Can CRISPRAnalyzeR be installed on AWS instances?

[xuguorong2016]

Hi Jan,

Thanks for your nice tool CRISPRAnalyzeR! I am wondering if CRISPRAnalyzeR can be installed an AWS instance though I have installed docker and the CRISPRAnalyzeR image on an AWS instance, but I just cannot open it from the browser.

In the security port, I have opened the 8000 port.

Your response would be really appreciated! Guorong

[jwinter6]

Hi Guorong, thats actually interesting, as the docker container should also work on AWS machines.

Have you used the latest version V 1.50? I updated it 3 days ago.

Please do me huge favour: can you login to the AWS instance and get the logs for me?

Either by logging into the docker container shell or by starting the docker container with mounting the log folder: docker run -e verbose_logfiles=TRUE -v /FOLDERONDISK:/srv/shiny-server/CRISPRAnalyzeR/log/ -v /FOLDERONDISK:/var/log/shiny-server/ -p 8000:8000 boutroslab/crispranalyzer:V1.50

Best, Jan

[xuguorong2016]

Hi Jan,

Thanks for your response! I run CRISPRAnalyzeR v1.5 on the AWS instance and then output the logs in the logs folder. Please see the below command and logs. I still have the same issue with the v1.5.

Please let me know if you need anything else.

Thanks, Guorong

[ec2-user@ip-172-31-17-138 ~]$ sudo docker run -e verbose_logfiles=TRUE -v /home/ec2-user/logs:/srv/shiny-server/CRISPRAnalyzeR/log/ -v /FOLDERONDISK:/var/log/shiny-server/ -p 8000:8000 boutroslab/crispranalyzer:1.50 [CUSTOM] setting enhanced websocket settings [CUSTOM] setting verbose shiny server and application logfiles [CUSTOM] setting the path to the COSMIC database [CUSTOM] EnrichR interface [CUSTOM] setting the EnrichR URL [CUSTOM] Set maximum upload Size [CUSTOM] setting number of threads for Bowtie2 [CUSTOM] setting Logs Starting Shiny-Server As a default, please navigate to http://localhost:8000/CRISPRAnalyzeR/ to access CRISPRAnalyzeR ^C[ec2-user@ip-172-31-17-138 ~]$ ls logs [ec2-user@ip-172-31-17-138 ~]$ cd logs/ [ec2-user@ip-172-31-17-138 logs]$ ls access.log [ec2-user@ip-172-31-17-138 logs]$ more access.log 108.83.5.212 - - [20/Jan/2018:17:07:32 +0000] 500 127.0.0.1 - - [20/Jan/2018:17:07:32 +0000] 500

[jwinter6]

Hi,

is there just an access.log? There should be way more, app.log, analysis.log, fastq_extraction.log etc.

And there is no CRISPRAnalyzer%X_%date.log ? COuld you start run it normal and then login to the docker container (docker ps then docker exec -it CONTAINERID /bin/bash and then get the shiny server log in /var/log/shiny-server/ ?

Thanks for your help, Jan

[xuguorong2016]

Hi Jan,

No, I did not find any other logs except access.log. And the access.log is only two lines. I just tried the command docker run --rm -p 8000:8000 boutroslab/crispranalyzer:latest

And then I run the commands you gave to me, I got the below error.

I am not sure if the contain id is correct or not.

Thanks, Guorong

[jwinter6]

HI,

oh sorry, the container ID needs to be retrieved by docker ps. It is the first entry when you do docker ps, in your case it was the 8de012309f52.

Best, Jan

Jan Winter Division of Signaling and Functional Genomics / B110 PhD Student

German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-1953 fax: +49 6221 42-1959

jan.winter@dkfz.demailto:jan.winter@dkfz.de www.dkfz.dehttp://www.dkfz.de/

[cid:image001.png@01D20DAD.91CE10B0]

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537

Von: Guorong Xu notifications@github.com Antworten an: boutroslab/CRISPRAnalyzeR reply@reply.github.com Datum: Samstag, 20. Januar 2018 um 22:05 An: boutroslab/CRISPRAnalyzeR CRISPRAnalyzeR@noreply.github.com Cc: Jan Winter jan.winter@Dkfz-Heidelberg.de, Assign assign@noreply.github.com Betreff: Re: [boutroslab/CRISPRAnalyzeR] Can CRISPRAnalyzeR be installed on AWS instances? (#36)

Hi Jan,

No, I did not find any other logs except access.log. And the access.log is only two lines. I just tried the command docker run --rm -p 8000:8000 boutroslab/crispranalyzer:latest

And then I run the commands you gave to me, I got the below error. [screen shot 2018-01-20 at 1 03 27 pm]https://user-images.githubusercontent.com/19210374/35187980-85d2a484-fde2-11e7-94c4-c6dc2afbaee4.png

I am not sure if the contain id is correct or not.

Thanks, Guorong

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[xuguorong2016]

Hi Jan,

Thanks a lot! I attached the shiny-server.log for you. Besides, I already opened all ports on my aws instance.

shiny-server.log.zip

Best, Guorong

[jwinter6]

Hi,

This error is something that I already observe in any docker container that I did with shiny-server included. I have no idea so far why and what, but it should not cause the issue.

Could you also drop me the log file that is located in /var/log/shiny-server/ apart from the shiny-server.log?

Thanks, Jan

Jan Winter Division of Signaling and Functional Genomics / B110 PhD Student

German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany phone: +49 6221 42-1953 fax: +49 6221 42-1959

jan.winter@dkfz.demailto:jan.winter@dkfz.de www.dkfz.dehttp://www.dkfz.de/

[cid:image001.png@01D20DAD.91CE10B0]

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537

Von: Guorong Xu notifications@github.com Antworten an: boutroslab/CRISPRAnalyzeR reply@reply.github.com Datum: Samstag, 20. Januar 2018 um 22:25 An: boutroslab/CRISPRAnalyzeR CRISPRAnalyzeR@noreply.github.com Cc: Jan Winter jan.winter@Dkfz-Heidelberg.de, Assign assign@noreply.github.com Betreff: Re: [boutroslab/CRISPRAnalyzeR] Can CRISPRAnalyzeR be installed on AWS instances? (#36)

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[xuguorong2016]

Hi Jan,

Thanks a lot for your help! I am still new to docker and just know how to copy the folder from the container to my local machine. So the whole log folder is attached for you. log.zip

Thanks again, Guorong

[jwinter6]

thanks I have a look at the logs :)