Try to install planemo within conda env

Author: mvdbeek

.travis.yml

@@ -13,11 +13,13 @@ before_install:
   - export PLANEMO_CONDA_PREFIX="$HOME/conda"
 
 install:
-  - pip install flake8 planemo
+  - pip install planemo
   - planemo conda_init
-  - $PLANEMO_CONDA_PREFIX/bin/conda update -y conda
-  - $PLANEMO_CONDA_PREFIX/bin/conda create -y -q -c bioconda --name iuc_conda samtools=0.1.19 bcftools
-  - . $PLANEMO_CONDA_PREFIX/bin/activate iuc_conda
+  - export PATH=$PLANEMO_CONDA_PREFIX/bin
+  - conda update -y conda
+  - conda create -y -q -c bioconda --name iuc_conda samtools=0.1.19 bcftools
+  - . activate iuc_conda
+  - pip install planemo
   - planemo --version
   - $PLANEMO_CONDA_PREFIX/bin/conda --version
   - git diff --quiet "$TRAVIS_COMMIT_RANGE" -- ; GIT_DIFF_EXIT_CODE=$?
@@ -37,7 +39,7 @@ install:
   - cat changed_repositories_chunk.list
 
 script:
-  - cd "$TRAVIS_BUILD_DIR" ## && flake8 --exclude=.git .
+  - cd "$TRAVIS_BUILD_DIR"
   - while read -r DIR; do planemo shed_lint --tools --ensure_metadata --urls --report_level warn --fail_level error --recursive "$DIR" || exit 1; done < changed_repositories_chunk.list
   - while read -r DIR; do planemo conda_install "$DIR"; done < changed_repositories_chunk.list
   - while read -r DIR; do planemo test --conda_dependency_resolution --galaxy_branch "$GALAXY_RELEASE" --galaxy_source "$GALAXY_REPO" "$DIR" || exit 1; done < changed_repositories_chunk.list