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slr: MISSING even after trying ete3_external_apps and upgrade-external-tools

Open drelo opened this issue 5 years ago • 0 comments

Dear users, although I have experience with conda installations, this is my first time trying to install ete, when I check the install I got this error.

ete3 build check
Current Toolchain path: /home/tucu/miniconda3/envs/etekit/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: 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]

Neither of these solutions seem to work

Install using conda (recomended):
 conda install -c etetoolkit ete3_external_apps
or manually compile by running:
 ete3 upgrade-external-tools

`conda install -c etetoolkit ete3_external_apps 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 each other:

Output in format: Requested package -> Available versions `

I am using miniconda and Ubuntu (14.04, it is not my machine ATM). I installed everything in a new environment created like this conda create --name etekit python=2

I didn't setup any channels before installing ete but I wonder if I can install everything from scratch to solve this missing package issue Thanks for your help

Cheers

drelo avatar Dec 09 '20 09:12 drelo