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etetoolkit / ete

Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
http://etetoolkit.org
GNU General Public License v3.0
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upgrade-external-tools is failed #543

Open Chronona opened 3 years ago

Chronona commented 3 years ago 
ete3 upgrade-external-tools

Compiling tcoffee ...ERROR
Compiling tcoffee. Check log .etetoolkit/ext_apps-latest/tcoffee.log

tcoffee.log

...
HTTP による接続要求を送信しました、応答を待っています... 404 Not Found
2021-06-24 15:25:01 エラー 404: Not Found。

!!!!!!! t_coffee        : Download of t_coffee binary failed
!!!!!!! t_coffee        : Check Address: http://www.tcoffee.org/Packages/
Binaries/linux/t_coffee
!!!!!!!! t_coffee compilation and  binary installation failed
------- Finishing The installation

the URL was not found. Could you fix it?

dengzq1234 commented 3 years ago

Hi, the upgrade-external-tools command is very outdated. If you need to install the external tools, I recommend you to install them via conda

conda install -c etetoolkit t_coffee

Chronona commented 3 years ago

Thank you for your reply. Is there a way to solve it without using conda ?

drelo commented 3 years ago

Dear @dengzq1234 the step conda install -c etetoolkit t_coffee

Failed for me. I got # All requested packages already installed. and it seems t_coffee is installed PROGRAM: T-COFFEE Version_11.00.8cbe486

I used this to install

mamba create -n ete3 python=3
conda activate ete3
conda install -c etetoolkit ete3 ete_toolchain
ete3 build check

Do you know how can I fix this? Thanks for your help

dengzq1234 commented 3 years ago

Thank you for your reply. Is there a way to solve it without using conda ?

yes but it would be a bit complicated. Once you install all the tools, it would be found at the same bin/ folder with ete3. Then create a a folder under the same directory by using mkdir -p ete3_apps/bin/ then create a symbolic link for all the tools to the directory above

I admit situation would be complicated without conda

dengzq1234 commented 3 years ago

Dear @dengzq1234 the step conda install -c etetoolkit t_coffee

Failed for me. I got # All requested packages already installed. and it seems t_coffee is installed PROGRAM: T-COFFEE Version_11.00.8cbe486

I used this to install

mamba create -n ete3 python=3
conda activate ete3
conda install -c etetoolkit ete3 ete_toolchain
ete3 build check

Do you know how can I fix this? Thanks for your help

so the tcoffee would be installed under the folder called ete3_apps/bin/ , which located at the same directory of bin folder of ete3, if ete3 build check shows tcoffee exists, the probably you are good to go

drelo commented 3 years ago

the ete3 build check doesn't show t_coffee installed that's why I was trying to fix this so I can finish the installation

Current Toolchain path: /home/andrespara/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: 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: OK - # SLR "Sitewise Likelihood Ratio" selection detection program. Version 1.4.3
         statal: OK - statAl v1.4.rev6 build[2012-02-02]
        tcoffee: MISSING
         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_apps
or manually compile by running:
 ete3 upgrade-external-tools

Do you know how can I fix this?

dengzq1234 commented 3 years ago

the ete3 build check doesn't show t_coffee installed that's why I was trying to fix this so I can finish the installation

Current Toolchain path: /home/andrespara/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: 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: OK - # SLR "Sitewise Likelihood Ratio" selection detection program. Version 1.4.3
         statal: OK - statAl v1.4.rev6 build[2012-02-02]
        tcoffee: MISSING
         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_apps
or manually compile by running:
 ete3 upgrade-external-tools

Do you know how can I fix this?

It indeed seems weird.

it's likely you have tcoffee installed before. My suggestion is to check the /home/andrespara/anaconda3/envs/ete3/bin/, to find if there is tcoffee installed, if yes, create a symbolic link with ln -s <tcoffee> /home/andrespara/anaconda3/envs/ete3/bin/ete3_apps/bin so the ete3 can detect tcoffee app

drelo commented 3 years ago

OK I removed a previous version of t_coffee, installed directly with conda -c bioconda and then moved to that folder (ete3/bin/ete3_apps/bin) and that seemed to work. Thanks for your help.