conda working with docker already installed and no minify-html

conda/build.sh

@@ -2,18 +2,25 @@
 
 VCF_VALIDATOR_VERSION=0.9.4
 BIOVALIDATOR_VERSION=2.1.0
+EVA_PYUTILS_VERSION=0.6.1
 
 EVA_SUB_CLI="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}"
 mkdir -p ${PREFIX}/bin ${EVA_SUB_CLI}
 
 # Install eva-sub-cli
-$PYTHON -m pip install -r requirements.txt
 $PYTHON -m pip install .
 cp bin/* ${PREFIX}/bin
 echo "Done with eva-sub-cli"
 
 cd ${EVA_SUB_CLI}
 
+# Install python dependencies not yet on conda
+curl -Lo eva-pyutils.zip https://github.com/EBIvariation/eva-common-pyutils/archive/refs/tags/v${EVA_PYUTILS_VERSION}.zip \
+    && unzip eva-pyutils.zip && rm eva-pyutils.zip \
+    && cd eva-common-pyutils-${EVA_PYUTILS_VERSION} \
+    && $PYTHON setup.py install \
+    && cd ..
+
 # Install biovalidator from source
 # Includes some workarounds that can be cleaned up once a new version is released
 curl -Lo biovalidator.zip https://github.com/elixir-europe/biovalidator/archive/refs/tags/v${BIOVALIDATOR_VERSION}.zip \

conda/meta.yaml

@@ -21,12 +21,20 @@ requirements:
   host:
     - nextflow >=21.10.0
     - python >=3.8
-    - pip
-    # biovalidator
     - nodejs >=10.19.1
+    - pyyaml
+    - jinja2
+    - openpyxl
+    - requests
+    - jsonschema
   run:
     - nextflow >=21.10.0
     - python >=3.8
+    - pyyaml
+    - jinja2
+    - openpyxl
+    - requests
+    - jsonschema
 
 test:
   imports:

eva_sub_cli/report.py

@@ -2,7 +2,6 @@
 import os.path
 
 from jinja2 import Environment, FileSystemLoader
-from minify_html import minify_html
 
 current_dir = os.path.dirname(__file__)
 
@@ -30,4 +29,9 @@ def generate_html_report(validation_results, validation_date, project_title=None
         validation_results=validation_results,
     )
 
-    return minify_html.minify(rendered_template, minify_js=True, remove_processing_instructions=True)
+    try:
+        # minify-html is not included in conda installation currently
+        from minify_html import minify_html
+        return minify_html.minify(rendered_template, minify_js=True, remove_processing_instructions=True)
+    except ImportError:
+        return rendered_template