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adding documentation for certificate change problems #162

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merged 4 commits into from
Jan 5, 2024
Merged

adding documentation for certificate change problems #162

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e181c4e
Main (#159)
WardDeb Aug 4, 2023
e10bf34
adding documentation for certificate change problems
Nov 29, 2023
e054ee8
updating certificate issue
Nov 29, 2023
6cc99ae
Update usage.rst
WardDeb Nov 29, 2023
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15 changes: 15 additions & 0 deletions docs/usage.rst
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Expand Up @@ -148,6 +148,21 @@ remove all the flags:

and rerun dissectBCL. Note that an existing demuxSheet in the folder won't be overwritten, allowing you to jump in.

Issues with Parkour verification
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
In this case (which is rare as it's caused by changing the certificate provider and it is not commonly listed), the certificate issuer is not recognized as dissect throws this error:

.. code-block:: console

requests.exceptions.SSLError: HTTPSConnectionPool(host='parkourURL', port=443): Max retries exceeded with url:
/api/analysis_list/analysis_list/?flowcell_id=XXXXXXXXX (Caused by SSLError(SSLCertVerificationError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate
verify failed: unable to get local issuer certificate (_ssl.c:1007)')))

then, the new certificate needs to be added in the system (i.e. for CentOS 7, copying it to /etc/pki/ca-trust/source/anchors/ and run "update-ca-trust").

Finally, the cert field under the parkour header in the configuration file needs to point to the file copied in the anchors directory.


Other issues
^^^^^^^^^^^^
It can happen that the pipeline just crashes. A point of entry there would be to have a look at the log files. These are written per flowcell.
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