Update Singularity (i-ADHoRe; pandas 1.2) + other fixes

[Cecilia-Sensalari]

Hi Arthur, I've edited the Singularity file so to add the use of i-ADHoRe and pandas 1.2. This pull request contains more than I anticipated because I had to fix other things. Below more details!

In Singularity recipe file:

• The first two lines now base your container image on the existing VIB-PSB/i-adhore container, so that i-ADHoRe is already installed in it and also wgd syn can be run.
• Among the environmental variables I added $TMPDIR and set it as the default temporary folder that is present in the container (/tmp). This change was motivated by the fact that wgd ksd runs mafft and this latter makes use of a $TMPDIR variable (see its source code); this variable is by default set from the host (i.e. in my case the cluster computer, which sets $TMPDIR to a personal folder inside /scratch), but this folder is clearly not available inside the container.
• PAML is installed from source website for compatibility issues
• I removed the line that is generating the alias for Fasttree because it was giving an error during installation, it doesn't seem to create problems, but needs further checks.

Insetup.py it is now asked to install pandas 1.2 because 0.24 was stalling the installation when using recent Python versions. On ksrates I don't have anything to report at the moment about using this version instead of 0.24, but in general it needs further checks.

In wgd_cli.py:

• I added arguments feature and attribute to functionwf1 because the user was otherwise not able to change their default values. I then added those two arguments in the syn_ function called in wf1.
• viz function was giving problems with some ticks (see this commit), probably due to pandas' new version, so I patched it.

I hope this can come in handy and let me know if you'd like to discuss something!

Best, Cecilia

[arzwa]

This is great, thanks Cecilia! Since I'm sure you have tested this extensively and I don't have much time to test it, I'll just merge this in. One thing: if there is anything about the Singularity container you wish to update in the README, you're very welcome to do so, I have not worked with Singularity in ages so the info on that in the README is probably outdated.