat-apps, the --devel flags set CONDA_INSTALL_TYPE_APPS=apps-devel.yml with TRAVIS_BRANCH=master, this resolves to

https://raw.githubusercontent.com/cgat-developers/cgat-apps/master/conda/environments/apps-devel.yml

while only cgat-apps.yml currently exists at the following link. https://raw.githubusercontent.com/cgat-developers/cgat-apps/master/conda/environments/cgat-apps.yml

Those raw.githubusercontent.com point to the following folder in the GitHub repository https://github.com/cgat-developers/cgat-apps/tree/master/conda/environments

That said, separately, I have managed to install cgat-apps as a regular user (i.e., not CGAT developer) using the recommended installation (that requires a pre-existing Miniconda installation, obviously)

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

Any feedback welcome.