From c1c8db9363fe70f95b5804dea94053d13f8e6087 Mon Sep 17 00:00:00 2001 From: MalinAhlberg Date: Tue, 3 Dec 2024 13:55:23 +0100 Subject: [PATCH] [tests] refactor: keep all installations together --- .github/integration/tests/sda/01_install_dependencies.sh | 2 ++ .github/integration/tests/sda/10_upload_test.sh | 2 -- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/integration/tests/sda/01_install_dependencies.sh b/.github/integration/tests/sda/01_install_dependencies.sh index 9020696c1..174d96c6d 100644 --- a/.github/integration/tests/sda/01_install_dependencies.sh +++ b/.github/integration/tests/sda/01_install_dependencies.sh @@ -13,3 +13,5 @@ for t in curl expect jq openssh-client postgresql-client xxd; do apt-get -o DPkg::Lock::Timeout=60 install -y "$t" >/dev/null fi done + +pip -q install s3cmd diff --git a/.github/integration/tests/sda/10_upload_test.sh b/.github/integration/tests/sda/10_upload_test.sh index 640045454..a5b8419de 100644 --- a/.github/integration/tests/sda/10_upload_test.sh +++ b/.github/integration/tests/sda/10_upload_test.sh @@ -20,8 +20,6 @@ done ## truncate database psql -U postgres -h postgres -d sda -At -c "TRUNCATE TABLE sda.files, sda.encryption_keys CASCADE;" -pip -q install s3cmd - for file in NA12878.bam NA12878_20k_b37.bam NA12878.bai NA12878_20k_b37.bai; do curl --retry 100 -s -L -o /shared/$file "https://github.com/ga4gh/htsget-refserver/raw/main/data/gcp/gatk-test-data/wgs_bam/$file" if [ ! -f "$file.c4gh" ]; then