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jwinter6 / CRISPRAnalyzeR-Site

CRISPRAnalyzeR Website
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installation of Crispr Analyzer #1

Open HugoGonzalezVelozo opened 6 years ago

HugoGonzalezVelozo commented 6 years ago

Hi Jan, I'm trying to install CRISPRAnalyzer by command line, because the use of CRISPRAnalyzer installed by kitematic fail during the re-evaluation step and now I want to do the sgRNA Re-evaluation using the reference genome directly from my mac, for that I need to re-install CRISPRAnalyzer using command line, but, the installation get stuck for many hours in the command "[CUSTOM] setting number of threads for Bowtie2", Any idea how I can fix this problem?, I leave you a copy of my terminal, see below.

Thanks,

Hugo

Copy of the terminal

NAME-MacBook-Pro:~ $ docker run --rm -p 80:3838 boutroslab/crispranalyzer:latest Unable to find image 'boutroslab/crispranalyzer:latest' locally latest: Pulling from boutroslab/crispranalyzer 693502eb7dfb: Pulling fs layer 8f59543f3f57: Pulling fs layer 3094a9c38da1: Pulling fs layer 84f4fa4175e2: Pulling fs layer e4b750e8b3d3: Pulling fs layer 12a9559dd987: Pulling fs layer dc2066609793: Pulling fs layer 53ac1f8ce835: Pulling fs layer e81534a6f221: Pulling fs layer 374c72e9f207: Pulling fs layer 660315d423bf: Pulling fs layer 0bf308d3eb7a: Pulling fs layer 2d02a624d77c: Pulling fs layer fd3dea4f8442: Pulling fs layer 3ff4e1aedd57: Pulling fs layer e7ce62b440c4: Pulling fs layer 10c7fafba55e: Pulling fs layer 2a5e709f2468: Pulling fs layer 0076c027cf28: Pulling fs layer 8893495398da: Pulling fs layer 385ec2ad0e5f: Pulling fs layer 667b9832d01e: Pulling fs layer 7b76b729f229: Pulling fs layer 62898fdcecbc: Pulling fs layer 922a94e50f94: Pulling fs layer 0e2ee0369975: Pulling fs layer 2c61515f0b8a: Pulling fs layer 8d5e0b85e554: Pulling fs layer d35f5870180e: Pulling fs layer f61ce4facbae: Pulling fs layer c188804ee01b: Pulling fs layer f76cacfc080f: Pulling fs layer e719d3b64c8a: Pulling fs layer 20c76e5b2cfd: Pulling fs layer 11b27ca5d98d: Pulling fs layer 6a5ba0a25381: Pulling fs layer 703f7e02ad22: Pulling fs layer 1e0da57fec16: Pulling fs layer f09fb0c90225: Pulling fs layer 63b6872a96d1: Pulling fs layer c078adeed163: Pulling fs layer 54498c9aeb1c: Pulling fs layer eaefeda22ec7: Pulling fs layer 129c5e6e534b: Pulling fs layer a70ac3f06908: Pulling fs layer 4c63f10625d2: Pulling fs layer b2089807e92e: Pulling fs layer 2a0aab6626ca: Pulling fs layer 369a58881862: Pulling fs layer b1baeaae9604: Pulling fs layer 034e75aa437f: Pulling fs layer ed6fb1dbafbe: Pulling fs layer 8f36db628e5f: Pulling fs layer 1cdd7f4e0b92: Pulling fs layer 72574134f16d: Pulling fs layer ebe7ab9551f4: Pulling fs layer a638abc6f1ad: Pulling fs layer 4f22c5e90bcb: Pulling fs layer bb52a48db1e1: Pulling fs layer 64dce0e4c7e1: Pulling fs layer 994fd9dce31c: Pulling fs layer 5b47f5033f52: Pulling fs layer 21f185495694: Pulling fs layer 9c4fbb4d713b: Pulling fs layer 7d86694fd613: Pulling fs layer e07b7a2f280b: Pulling fs layer 08b9acf9a388: Pulling fs layer bb2fd6657876: Pulling fs layer a3f16fda18f4: Pulling fs layer 7a985e4a8616: Pulling fs layer 9c7498b5e211: Pulling fs layer f1875d57734c: Pulling fs layer 57ad46d52904: Pulling fs layer b33ededd1bc8: Pulling fs layer f1ad88d367c5: Pulling fs layer 90ba6f406570: Pulling fs layer 69e8d193c2de: Pulling fs layer 18d39b0bf997: Pulling fs layer 7b9121682934: Pull complete afd20485c29b: Pull complete 9d9a8e8e403b: Pull complete 19b0565edc42: Pull complete 705b4d474732: Pull complete 9ba827d3148f: Pull complete 8dc9313a1689: Pull complete c1b1f34d5db1: Pull complete 3c6fcb7bfb13: Pull complete 8efc651fead0: Pull complete e90978af293e: Pull complete e10f7d1e64b1: Pull complete cb1955aae8cf: Pull complete 05771dc56441: Pull complete 74f24bc3948c: Pull complete 2c0e8ab6d25e: Pull complete 5f14ff31c7cc: Pull complete 8822bf7090fe: Pull complete baa038dc68d5: Pull complete ca805e66d583: Pull complete 07ffb6c9705d: Pull complete 8e75e8fbd3ee: Pull complete 75b8c939f056: Pull complete Digest: sha256:1172a7529d367c065292603f6d063c9935db6e2aba34b0a0fea7188b7a53b9d9 Status: Downloaded newer image for 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

