Merge pull request #21 from apriltuesday/conda

EVA-3439 - Conda build

README.md

@@ -4,7 +4,48 @@ EVA Submission Command Line Interface for Validation
 
 ## Installation
 
-TBD
+There are currently three ways to install and run the tool: using conda, from source using Docker,
+and from source natively (i.e. managing dependencies on your own).
+
+### Conda
+
+The most straightforward way to install eva-sub-cli and its dependencies is through conda.
+For example the following installs eva-sub-cli in a new environment called `eva`, activates the environment, and prints
+the help message:
+```bash
+conda create -n eva -c conda-forge -c bioconda eva-sub-cli
+conda activate eva
+eva-sub-cli.py --help
+````
+
+### From source using Docker
+
+This method requires just Python 3.8+ and [Docker](https://docs.docker.com/engine/install/) to be installed.
+Then either clone the git repository, or download the newest tagged release from [here](https://github.com/EBIvariation/eva-sub-cli/tags):
+```bash
+git clone git@github.com:EBIvariation/eva-sub-cli.git
+# OR
+wget -O eva-sub-cli.zip https://github.com/EBIvariation/eva-sub-cli/archive/refs/tags/v0.2.zip
+unzip eva-sub-cli.zip
+```
+
+Then install the library and its dependencies as follows (e.g. in a virtual environment):
+```bash
+cd eva-sub-cli
+pip install -r requirements.txt
+python setup.py install
+```
+
+### From source natively
+
+This method requires the following:
+* Python 3.8+
+* [Nextflow](https://www.nextflow.io/docs/latest/getstarted.html) 21.10+
+* [biovalidator](https://github.com/elixir-europe/biovalidator) 2.1.0+
+* [vcf-validator](https://github.com/EBIvariation/vcf-validator) 0.9.6+
+
+Install each of these and ensure they are available on the path.
+Then git clone the repo or install the newest release as described above.
 
 ## Input files for the validation and submission tool
 
@@ -46,6 +87,9 @@ More detail documentation to follow
 
 ## Execution
 
+Note for Docker users: for each of the below commands, add the command line option `--executor docker`, which will
+fetch and manage the docker container for you.
+
 ### Validate and submit your dataset
 
 To validate and submit run the following command

bin/eva-sub-cli.py

@@ -55,7 +55,7 @@ def validate_command_line_arguments(args, argparser):
                                 'previous runs. Selecting SUBMIT will run validate only if the validation was not performed '
                                 'successfully before and then run the submission.')
     argparser.add_argument('--executor', choices=[DOCKER, NATIVE], default=NATIVE,
-                           help='Select an execution type for running validation')
+                           help='Select an execution type for running validation (default native)')
     credential_group = argparser.add_argument_group('Credential', 'Specify the Webin credential you want to use to '
                                                                   'upload to the EVA')
     credential_group.add_argument("--username", help="Username used for connecting to the ENA webin account")

conda/build.sh

@@ -0,0 +1,48 @@
+#!/bin/bash
+
+VCF_VALIDATOR_VERSION=0.9.6
+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 .
+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 \
+    && unzip biovalidator.zip && rm biovalidator.zip \
+    && cd biovalidator-${BIOVALIDATOR_VERSION} \
+    && bash -c "cat <(echo '#!/usr/bin/env node') <(cat src/biovalidator.js) > tmp" \
+    && mv tmp src/biovalidator.js \
+    && chmod +x src/biovalidator.js \
+    && sed -i 's/dist/src/' package.json \
+    && npm install && npm install -g \
+    && cd ..
+echo "Done with biovalidator"
+
+# Download pre-built vcf-validator
+# Check if linux or osx
+if [ -z ${OSX_ARCH+x} ]; then
+  curl -LJo ${PREFIX}/bin/vcf_validator  https://github.com/EBIvariation/vcf-validator/releases/download/v${VCF_VALIDATOR_VERSION}/vcf_validator_linux \
+    && curl -LJo ${PREFIX}/bin/vcf_assembly_checker  https://github.com/EBIvariation/vcf-validator/releases/download/v${VCF_VALIDATOR_VERSION}/vcf_assembly_checker_linux \
+    && chmod 755 ${PREFIX}/bin/vcf_assembly_checker ${PREFIX}/bin/vcf_validator
+else
+  curl -LJo ${PREFIX}/bin/vcf_validator  https://github.com/EBIvariation/vcf-validator/releases/download/v${VCF_VALIDATOR_VERSION}/vcf_validator_macos \
+    && curl -LJo ${PREFIX}/bin/vcf_assembly_checker  https://github.com/EBIvariation/vcf-validator/releases/download/v${VCF_VALIDATOR_VERSION}/vcf_assembly_checker_macos \
+    && chmod 755 ${PREFIX}/bin/vcf_assembly_checker ${PREFIX}/bin/vcf_validator
+fi
+echo "Done with vcf-validator"

conda/meta.yaml

@@ -0,0 +1,57 @@
+{% set name = "eva-sub-cli" %}
+{% set version = "0.2" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  path: ../
+# For submission to bioconda recipes, replace 'path' with the following (filling in the appropriate sha256):
+#  url: https://github.com/EBIvariation/eva-sub-cli/archive/v{{version}}.tar.gz
+#  sha256:
+
+build:
+  number: 0
+  noarch: generic
+  preserve_egg_dir: True
+# For submission to bioconda recipes, replace 'preserve_egg_dir' with the following:
+#  run_exports:
+#    - {{ pin_subpackage(name, max_pin="x.x") }}
+
+requirements:
+  host:
+    - nextflow >=21.10.0
+    - python >=3.8
+    - 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
+  commands:
+    - biovalidator --help
+    - vcf_validator --help
+    - eva-sub-cli.py --help
+
+about:
+  home: https://github.com/EBIvariation/eva-sub-cli
+  summary: EVA Submission Command Line Interface
+  license: Apache-2.0
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - apriltuesday

eva_sub_cli/VERSION

@@ -1 +1 @@
-0.1
+0.2

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