Installation help

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Anoop Sendamarai

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Jul 8, 2021, 4:31:42 AMJul 8
to cBioPortal for Cancer Genomics Discussion Group
Hello,

I am new to both CBP and docker. I was trying to install the portal on my windows machine using the instructions in: 

I am having trouble running the docker because of the mysql port. I get the following error:
cbioportal-container                   | Database not available yet (first time can take a few minutes to load seed database)... Attempting reconnect...
')used for variable 'port' (value '3306| Unknown suffix '
' to 'port'container                   | mysqladmin: Error while setting value '3306
 -psomepasswordainer                   | mysqladmin ping -s -hcbioportal-database -P3306

I was not able to find any help on this error, any help would be greatly appreciated!

Thanks!

Pim van Nierop

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Jul 8, 2021, 6:10:09 AMJul 8
to Anoop Sendamarai, cBioPortal for Cancer Genomics Discussion Group
Hi Anoop,

At what step in the docs does this occur. Also, can you clarify the error that you recieve? Is this literally what is shown on screen? It looks a bit garbled. Can you provide a screenshot?

Bye,
Pim 

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Anoop Sendamarai

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Jul 9, 2021, 2:46:38 PMJul 9
to cBioPortal for Cancer Genomics Discussion Group
Hi Pim,

Thanks for your response.

I get the error during initializing: docker compose up

I have attached a screen shot.


Capture.JPG

Anoop Sendamarai

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Jul 9, 2021, 2:46:38 PMJul 9
to cBioPortal for Cancer Genomics Discussion Group
Hi Pim,

Thanks for the reply.

I get this error during initializing the docker: docker compose up

I have attached a screenshot.

Thanks again!

On Thursday, July 8, 2021 at 6:10:09 AM UTC-4 p...@thehyve.nl wrote:

Pim van Nierop

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Jul 16, 2021, 3:36:32 AMJul 16
to Anoop Sendamarai, cBioPortal for Cancer Genomics Discussion Group
Hi Anoop,

I suspect that you edited the portal.properties file on a windows computer thereby using line endings that are not correctly interpreted by the bash scripts in the docker entrypoint script. Can you try to transform line endings to unix and try again?

All the best,
Pim

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