jwinter6 commented 6 years ago

Hi Hugo,

You are already done :) If you start it like this, it runs in the foreground and all you need to do is going to ur web browser and navigate to http://localhost:80 . Please not this only works if docker is run as administrator. Otherwise use ... -p 3838:3838 boutroslab/crispranalyzer:latest and navigate to localhost:3838 .

That should be it.

What you see in the terminal is fine, since the docker container runs in the foreground, providing you a web interface via the address shown above.

Also check out http://www.crispr-analyzer.org for how it will look like and the official github repository. You can also give the latest beta a try available as boutroslab/crispranalyzer:1.31BETA .

Cheers Jan

Am 28. Oktober 2017 18:57:17 schrieb HugoGonzalezVelozo notifications@github.com:

Hi Jan, I'm trying to install CRISPRAnalyzer by command line, because the use of CRISPRAnalyzer installed by kinematic fail during the re-evaluation step and now I want to do the sgRNA Re-evaluation using the reference genome directly from my mac, for that I need to re-install CRISPRAnalyzer using command line, but, the installation get stuck for many hours in the command "[CUSTOM] setting number of threads for Bowtie2", Any idea how I can fix this problem?, I leave you a copy of my terminal, see below.

Thanks,

Hugo

Copy of the terminal

NAME-MacBook-Pro:~ $ docker run --rm -p 80:3838 boutroslab/crispranalyzer:latest Unable to find image 'boutroslab/crispranalyzer:latest' locally latest: Pulling from boutroslab/crispranalyzer 693502eb7dfb: Pulling fs layer 8f59543f3f57: Pulling fs layer 3094a9c38da1: Pulling fs layer 84f4fa4175e2: Pulling fs layer e4b750e8b3d3: Pulling fs layer 12a9559dd987: Pulling fs layer dc2066609793: Pulling fs layer 53ac1f8ce835: Pulling fs layer e81534a6f221: Pulling fs layer 374c72e9f207: Pulling fs layer 660315d423bf: Pulling fs layer 0bf308d3eb7a: Pulling fs layer 2d02a624d77c: Pulling fs layer fd3dea4f8442: Pulling fs layer 3ff4e1aedd57: Pulling fs layer e7ce62b440c4: Pulling fs layer 10c7fafba55e: Pulling fs layer 2a5e709f2468: Pulling fs layer 0076c027cf28: Pulling fs layer 8893495398da: Pulling fs layer 385ec2ad0e5f: Pulling fs layer 667b9832d01e: Pulling fs layer 7b76b729f229: Pulling fs layer 62898fdcecbc: Pulling fs layer 922a94e50f94: Pulling fs layer 0e2ee0369975: Pulling fs layer 2c61515f0b8a: Pulling fs layer 8d5e0b85e554: Pulling fs layer d35f5870180e: Pulling fs layer f61ce4facbae: Pulling fs layer c188804ee01b: Pulling fs layer f76cacfc080f: Pulling fs layer e719d3b64c8a: Pulling fs layer 20c76e5b2cfd: Pulling fs layer 11b27ca5d98d: Pulling fs layer 6a5ba0a25381: Pulling fs layer 703f7e02ad22: Pulling fs layer 1e0da57fec16: Pulling fs layer f09fb0c90225: Pulling fs layer 63b6872a96d1: Pulling fs layer c078adeed163: Pulling fs layer 54498c9aeb1c: Pulling fs layer eaefeda22ec7: Pulling fs layer 129c5e6e534b: Pulling fs layer a70ac3f06908: Pulling fs layer 4c63f10625d2: Pulling fs layer b2089807e92e: Pulling fs layer 2a0aab6626ca: Pulling fs layer 369a58881862: Pulling fs layer b1baeaae9604: Pulling fs layer 034e75aa437f: Pulling fs layer ed6fb1dbafbe: Pulling fs layer 8f36db628e5f: Pulling fs layer 1cdd7f4e0b92: Pulling fs layer 72574134f16d: Pulling fs layer ebe7ab9551f4: Pulling fs layer a638abc6f1ad: Pulling fs layer 4f22c5e90bcb: Pulling fs layer bb52a48db1e1: Pulling fs layer 64dce0e4c7e1: Pulling fs layer 994fd9dce31c: Pulling fs layer 5b47f5033f52: Pulling fs layer 21f185495694: Pulling fs layer 9c4fbb4d713b: Pulling fs layer 7d86694fd613: Pulling fs layer e07b7a2f280b: Pulling fs layer 08b9acf9a388: Pulling fs layer bb2fd6657876: Pulling fs layer a3f16fda18f4: Pulling fs layer 7a985e4a8616: Pulling fs layer 9c7498b5e211: Pulling fs layer f1875d57734c: Pulling fs layer 57ad46d52904: Pulling fs layer b33ededd1bc8: Pulling fs layer f1ad88d367c5: Pulling fs layer 90ba6f406570: Pulling fs layer 69e8d193c2de: Pulling fs layer 18d39b0bf997: Pulling fs layer 7b9121682934: Pull complete afd20485c29b: Pull complete 9d9a8e8e403b: Pull complete 19b0565edc42: Pull complete 705b4d474732: Pull complete 9ba827d3148f: Pull complete 8dc9313a1689: Pull complete c1b1f34d5db1: Pull complete 3c6fcb7bfb13: Pull complete 8efc651fead0: Pull complete e90978af293e: Pull complete e10f7d1e64b1: Pull complete cb1955aae8cf: Pull complete 05771dc56441: Pull complete 74f24bc3948c: Pull complete 2c0e8ab6d25e: Pull complete 5f14ff31c7cc: Pull complete 8822bf7090fe: Pull complete baa038dc68d5: Pull complete ca805e66d583: Pull complete 07ffb6c9705d: Pull complete 8e75e8fbd3ee: Pull complete 75b8c939f056: Pull complete Digest: sha256:1172a7529d367c065292603f6d063c9935db6e2aba34b0a0fea7188b7a53b9d9 Status: Downloaded newer image for 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

