planemo/docs/tests/tests_conda.sh at fde104728b253ffa28143f5a00048b3067b38604 · nsoranzo/planemo · GitHub

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#!/bin/bash

set -o xtrace

set -e

shopt -s expand_aliases  # Needed for conda_env test

# Preconditions:
# - seqtk_example doesn't exist and in home directory
# - conda_exercises doesn't exist in home directory.
# - seqtk environment is absent
# - conda on the PATH

cd

rm -rf seqtk_example
rm -rf conda_exercises
echo "Remove existing seqtk environment - it is fine if it doesn't exist."
conda remove --force --yes --name '__seqtk@1.2' --all || true

# Tests

echo "Try planemo conda_init - this may fail and will always fail on planemo-machine"
echo "still good to see a decent error message though."
planemo conda_init || true

echo "Setup completed seqtk example"
planemo project_init --template=seqtk_complete seqtk_example
cd seqtk_example

echo "Check conda_requirements - should see them linting properly"
planemo lint --conda_requirements seqtk_seq.xml


planemo conda_install seqtk_seq.xml

echo "Checking for seqtk - shouldn't be present"
which seqtk || true

echo "Simulating '. <(planemo conda_env seqtk_seq.xml)', subshell-ism doesn't seem to work in script"
planemo conda_env seqtk_seq.xml > .conda_env
. .conda_env

echo "Inside conda_env I should see seqtk"
which seqtk

conda_env_deactivate

sleep 5  # Need to wait for the package to get cleaned up.

planemo test seqtk_seq.xml

echo "Doing a search - should see seqtk in bioconda results along with versions"
planemo conda_search seqt

cd

planemo project_init --template conda_exercises conda_exercises
cd conda_exercises/exercise_1
ls

echo "Running test wrong - this should fail"
planemo test pear.xml || true
echo "Linting pear without requirements - this should fail"
planemo lint --conda_requirements pear.xml || true

echo "Should see pear from bioconda at 0.9.6"
planemo conda_search pear

wget https://raw.githubusercontent.com/galaxyproject/planemo/master/project_templates/conda_answers/exercise_1/pear.xml -O pear.xml
planemo lint --conda_requirements pear.xml || true

planemo test pear.xml

cd ../exercise_2

# Fetch and build recipe.

mkdir fleeqtk
cd fleeqtk

wget https://raw.githubusercontent.com/galaxyproject/planemo/master/project_templates/conda_answers/exercise_2/fleeqtk/build.sh
wget https://raw.githubusercontent.com/galaxyproject/planemo/master/project_templates/conda_answers/exercise_2/fleeqtk/meta.yaml

cd ..
conda build fleeqtk

# Update to fix tool and see it work.

wget https://raw.githubusercontent.com/galaxyproject/planemo/master/project_templates/conda_answers/exercise_2/fleeqtk_seq.xml -O fleeqtk_seq.xml
planemo test --conda_use_local fleeqtk_seq.xml