ETE3 install on Ubuntu 22.04 via WSL2

[denjixx]

Hi! I was trying to get a workaround with installing ete3. I somewhat messed up at first, but I was able to install ete3 later. Afterwards, I tried $ ete3 build check, and this was the output:

Current Toolchain path: /home/rene/anaconda3/envs/ete3/bin/ete3_apps/bin
Current Toolchain version: unknown
       clustalo: OK - 1.2.4
         codeml: OK - AAML in paml version 4.8a, July 2014
      dialigntx: OK - This is DIALIGN-TX Version 1.0.2 - A Multiple Sequence alignment program.
       fasttree: OK - Usage for FastTree version 2.1.8 Double precision (No SSE3), OpenMP (1 threads):
         iqtree: OK - IQ-TREE multicore version 1.5.5 for Linux 64-bit built Jun  2 2017
         kalign: OK - Kalign version 2.04, Copyright (C) 2004, 2005, 2006 Timo Lassmann
          mafft: OK - MAFFT v6.861b (2011/09/24)
         muscle: MISSING
          phyml: OK - . This is PhyML version 20160115.
     pmodeltest: OK - pmodeltest.py v1.4
          raxml: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
 raxml-pthreads: OK - This is RAxML version 8.2.11 released by Alexandros Stamatakis on June 2017.
         readal: OK - readAl v1.4.rev6 build[2012-02-02]
            slr: MISSING
         statal: OK - statAl v1.4.rev6 build[2012-02-02]
        tcoffee: OK - PROGRAM: T-COFFEE Version_11.00.8cbe486 (2014-08-12 22:05:29 - Revision 8cbe486 - Build 477)
         trimal: OK - trimAl v1.4.rev6 build[2012-02-02]

WARNING: 2 external tools seem to be missing or unfunctional
Install using conda (recomended):
 conda install -c etetoolkit ete3_external_apps
or manually compile by running:
 ete3 upgrade-external-tools

Then I tried using $ conda install -c etetoolkit ete3_external_apps, which gave me this:

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - ete3_external_apps -> python[version='2.7.*|3.4.*']

Your python: python=3

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.35=0
  - feature:|@/linux-64::__glibc==2.35=0

Your installed version is: 2.35

I was looking for answers here but there seems to be none, or my layman head cannot understand how technical it is to troubleshoot. I am just learning the WSL CLI so please bear with me, just a beginner. Thanks a lot!

[denjixx]

UPDATE: I tried installing slr and muscle via $ conda install -c etetoolkit slr muscle but it says # All requested packages already installed.. Could there be any work around with this?

[denjixx]

Hi! Took it months to finally reach the end of this... but well we good! So, here is the workaround for those who has this problem:

FOR MUSCLE First, sudo apt install muscle to install MUSCLE v3.8.1551 by Robert C. Edgar, independent of ete3. Then, create a symbolic link by using ln -s $(which muscle) [Current Toolchain path] (use ete3 build check to know here the apps are located.) Detailed explanation is here: https://groups.google.com/g/etetoolkit/c/mlqJHJcu87E

FOR SLR There is no workaround but to manually install SLR "Sitewise Likelihood Ratio" selection detection program. Version 1.3. Detailed explanation and instruction is here: https://groups.google.com/g/etetoolkit/c/1rWr4GV3zO0

1. First, download SLR binary using either wget or curl. For me, I used wget -O slr https://www.ebi.ac.uk/goldman-srv/SLR/download/v1.3/slr_linux.tgz.
2. After which, uncompress binary using tar xzvf slr.
3. Then, copy binary to ete3 using cp slr/bin/Slr_shared [Current Toolchain Path]/Slr.
4. Lastly, install libatlas3-base by using sudo apt install libatlas3-base.

Thank you to all!