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miRBase certificate error #3721

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rchekaluk opened this issue Nov 1, 2023 · 0 comments · Fixed by chapmanb/cloudbiolinux#413
Closed

miRBase certificate error #3721

rchekaluk opened this issue Nov 1, 2023 · 0 comments · Fixed by chapmanb/cloudbiolinux#413

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@rchekaluk
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Attempting to install hg38 throws this error (here reproduced manually):

$ wget --random-wait --retry-connrefused -c -O hsa.gff3 https://www.mirbase.org/ftp/21/genomes/hsa.gff3
--2023-11-01 07:19:53--  https://www.mirbase.org/ftp/21/genomes/hsa.gff3
Resolving www.mirbase.org (www.mirbase.org)... 130.88.97.249
Connecting to www.mirbase.org (www.mirbase.org)|130.88.97.249|:443... connected.
ERROR: no certificate subject alternative name matches
	requested host name ‘www.mirbase.org’.
To connect to www.mirbase.org insecurely, use `--no-check-certificate'.
$ echo $?
5

Reviewing the certificate shows this (edited for clarity):

$ host=www.mirbase.org
$ echo "QUIT" | openssl s_client -connect $host:443 -showcerts 2>&1 | sed -n "/BEGIN CERTIFICATE/,/END CERTIFICATE/p" > /tmp/$host.pem
$ openssl x509 -in /tmp/$host.pem -noout -text
...
        Issuer: C = US, O = Let's Encrypt, CN = R3
        Validity
            Not Before: Oct 10 18:39:26 2023 GMT
            Not After : Jan  8 18:39:25 2024 GMT
        Subject: CN = mirbase.org
...
            X509v3 Subject Alternative Name: 
                DNS:mirbase.org

Which indicates that URLs must now use mirbase.org not www.mirbase.org.

rchekaluk pushed a commit to rchekaluk/cloudbiolinux that referenced this issue Nov 1, 2023
naumenko-sa pushed a commit to chapmanb/cloudbiolinux that referenced this issue Dec 11, 2023
* Update mirbase.org URLs fixes bcbio/bcbio-nextgen#3721 fixes bcbio/bcbio-nextgen#3722

* Some miRBase downloads no longer require uncompressing. Fixes bcbio/bcbio-nextgen#3723

---------

Co-authored-by: Rob Chekaluk <rchekaluk@ppolitics.org>
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