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 1/2] 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"

From 2e6557a9086715cd5bb3eea572793641d08761e3 Mon Sep 17 00:00:00 2001
From: April Shen <ashen@ebi.ac.uk>
Date: Wed, 18 Sep 2024 11:36:26 +0100
Subject: [PATCH 2/2] update meta.yaml

---
 conda/meta.yaml | 28 +++++++++++++++++-----------
 1 file changed, 17 insertions(+), 11 deletions(-)

diff --git a/conda/meta.yaml b/conda/meta.yaml
index 40ba37e..b54c05a 100644
--- a/conda/meta.yaml
+++ b/conda/meta.yaml
@@ -1,37 +1,42 @@
 {% set name = "eva-sub-cli" %}
-{% set version = "0.2" %}
+{% set version = "0.4" %}
 
 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:
+  url: https://github.com/EBIvariation/eva-sub-cli/archive/v{{version}}.tar.gz
+  sha256: be4d4109d9879ad94ccc01a3bd534ff6077775f126977dfb3f2d6fd9cfb251ba
 
 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") }}
+  script_env:
+    - SETUPTOOLS_SCM_PRETEND_VERSION={{ version }}
+  run_exports:
+    - {{ pin_subpackage(name, max_pin="x.x") }}
 
 requirements:
   host:
     - nextflow >=21.10.0
     - python >=3.8
     - nodejs >=10.19.1
+    - vcf-validator >=0.9.7
+    - ebi-eva-common-pyutils >=0.6.1
     - pyyaml
     - jinja2
     - openpyxl
     - requests
     - jsonschema
+    - unzip
+    - setuptools-scm
   run:
     - nextflow >=21.10.0
     - python >=3.8
+    - nodejs >=10.19.1
+    - vcf-validator >=0.9.7
+    - ebi-eva-common-pyutils >=0.6.1
     - pyyaml
     - jinja2
     - openpyxl
@@ -43,7 +48,6 @@ test:
     - eva_sub_cli
   commands:
     - biovalidator --help
-    - vcf_validator --help
     - eva-sub-cli.py --help
 
 about:
@@ -54,4 +58,6 @@ about:
 
 extra:
   recipe-maintainers:
-    - apriltuesday
\ No newline at end of file
+    - apriltuesday
+    - tcezard
+    - ebi-variation
\ No newline at end of file