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This commit is contained in:
mvdbeek
2020-09-15 17:17:19 +02:00
parent 08cde1aca7
commit f31b071112
2 changed files with 4 additions and 0 deletions
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lib/galaxy/datatypes/binary.py
+2
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@@ -33,6 +33,8 @@ from galaxy.util.checkers import is_bz2, is_gzip
from . import data, dataproviders
log = logging.getLogger(__name__)
# pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
# Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
pysam.set_verbosity(0)
# Currently these supported binary data types must be manually set on upload
lib/galaxy/visualization/data_providers/genome.py
+2
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@@ -27,6 +27,8 @@ from galaxy.visualization.data_providers.cigar import get_ref_based_read_seq_and
# Utility functions.
#
# pysam 0.16.0.1 emits logs containing the word 'Error', this can confuse the stdout/stderr checkers.
# Can be be removed once https://github.com/pysam-developers/pysam/issues/939 is resolved.
pysam.set_verbosity(0)
PYSAM_INDEX_SYMLINK_NECESSARY = packaging.version.parse(pysam.__version__) <= packaging.version.parse('0.13.0')