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HugoGonzalezVelozo commented 6 years ago

Thanks Jan, I installed the analyzer by command line and I downloaded the reference genome to my laptop, following the instructions to do the local SgRNA Re-evaluation (https://github.com/boutroslab/CRISPRAnalyzeR ), then I run CRISPRAnalyzer using (docker run --rm -v /Users/USERXXX/databases/:/srv/shiny-server/CRISPRAnalyzeR/database -p 80:3838 boutroslab/crispranalyzer:latest), but I got the same error during the analysis "Sorry, CRISPRAnalyzeR had trouble communicating with E-CRISP / Re-evaluation tool", I'm doing something wrong?

Thanks,

Hugo

jwinter6 commented 6 years ago

Hi Hugo,

I will release an update tomorrow which will have all of this fixed in case you use any Addgene-available CRISPR library.

Cheers Jan

HugoGonzalezVelozo commented 6 years ago

Cool, I'll look forward try again tomorrow. Thanks Jan

jwinter6 commented 6 years ago

HI Hugo,

I am in the last phases of testing and will upload the new version hopefully today ☺ Cheers 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/

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

Von: HugoGonzalezVelozo notifications@github.com Antworten an: jwinter6/CRISPRAnalyzeR-Site reply@reply.github.com Datum: Sonntag, 29. Oktober 2017 um 16:34 An: jwinter6/CRISPRAnalyzeR-Site CRISPRAnalyzeR-Site@noreply.github.com Cc: Jan Winter jan.winter@Dkfz-Heidelberg.de, Comment comment@noreply.github.com Betreff: Re: [jwinter6/CRISPRAnalyzeR-Site] installation of Crispr Analyzer (#1)

Cool, I'll look forward try again tomorrow. Thanks Jan

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HugoGonzalezVelozo commented 6 years ago

Hi Jan, thanks, do you know if the new version will work well with the libraries TKO90K and mGeCKO-A?

thanks

jwinter6 commented 6 years ago

Hi,

for mouse Gecko I have no data, but for the TKO for sure it works, just tested it ☺

cheers 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/

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

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

Von: HugoGonzalezVelozo notifications@github.com Antworten an: jwinter6/CRISPRAnalyzeR-Site reply@reply.github.com Datum: Donnerstag, 2. November 2017 um 15:29 An: jwinter6/CRISPRAnalyzeR-Site CRISPRAnalyzeR-Site@noreply.github.com Cc: Jan Winter jan.winter@Dkfz-Heidelberg.de, Comment comment@noreply.github.com Betreff: Re: [jwinter6/CRISPRAnalyzeR-Site] installation of Crispr Analyzer (#1)

Hi Jan, thanks, do you know if the new version will work well with the libraries TKO90K and mGeCKO-A?

thanks

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