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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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Broken clustalo version in conda #670

Open sbliven opened 1 year ago

sbliven commented 1 year ago

When installing via the etetoolkit conda channel the following packages are installed on OSX:

$ conda create -n ete3 -c etetoolkit python=3 ete3 ete_toolchain
...
 argtable2          etetoolkit/osx-64::argtable2-2.13-0
 clustalo           etetoolkit/osx-64::clustalo-1.2.4-h8fd5eaf_0

These versions appear to be incompatible:

$ /usr/local/miniconda/envs/ete3/bin/ete3_apps/bin/clustalo
dyld[8079]: Library not loaded: '/Users/jhc/_Devel/ext_apps/local/lib/libargtable2.0.dylib'
  Referenced from: '/usr/local/miniconda/envs/ete3/bin/ete3_apps/bin/clustalo'
  Reason: tried: '/Users/jhc/_Devel/ext_apps/local/lib/libargtable2.0.dylib' (no such file), '/usr/local/lib/libargtable2.0.dylib' (no such file), '/usr/lib/libargtable2.0.dylib' (no such file)

Aborted

I was able to fix it by installing clustalo from bioconda, then symlinking it to the correct location:

$ conda install -c bioconda clustalo
...

  clustalo            etetoolkit::clustalo-1.2.4-h8fd5eaf_0 --> bioconda::clustalo-1.2.4-h9722bc1_5

$ ln -s $CONDA_PREFIX/bin/clustalo $CONDA_PREFIX/bin/ete3_apps/bin/
$ /usr/local/miniconda/envs/ete3/bin/ete3_apps/bin/clustalo --version
1.2.4

After this the ete3 build check command is successful.