From b1844aced2a326fb19a254fbf5425fd5c601681a Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Tue, 6 Feb 2024 07:19:14 -0700 Subject: [PATCH 1/2] afterok --- scripts/start_meta | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/start_meta b/scripts/start_meta index 964f879..136cf0b 100755 --- a/scripts/start_meta +++ b/scripts/start_meta @@ -52,7 +52,7 @@ def execute(url, job_id, out_dir): # Submitting jobs and returning id main_job = run(['sbatch', main_fp], stdout=PIPE) main_job_id = main_job.stdout.decode('utf8').split()[-1] - finish = run(['sbatch', '-d', f'afterany:{main_job_id}', finish_fp], + finish = run(['sbatch', '-d', f'afterok:{main_job_id}', finish_fp], stdout=PIPE) finish_job_id = finish.stdout.decode('utf8').split()[-1] print(f'{main_job_id}, {finish_job_id}') From dd972bc46b5e7db7dac9eee6a70ffe4e104ea92e Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Tue, 6 Feb 2024 08:09:33 -0700 Subject: [PATCH 2/2] QIITA_SERVER_CERT --- .github/workflows/qiita-plugin-ci.yml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/.github/workflows/qiita-plugin-ci.yml b/.github/workflows/qiita-plugin-ci.yml index a8ad7b4..529aa74 100644 --- a/.github/workflows/qiita-plugin-ci.yml +++ b/.github/workflows/qiita-plugin-ci.yml @@ -84,8 +84,9 @@ jobs: conda create -q --yes -n qp-meta python=3.9 biom-format sortmerna=2.1b samtools pigz conda activate qp-meta - export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt + export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg + pip --quiet install -U pip pip --quiet install . pip --quiet install coveralls @@ -105,7 +106,7 @@ jobs: shell: bash -l {0} run: | conda activate qiita - export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt + export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg sed "s#/home/runner/work/qiita/qiita#${PWD}/qiita-dev/#g" `pwd`/qiita-dev/qiita_core/support_files/config_test.cfg > ${QIITA_CONFIG_FP} @@ -138,7 +139,7 @@ jobs: run: | conda activate qp-meta - export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/server.crt + export QIITA_SERVER_CERT=`pwd`/qiita-dev/qiita_core/support_files/ci_rootca.crt export QIITA_CONFIG_FP=`pwd`/qiita-dev/qiita_core/support_files/config_test_local.cfg export QC_SORTMERNA_DB_DP=$PWD/qp_meta/sortmerna/databases/rRNA_databases/ export ENVIRONMENT="source /home/runner/.profile; conda activate qp-meta"