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Source the full path of conda activate script

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Otherwise, if a virtualenv is active on top of conda base env (e.g. when
running py37-first_startup tox test in TravisCI), the wrong `activate`
script is sourced.

Also fix `CONDA_PREFIX` environment variable definition when using a shell
not supported by conda.
This commit is contained in:
Nicola Soranzo
2020-02-23 23:06:01 +00:00
parent f61ae2c42a
commit da256571e6
1 changed files with 9 additions and 3 deletions
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scripts/common_startup_functions.sh
+9 -3
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@@ -88,9 +88,9 @@ conda_activate() {
echo " starting Galaxy."
PATH="$(get_conda_env_path $GALAXY_CONDA_ENV)/bin:$PATH"
CONDA_DEFAULT_ENV="$GALAXY_CONDA_ENV"
CONDA_PREFIX="$(get_conda_root_path)"
CONDA_PREFIX="$(get_conda_active_prefix)"
else
source activate "$GALAXY_CONDA_ENV"
source "$(get_conda_root_prefix)"/bin/activate "$GALAXY_CONDA_ENV"
fi
}
@@ -225,7 +225,13 @@ set_conda_info() {
fi
}
get_conda_root_path() {
get_conda_active_prefix() {
set_conda_info
printf "%s" "$__CONDA_INFO" \
| python -c "import json, sys; print(json.load(sys.stdin)['active_prefix'])"
}
get_conda_root_prefix() {
set_conda_info
printf "%s" "$__CONDA_INFO" \
| python -c "import json, sys; print(json.load(sys.stdin)['root_prefix'])"