From d449d54dd6ca5f67f054560156bdbeb307c48354 Mon Sep 17 00:00:00 2001
From: April Shen <ashen@ebi.ac.uk>
Date: Wed, 18 Sep 2024 11:34:34 +0100
Subject: [PATCH] Update build.sh

---
 conda/build.sh | 34 +++-------------------------------
 1 file changed, 3 insertions(+), 31 deletions(-)

diff --git a/conda/build.sh b/conda/build.sh
index 5921457..695dd90 100644
--- a/conda/build.sh
+++ b/conda/build.sh
@@ -1,48 +1,20 @@
 #!/bin/bash
 
-VCF_VALIDATOR_VERSION=0.9.6
-BIOVALIDATOR_VERSION=2.1.0
-EVA_PYUTILS_VERSION=0.6.1
+BIOVALIDATOR_VERSION=2.2.1
 
 EVA_SUB_CLI="${PREFIX}/share/${PKG_NAME}-${PKG_VERSION}"
-mkdir -p ${PREFIX}/bin ${EVA_SUB_CLI}
+mkdir -p ${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 \
+    && unzip -q 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"