slr: MISSING

[Daniela Tejada Martinez]

Hi

I am using ete-evol and all the models run perfect except the slr. Apparently it doesen't download well.

Could you help me with this?

Thank you.

killer-whale@localhost:~$ ete3 build check

Current Toolchain path: /home/killer-whale/anaconda_ete/bin/ete3_apps 

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: OK - MUSCLE v3.8.31 by Robert C. Edgar

          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: 1 external tools seem to be missing or unfunctional

Install using conda (recomended):

 conda install -c etetoolkit ete3_external_tools

or manually compile by running:

 ete3 upgrade-external-tools

[fransua]

Hi Daniela,

we are having troubles installing Slr automatically in many systems...

If you need to use it you could install it manually:

- download the binary from: https://www.ebi.ac.uk/goldman-srv/SLR/#download

- uncompress: tar xzvf slr_linux.tgz

- copy the binay to the etetoolkit folder (most probably ~/.etetoolkit/ext_apps-latest/bin/): cp slr/bin/Slr_shared ~/.etetoolkit/ext_apps-latest/bin/Slr

- In my case (ubuntu 18) I also had to install libatlas3-base: sudo apt install libatlas3-base

hope this helps

cheers

francois