Installation problems SSL certificate

[ghost]

Hi Ale,
I just tried to install EpiCSeg in a new Conda environment configured as follows:

name: epicsegenv
channels:
  - bioconda
  - r
dependencies:
  - openssl
  - curl
  - r-base=3.3.*
  - r-openssl
  - r-curl
  - r-devtools
  - bioconductor-biostrings
  - bioconductor-genomicranges
  - bioconductor-iranges
  - bioconductor-edger
  - bioconductor-biocinstaller

Following the relevant installation instructions leads to the following:

> source("http://bioconductor.org/biocLite.R")
> biocLite(c("bamsignals"))
> library(devtools)
> install_github("lamortenera/kfoots")
Downloading GitHub repo lamortenera/kfoots@master
from URL https://api.github.com/repos/lamortenera/kfoots/zipball/master
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Problem with the SSL CA cert (path? access rights?)

A possible workaround/temporary fix would be as follows (deactivate checking the certificate, which is then probably a security issue):

> library(httr)
> set_config( config( ssl_verifypeer = 0L ) )
> library(devtools)
> install_github("lamortenera/kfoots")
Downloading GitHub repo lamortenera/kfoots@master
from URL https://api.github.com/repos/lamortenera/kfoots/zipball/master
Installing kfoots
> install_github("lamortenera/epicseg")
Downloading GitHub repo lamortenera/epicseg@master
from URL https://api.github.com/repos/lamortenera/epicseg/zipball/master
Installing epicseg

I guess this is not really an issue that can be fixed by you for good, so maybe you want to consider to hint at this problem in the installation instructions.

Best,
Peter

[lamortenera]

Hi Peter, thanks for the hint. I have the vague impression that I have discussed a similar issue already, but i can't find it among the closed issues.
Anyway you are correct, this issue has to do with the install_github function, so I can't do very much about it.
In the near future I am planning to deploy epicseg in a docker container, so that you shouldn't be dealing with these problems anymore. Would you be interested in such a solution? Does your computing cluster support docker?

[ghost]

Unfortunately no, when our cluster was installed, Docker was considered too immature to be running on a production system, and now, the setup will not/cannot be changed with reasonable effort.
Personally, I have moved to Conda on a "one environment per project" basis, hence, I would love to see EpiCSeg in the Bioconda channel. Apart from that, I also think that a Docker container would be appreciated by many users.