Docker trouble

[stephen mclaughlin]

Hi there,

   I'm trying to get CRISPRAnalyzeR working using your Docker container and test data and I'm running into an issue and would appreciate some help.

   I will walk you through exactly what I did.  I should mention I ran into the exact same issue using an ubuntu AWS instance as well as my local laptop (Windows 10). 

  1. I did a docker pull of the image: boutroslab/crispranalyzer:latest

  2. I started the server as described in the docs:

C:\WINDOWS\system32>docker run --rm -p 8000:8000 boutroslab/crispranalyzer:latest

[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

  3. I am able to open up CRISPRAnalyzeR  in the browser

  4. I am testing it using this test data set: https://cdn.rawgit.com/boutroslab/CRISPRAnalyzeR/fc2d9b6b/sampledata/caR_Readcount_sample-data.zip

  5. I upload pilotscreen.fasta as shown in the first screenshot.

  6. I upload the 4 files (PBS-Replicate1.txt, PBS-Replicate2.txt, TRAIL-Replicate1.txt, and TRAIL-Replicate2.txt) simultaneously (by holding down CTRL to select all of them) as shown in the second screenshot.

  7. I rename the samples so that there are only numbers and letters (also as shown in the second screenshot).

  8. I hit the green Upload and Check Files button on the bottom.

  9. I get a Disconnected from the Server message as shown in the third screenshot.

  Should all of that have worked or am I missing something?  Please let me know.

Thank you!

Stephen

[Jan Winter]

Hi Stephen,

thanks for your post.

And I know what happened :)

I guess you downloaded the readcount package from the HELP menu section, right?

I must admit that I completely forgot to update the links in there! Shame on me...

Please download the updated read count package from here:

1. Select the EXAMPLE TRAIL Screen in the library settings

2. then the read count and FASTQ packages are shown for download, please get them and try them, they will work.

Alternatively, use this:

https://cdn.rawgit.com/boutroslab/CRISPRAnalyzeR/fc2d9b6b/sampledata/caR_Readcount_sample-data.zip

I hope this will solve the issue :)

Please let me know if it worked and sorry for the circumstances.

cheers

Jan

[stephen mclaughlin]

Thank you Jan!  This fixes my problem.

Best,

Stephen