student from Wuhan University

[宋日进]

Hello, I'm a student of Wuhan University in China.
I want to localize UCSC now and have encountered some problems.
I want to use the docker method to install UCSC. However, an error occurred in step 7 of the command "docker build - t Dockerfile UCSC:V1.". Dockerfile is the official file of UCSC.
The error is
“The command '/bin/sh -c apt-get install -yq wget rsync && 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' returned a non-zero code: 1“.
Thank you for your answer

[Matthew Speir]

Hello!

Thank you for your question about setting up a Genome Browser using Docker.

Can you explain more about what you are hoping to do with your Genome Browser mirror? Are you attempting to visualize a custom genome? Or do you have custom data for an existing genome assembly (e.g. hg38, mm10, etc)? There are other options besides Docker that may be easier for you, such as GBiB or GBiC: https://genome.ucsc.edu/goldenPath/help/mirror.html#considerations-before-installing-a-genome-browser. 

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.

Training videos & resources: http://genome.ucsc.edu/training/index.html

Want to share the Browser with colleagues? Host a workshop: http://bit.ly/ucscTraining

---

Matthew Speir

UCSC Cell Browser, Quality Assurance and Data Wrangler

Human Cell Atlas, User Experience Researcher

UCSC Genome Browser, User Support

UC Santa Cruz Genomics Institute

Revealing life’s code.

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[宋日进]

Hello,  I am attempting to visualize a custom genome.I installed UCSC through GBIC, and the install command is "bash browsersetup sh install". But the problem is that after the installation, such an error message appears,

                        “handleRefreshState: error from server: Mysql error during sqlTableExists(defaultKnown) 2006: MySQL server has gone away”.

Moreover, I downloaded all files of gbdb and MySQL of caeJap1 from the official website of UCSC and put them in / gbdb and / var / lib / MySQL of Ubuntu18.04 system respectively, but there was still an error,

                         "couldn't connect to database caejap1 on genome-mysql.soe.ucsc.edu as genome

                          Unknown MySQL server host 'genome-mysql. soe. ucsc. Edu '(- 2) ".

I don't know why. I hope to get your help. Thank you very much.

-----原始邮件-----
发件人:"Matthew Speir" <msp...@ucsc.edu>
发送时间:2021-12-09 03:38:30 (星期四)
收件人: "宋日进" <201732...@whu.edu.cn>
抄送: genome-mirror <genome...@soe.ucsc.edu>
主题: Re: [genome-mirror] student from Wuhan University

[Daniel Schmelter]

Hello,

Thanks for using the Genome Browser and writing to our support team. We apologize for the delay in our reply.

It appears that your MySQL server is not functioning correctly. You may want to reinstall MySQL or consider switching to a GBIB installation.

https://genome.ucsc.edu/goldenpath/help/gbib.html

You may also want to check that your genome of interest is not in our system, which now includes many GenBank and RefSeq assemblies. You can search for it here:

https://genome.ucsc.edu/cgi-bin/hgGateway

The easiest way to work within non-reference genomes is by visualizing your custom genome through an assembly hub. No local installation is needed. Is there any reason this does not work for you?

https://genome.ucsc.edu/goldenpath/help/hubQuickStartAssembly.html

I hope this was helpful. If you have any more questions, please reply-all to gen...@soe.ucsc.edu. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

All the best,

Daniel Schmelter
UCSC Genome Browser

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome-mirror/5bea5ec3.4ec14.17db254ecdb.Coremail.songiljin%40whu.edu.cn.