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)

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Akira Hasegawa

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Aug 4, 2022, 12:00:40 PM8/4/22
to genome...@soe.ucsc.edu
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:


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
------
 > [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

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Aug 12, 2022, 8:14:33 PM8/12/22
to Akira Hasegawa, genome...@soe.ucsc.edu

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

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Sep 7, 2022, 9:30:07 PM9/7/22
to Akira Hasegawa, genome...@soe.ucsc.edu

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

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