vanheeringen-lab/genomepy

details of external databases

zhichengwang59 opened this issue · 1 comments

zhichengwang59 commented

Hi

It seems that our firewall prevents accessing the external databases, see errors below. Please what is the IP or hostname and ports numbers of the external databases? we need to open ports on our firewall.

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/lmod/apps/gimmemotifs/0.17.0_python-3.8.6/lib/python3.8/site-packages/mysql/connector/connection_cext.py", line 236, in _open_connection
self._cmysql.connect(**cnx_kwargs)
_mysql_connector.MySQLInterfaceError: Lost connection to MySQL server at 'reading initial communication packet', system error: 104

During handling of the above exception, another exception occurred:

thanks

zhicheng wang

siebrenf commented

Hey zhicheng,

This error is happening while connecting to the UCSC database. Their host is "genome-mysql.soe.ucsc.edu" and port is 3306.

Here are some workarounds in case this does not work:

  • If you are not set on UCSC, you can specify a provider (for example genomepy search GENOME --provider Ensembl). The full list of providers can be seen with genomepy providers.
  • You could try using genomepy version 0.9.3, which does not use SQL for UCSC.

Good luck!

Siebren