Installing genome browser on my local computer failed with ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

[Akira Hasegawa]

Dear Genome Browser staffs,

I truly enjoy using your Genome Browser for viewing genomes so I've tried installing onto my local computer following instruction:

https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions

But installation failed with MySQL socket problem.

Here are the last part of the log:

#10 198.3 To activate the new configuration, you need to run:

#10 198.3   service apache2 reload

#10 198.4 Site 000-default disabled.

#10 198.4 To activate the new configuration, you need to run:

#10 198.4   service apache2 reload

#10 198.4  * Restarting Apache httpd web server apache2

#10 199.7 AH00112: Warning: DocumentRoot [/usr/local/apache/htdocs] does not exist

#10 200.7    ...done.

#10 200.7 | Checking for Mysql version >= 8

#10 200.8 ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

#10 200.8 Exit error 1 occurred on line 1

#10 200.8 The UCSC Genome Browser installation script exited with an error.

#10 200.8 Please contact us at genome...@soe.ucsc.edu and send us an output log

#10 200.8 of the command prefixed with "bash -x", e.g.

#10 200.8 bash -x browserSetup.sh install 2>&1 > install.log

#10 ERROR: executor failed running [/bin/sh -c apt-get install -yq wget rsync mariadb-server && sed -i 's/101/0/g' /usr/sbin/policy-rc.d && apt-get install udev || sed -i '2iexit 0' /etc/init.d/udev && service udev start && chmod a+x /root/browserSetup.sh && /root/browserSetup.sh -b install && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && chmod a+x /etc/service/mysqld/run /etc/service/apache/run]: exit code: 1

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 > [6/7] RUN apt-get install -yq wget rsync mariadb-server && sed -i 's/101/0/g' /usr/sbin/policy-rc.d && apt-get install udev || sed -i '2iexit 0' /etc/init.d/udev && service udev start && chmod a+x /root/browserSetup.sh && /root/browserSetup.sh -b install && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && chmod a+x /etc/service/mysqld/run /etc/service/apache/run:

------

executor failed running [/bin/sh -c apt-get install -yq wget rsync mariadb-server && sed -i 's/101/0/g' /usr/sbin/policy-rc.d && apt-get install udev || sed -i '2iexit 0' /etc/init.d/udev && service udev start && chmod a+x /root/browserSetup.sh && /root/browserSetup.sh -b install && apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/* && chmod a+x /etc/service/mysqld/run /etc/service/apache/run]: exit code: 1

Is there any way to go around this problem?

Thank you in advance.

Akira Hasegawa

[Gerardo Perez]

Hello, Akira.

Thank you for your interest in the Genome Browser and for bringing this installation error to our attention.

The installation error is due to the docker image getting changed. A docker image contains a pointer to another base docker image that contains the Linux distro. This Linux distro sometimes gets updated for security fixes or when ubuntu does a major change. We are working on fixing the issue, and should be fixed very soon. We will follow up with you when the issue has been fixed.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

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[Gerardo Perez]

Hello, Akira.

Thank you again for bringing this issue to our attention.

We have fixed the issue, and you should now be able to run the Docker installation instructions:
https://genome.ucsc.edu/goldenPath/help/mirror.html#docker-installation-instructions

Thank you again for using the UCSC Genome Browser and helping to improve the software for everyone.

I hope this is helpful. If you have any further questions, please reply to genome...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute