search

ait5 / CNApp

CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either aCGH, SNP-array, whole-exome sequencing or whole-genome sequencing to assess sample profiles and CNA levels, establishing associations with molecular and clinical features. CNApp has three main sections: Re-Seg & Score, Region profile and Classifier model
Other
18 stars 7 forks source link

ubuntu install, and issues #1

Closed colindaven closed 5 years ago

colindaven commented 5 years ago

Hi,

interesting looking app.

On ubuntu 16.04 I needed these packages to install everything successfully.

sudo apt install libmariadb-client-lgpl-dev

sudo apt install libv8-3.14-dev

Unfortunately, selecting the demo data doesn't do anything, and the whole app is kind of grey so I must be missing other packages. R-3.4.4

Any ideas ?

ait5 commented 5 years ago

Hi @colindaven,

thanks a lot for trying out our app!

I have just re-downloaded and re-installed the whole app into my Mac and it works fine (just to be sure anything happened since my last test...).

I haven't tried to install it on Ubuntu 16.0.4 (I have 14.04 at my work-place and it worked fine by testing the installation. Still haven't upgraded my ubuntu OS...).

Any error coming out at R-studio terminal when running the app?? It seems strange that everything is going fine till selecting the demo data... :S

Have you tried to upload data of your own? (or try to use demo data as input data, just as it was your owns!)

Let me know how it goes!!

ait5 commented 5 years ago

Sorry, @colindaven, I have 16.04 Ubunut installed indeed and all worked fine for me...

colindaven commented 5 years ago

hey @ait5 , thanks for looking into this.

I just upgraded my R from 3.4.4 to 3.5 (locally at least), is R3.5 required ?

ait5 commented 5 years ago

Hi @colindaven ,

CNApp is working with R 3.4.2 in our server, but I have installed also using new version (e.g. using my Mac with R 3.5.1)

colindaven commented 5 years ago

Hey,

the main error which I can't resolve is phantomjs. Is this likely to be a major issue ?

2018-12-14 13:26:13 (2,38 MB/s) - ‘phantomjs-2.1.1-linux-x86_64.tar.bz2’ saved [23415665/23415665]

phantomjs has been installed to /home/davenpor/bin
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘phantomjs’
colindaven commented 5 years ago

Thanks, it works now with Ubuntu 16.04 and R3.5.1, despite the phantomjs warning mentioned above. I had to download the demo data separately and manually add.