Usage: task 5 error

[ElitaJaun]

Dear Florent,

Tasks/steps 0-4 seem to be working fine, but when I get to task 5 I get the following error:

Traceback (most recent call last): File "/home/elita/pantagruel_pipeline/pantagruel/scripts/replace_species_by_pop_in_gene_trees.py", line 3, in import tree2 ImportError: No module named tree2 tail: cannot open '/home/elita/databasename/05.core_genome/core-genome-based_reference_tree_databasename_populations' for reading: No such file or directory Found 0 disctinct populations in the species tree Traceback (most recent call last): File "", line 1, in ImportError: No module named tree2 ERROR:

Thank you.

Bw, Elita

[flass]

Hi Elita, OK so the tree2 python package is not seen. It should be installed with the install_dependencies.sh script, and its location should be added to your $PYTHONPATH environement variable through editing of your ~/.bashrc file. Now I realize it may be that you provided a relative path for the target installation directory (argument of install_dependencies.sh), which might result in the $PYTHONPATH being defined but not pointing to an absolute path and thus in most cases, not the correct place. Can you please provide the value of this variable? Best wishes, Florent

[flass]

I realize the situation described above could happen if you installed the software with a previous version, before I enforced the interpretation of relative paths into absolute paths (see similar point in #4). I added a more stringent test on the previous presence of $PYTHONPATH definition in ~/.bashrc in commit 4a4b63d. If that was the case, please either re-run the install script, or just edit your ~/.bashrc so to have absolute path in the $PYTHONPATH definition.

[flass]

This possibility of bug should now be completely avoided through the integration of the tree2 git repository as a submodule of this repo (commits 7a71315, bdebd1a and 7a8c449).