PAML installation from source

[Cecilia-Sensalari]

• In containers PAML is now installed from source

• Installation.rst updated for PAML local installation

• Renamed "Paralog1" to "Ortholog1" in ortholog TSV file

• Nextflow command is now without square brackets for the "-c" parameter

• Lincense has now "ksrates" instead of "ks rate-correction"

[Cecilia-Sensalari]

Renaming "wgd" module to "wgd_ksrates": We have called the wgd module integrated in ksrates simply "wgd", however this is also how wgd is called when installed separately (one might have wgd already installed or might want to install it later on). If for example you install first ksrates and then wgd, the most recent wgd will take over when "wgd" is called in the commands during our ksrates pipeline. This leads to some incompatibilities... To solve this I'm giving a new name to our integrated wgd directory ("wgd_ksrates") and I'm changing it in the files where needed.

[lohausr]

Renaming "wgd" module to "wgd_ksrates": We have called the wgd module integrated in ksrates simply "wgd", however this is also how wgd is called when installed separately (one might have wgd already installed or might want to install it later on). If for example you install first ksrates and then wgd, the most recent wgd will take over when "wgd" is called in the commands during our ksrates pipeline. This leads to some incompatibilities... To solve this I'm giving a new name to our integrated wgd directory ("wgd_ksrates") and I'm changing it in the files where needed.

Hmm. We do not use the wgd command anywhere anymore, or do we? Is this also the case for the import statements, would it rather import from a separately installed wgd than the module integrated within ksrates?