diff --git a/Singularity b/Singularity index fac66fabf..2e8f96937 100644 --- a/Singularity +++ b/Singularity @@ -83,7 +83,7 @@ From: centos:7 echo ===== Installing Rust and merge-mates ===== >/dev/null yum install -q -y rust cargo - cargo install --root / --git https://github.com/jeff-k/merge-mates.git + cargo install --quiet --root / --git https://github.com/jeff-k/merge-mates.git ## Miniconda (Python 2) (Don't use this) #wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh diff --git a/release_test_microtest.py b/release_test_microtest.py index ab0154775..d8fadb9ba 100644 --- a/release_test_microtest.py +++ b/release_test_microtest.py @@ -93,9 +93,6 @@ def check_1234(self): def check_2000(self): expected_counts = """\ -1 0 0 0 0 -2 0 0 0 0 -3 0 0 0 0 4 10 0 0 0 5 0 10 0 0 6 10 0 0 0 @@ -342,10 +339,13 @@ def check_2180(self): assert 10 < coverage, coverage_message elif 380 < pos: assert coverage < 10, coverage_message - else: - assert row['region'] == 'V3LOOP', row['region'] + elif row['region'] == 'V3LOOP': assert row['seed'] == 'HIV1-CON-XX-Consensus-seed', row['seed'] assert 10 < coverage, coverage_message + else: + # Last codon of vpu has coverage. + assert row['region'] == 'HIV1B-vpu', row['region'] + assert row['query.nuc.pos'] == '6305', row['query.nuc.pos'] def check_2190(self): mutation_rows = self.read_file('2190A-SARSCOV2_S23', 'nuc_mutations.csv') @@ -361,7 +361,7 @@ def check_2200(self): pos = int(row['refseq.aa.pos']) coverage = int(row['coverage']) coverage_message = f'{coverage} coverage at {pos}' - assert row['region'] in ('SARS-CoV-2-nsp1', 'SARS-CoV-2-ORF1ab'), row + assert row['region'] in ('SARS-CoV-2-nsp1', 'SARS-CoV-2-ORF1a'), row if 27 <= pos <= 102: assert coverage == 100, coverage_message else: