Comments (9)
Yes I did - use Exome Depth for CNV calling - works perfectly fine.
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I've a similar error....did you find the solution?
I've R version 3.6.0
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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.
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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.
from decon.
I've a similar error....did you find the solution?
I've R version 3.6.0The 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!
from decon.
I've a similar error....did you find the solution?
I've R version 3.6.0The 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
from decon.
I've a similar error....did you find the solution?
I've R version 3.6.0The 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
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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
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@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
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Related Issues (20)
- ERROR when running makeCNVcalls.R HOT 6
- makeCNVcalls.R failed HOT 11
- Installation Issue
- error when running ReadInBams.R
- Error when running makeCNVcalls.R
- makeCNVcalls.R Error in cnv.calls_ids[i, ]$start.p:cnv.calls_ids[i, ]$end.p : HOT 5
- Rsamtools version not compatible with VN:1.4 BAM files?
- Error in running IdentifyFailures HOT 1
- Congratulations! HOT 2
- IdentifyFailures Error HOT 3
- Error in if (MaxCorr[i] < corr_thresh) { : missing value where TRUE/FALSE needed HOT 2
- Installation of DECoN failed HOT 1
- samples off by one HOT 3
- DECoN installation error HOT 5
- Problem while running Rscript makeCNVcalls.R HOT 2
- CNV offsets by one in makeCNVcalls. HOT 1
- DECoN v2.0.1 installation error, Rscript error and question. HOT 4
- How to select meaningful CNVs?
- Differences between V1 and V2
- DECoN packages management
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