Closed litaifang closed 3 months ago
Thanks for the additional report. This problem exists when using a pre-built pysam wheel on Debian or Ubuntu. The problem is that the underlying libcurl is looking for SSL CA certificates at a path that does not exist on your machine. This can be fixed by telling it where to look; e.g., on Debian/Ubuntu this will probably be
export CURL_CA_BUNDLE=/etc/ssl/certs/ca-certificates.crt
See https://github.com/pysam-developers/pysam/issues/1257#issuecomment-2102480113 for details.
Thanks. Also was able to do os.environ["CURL_CA_BUNDLE"] = "/etc/ssl/certs/ca-certificates.crt"
in a python script.
Hi,
In pysam v0.22.0 (but not in 0.21.0),
pysam.AlignmentFile(REMOTE_BAM_FILE)
returns with the following error messages. Not sure what the issue is, but those errors go away when I use 0.21.0. This seems to happen for bam files on GCS, HTTP, or HTTPS.