search

LewisLabUCSD / PinAPL-Py

A no hassle tool for analyzing your favorite CRISPR screen dataset!
11 stars 9 forks source link

How do I run these scripts on Linux? The Web-application is not working. #2

Open geng-lee opened 2 years ago

geng-lee commented 2 years ago

Hi Philipp,

How do I run these scripts on Linux? The Web-application is not working. Uploading data at http://pinapl-py.ucsd.edu is very slow, and the file cannot be uploaded successfully. Could you please provide a tutorial? I really hope to use your analysis method.

Best Wishes,
Geng

oharismendy commented 2 years ago

Dear Geng

there is a docker container running PinAPL-py with command line. You are welcome to try it, hoping it can solve your issues. Unfortunately, the documentation is not available. The docker container was used in a UCSD workshophttp://sdcsb.ucsd.edu/crispr-screening-workshop/ in 2016, for which we provided high level instructionhttps://docs.google.com/document/d/11V1LZ9hPECiJkd_MEDzGhUMx9azz4XTtot7bypaTBoo/edit. But these may differ with the current versions.

https://hub.docker.com/r/oncogx/pinaplpy_docker https://github.com/oharismendy/pinaplpy_docker https://github.com/LewisLabUCSD/PinAPL-Py

Olivier

On Mar 29, 2022, at 11:19 AM, Geng Lee @.**@.>> wrote:

Hi Philipp,

How do I run these scripts on Linux? The Web-application is not working. Uploading data at http://pinapl-py.ucsd.eduhttps://urldefense.com/v3/__http://pinapl-py.ucsd.edu__;!!LLK065n_VXAQ!1p8xch7XvoWTjZgqLM2wwdf1hfO9tcH5BT18q6eWsZG6B4A9Sl1WJ_fPLsly2mVw0GMK$ is very slow, and the file cannot be uploaded successfully. Could you please provide a tutorial? I really hope to use your analysis method.

Best Wishes, Geng

— Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LewisLabUCSD_PinAPL-2DPy_issues_2&d=DwMCaQ&c=-35OiAkTchMrZOngvJPOeA&r=Nzbs-WeFEcdH7mpkJhlS7A&m=gC0pi39CtKSwhIgz8mtF4BAQX_jstHdZb3BE9yx79NxOVGL7W8NXrVEtjCoDuNqZ&s=DpgYlaYqnWFqwKer4dmSj7IsrTeYiQ0jTfAEU8DL57o&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ACN4RSNDUAKPJVVLF5AQDG3VCNCRRANCNFSM5R7IFANQ&d=DwMCaQ&c=-35OiAkTchMrZOngvJPOeA&r=Nzbs-WeFEcdH7mpkJhlS7A&m=gC0pi39CtKSwhIgz8mtF4BAQX_jstHdZb3BE9yx79NxOVGL7W8NXrVEtjCoDuNqZ&s=j6mxy3gJqeJum40SYmNyE_-EIy1gxgNISjvughQuF4Y&e=. You are receiving this because you are subscribed to this thread.Message ID: @.***>

geng-lee commented 2 years ago

Dear Geng there is a docker container running PinAPL-py with command line. You are welcome to try it, hoping it can solve your issues. Unfortunately, the documentation is not available. The docker container was used in a UCSD workshophttp://sdcsb.ucsd.edu/crispr-screening-workshop/ in 2016, for which we provided high level instructionhttps://docs.google.com/document/d/11V1LZ9hPECiJkd_MEDzGhUMx9azz4XTtot7bypaTBoo/edit. But these may differ with the current versions. https://hub.docker.com/r/oncogx/pinaplpy_docker https://github.com/oharismendy/pinaplpy_docker https://github.com/LewisLabUCSD/PinAPL-Py Olivier On Mar 29, 2022, at 11:19 AM, Geng Lee @.**@.>> wrote: Hi Philipp, How do I run these scripts on Linux? The Web-application is not working. Uploading data at http://pinapl-py.ucsd.edu<https://urldefense.com/v3/http://pinapl-py.ucsd.edu;!!LLK065n_VXAQ!1p8xch7XvoWTjZgqLM2wwdf1hfO9tcH5BT18q6eWsZG6B4A9Sl1WJ_fPLsly2mVw0GMK$> is very slow, and the file cannot be uploaded successfully. Could you please provide a tutorial? I really hope to use your analysis method. Best Wishes, Geng — Reply to this email directly, view it on GitHubhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_LewisLabUCSD_PinAPL-2DPy_issues_2&d=DwMCaQ&c=-35OiAkTchMrZOngvJPOeA&r=Nzbs-WeFEcdH7mpkJhlS7A&m=gC0pi39CtKSwhIgz8mtF4BAQX_jstHdZb3BE9yx79NxOVGL7W8NXrVEtjCoDuNqZ&s=DpgYlaYqnWFqwKer4dmSj7IsrTeYiQ0jTfAEU8DL57o&e=, or unsubscribehttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ACN4RSNDUAKPJVVLF5AQDG3VCNCRRANCNFSM5R7IFANQ&d=DwMCaQ&c=-35OiAkTchMrZOngvJPOeA&r=Nzbs-WeFEcdH7mpkJhlS7A&m=gC0pi39CtKSwhIgz8mtF4BAQX_jstHdZb3BE9yx79NxOVGL7W8NXrVEtjCoDuNqZ&s=j6mxy3gJqeJum40SYmNyE_-EIy1gxgNISjvughQuF4Y&e=. You are receiving this because you are subscribed to this thread.Message ID: @.***>

I really appreciate your help!

Best Wishes,
Geng