Failed installation about decon

[zgtman]

Yes I did - use Exome Depth for CNV calling - works perfectly fine.

[flapa86]

I've a similar error....did you find the solution?
I've R version 3.6.0

[zgtman]

Absolutely agree. I try to install this tools with no success. I do not understand why developers do not put all necessary packages under the packrat directory. Still with some error. I think this project is dead. I would everybody recommend rather ExomeDepth.

Thank you.

[seon22break]

I've a similar error....did you find the solution?
I've R version 3.6.0

The R version is very important and in a project like this, where they are not updating the code, I would recommend you to install the R 3.1.2 version. I am creating a Docker image with DeCoN installed. As soon as I have it, I will post it.

[ClaraffD]

I've a similar error....did you find the solution?
I've R version 3.6.0

The R version is very important and in a project like this, where they are not updating the code, I would recommend you to install the R 3.1.2 version. I am creating a Docker image with DeCoN installed. As soon as I have it, I will post it.

Hi, have you created your Docker image? Running out of options to successfully use DECoN here.. thank you!

[seon22break]

I've a similar error....did you find the solution?
I've R version 3.6.0

The R version is very important and in a project like this, where they are not updating the code, I would recommend you to install the R 3.1.2 version. I am creating a Docker image with DeCoN installed. As soon as I have it, I will post it.

Hi, have you created your Docker image? Running out of options to successfully use DECoN here.. thank you!

Yes , I have a docker image with DeCoN. Works correctly

[ClaraffD]

I've a similar error....did you find the solution?
I've R version 3.6.0

The R version is very important and in a project like this, where they are not updating the code, I would recommend you to install the R 3.1.2 version. I am creating a Docker image with DeCoN installed. As soon as I have it, I will post it.

Hi, have you created your Docker image? Running out of options to successfully use DECoN here.. thank you!

Yes , I have a docker image with DeCoN. Works correctly

Would it be possible for you to link it please? Thank you for your help

[worker000000]

Yes I did - use Exome Depth for CNV calling - works perfectly fine.

do you kown which column of exomedepth stands for copy number, thanks a lot
and have you ever met this vplagnol/ExomeDepth#44

[worker000000]

@ClaraffD
i once download one, not writen by me, but it needs to enter the docker, can not concatate argument directly, not that convenient

#################################################################

Dockerfile # # Version: 0.1

Software: DECoN V1.0.2

Description: DECoN Detection of Exon Copy Number variants

Website: http://www.thetgmi.org/tgmi-news/detecting-tricky-gene-mutations/

Tags: None, for the moment

Base Image: r-base:3.1.2

#################################################################
From r-base:3.1.2
ENTRYPOINT ["/bin/bash"]

Adding user decon

RUN useradd -ms /bin/bash decon

Adding Certificates for wget tu download from git

RUN apt-get update &&
apt-get install -y --no-install-recommends
ca-certificates
&& rm -rf /var/lib/apt/lists/*

Running Container as decon and install decon from git

USER decon
WORKDIR /home/decon/
RUN wget https://github.com/RahmanTeam/DECoN/archive/v1.0.2.tar.gz
RUN tar -xzvf v1.0.2.tar.gz
Run rm v1.0.2.tar.gz
WORKDIR /home/decon/DECoN-1.0.2/Linux/

Starting setup

RUN mkdir /home/decon/DECoN-1.0.2/Linux/packrat/src/VGAM/
RUN wget https://cran.r-project.org/src/contrib/Archive/VGAM/VGAM_0.9-8.tar.gz -O /home/decon/DECoN-1.0.2/Linux/packrat/src/VGAM/VGAM_0.9-8.tar.gz
RUN ./setup.sh