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etetoolkit
upgrade-external-tools is failed
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?
Hi, the upgrade-external-tools command is very outdated.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
Thank you for your reply. Is there a way to solve it without using conda ?
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
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
Dear @dengzq1234 the step
conda install -c etetoolkit t_coffeeFailed for me. I got
# All requested packages already installed.and it seems t_coffee is installed PROGRAM: T-COFFEE Version_11.00.8cbe486I used this to install
mamba create -n ete3 python=3 conda activate ete3 conda install -c etetoolkit ete3 ete_toolchain ete3 build checkDo 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
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?
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-toolsDo 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
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.