update Dockerfile

[tgambin]

Hi, I am trying to use ximmer with hg38 so I noticed its better to try with 3.0 alpha branch. Now I am trying to update Dockerfile. was able to fix few issues because of missing directories and now I am getting the error on installation of R packages through bpipe. It looks there are some incompatibilities with R version, BiocManager. Do you have any suggestion how to start fixing these problems? Should I try to modify bpipe package ?

Installing package into '/usr/local/lib/R/site-library'                                                                                                                                                                                                                        
(as 'lib' is unspecified)                                                                                                                                                                                                                                                      
trying URL 'http://cran.r-project.org/src/contrib/BiocManager_1.30.18.tar.gz'                                                                                                                                                                                                  
Content type 'application/x-gzip' length 289602 bytes (282 KB)                                                                                                                                                                                                                 
==================================================                                                                                                                                                                                                                             
downloaded 282 KB                                                                                                                                                                                                                                                              
                                                                                                                                                                                                                                                                               
* installing *source* package 'BiocManager' ...                                                                                                                                                                                                                                
** package 'BiocManager' successfully unpacked and MD5 sums checked                                                                                                                                                                                                            
** R                                                                                                                                                                                                                                                                           
** inst                                                                                                                                                                                                                                                                        
** preparing package for lazy loading                                                                                                                                                                                                                                          
** help                                                                                                                                                                                                                                                                        
*** installing help indices                                                                                                                                                                                                                                                    
** building package indices                                                                                                                                                                                                                                                    
** installing vignettes                                                                                                                                                                                                                                                        
** testing if installed package can be loaded                                                                                                                                                                                                                                  
* DONE (BiocManager)                                                                                                                                                                                                                                                           
                                                                                                                                                                                                                                                                               
The downloaded source packages are in                                                                                                                                                                                                                                          
        '/tmp/RtmpL8IBgs/downloaded_packages'                                                                                                                                                                                                                                  
Warning message:                                                                                                                                                                                                                                                               
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :                                                                                                                                                                                        
  there is no package called 'BiocManager'                                                                                                                                                                                                                                     
'getOption("repos")' replaces Bioconductor standard repositories, see                                                                                                                                                                                                          
'?repositories' for details                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                               
replacement repositories:                                                                                                                                                                                                                                                      
    CRAN: http://cran.r-project.org                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                               
Bioconductor version 3.6 (BiocManager 1.30.18), R 3.4.4 (2018-03-15)                                                                                                                                                                                                           
Installing package(s) 'BiocVersion', 'ExomeDepth'                                                                                                                                                                                                                              
also installing the dependencies 'formatR', 'lambda.r', 'futile.options', 'matrixStats', 'RCurl', 'GenomeInfoDbData', 'futile.logger', 'snow', 'BH', 'Biobase', 'DelayedArray', 'fansi', 'pkgconfig', 'ellipsis', 'purrr', 'cli', 'utf8', 'BiocGenerics', 'S4Vectors', 'XVector
', 'GenomeInfoDb', 'zlibbioc', 'bitops', 'BiocParallel', 'SummarizedExperiment', 'generics', 'glue', 'lifecycle', 'R6', 'rlang', 'tibble', 'tidyselect', 'vctrs', 'pillar', 'Biostrings', 'IRanges', 'Rsamtools', 'GenomicRanges', 'aod', 'GenomicAlignments', 'dplyr', 'magrit
tr'                                                                                                                                                                                                                                                                            
                                                                                                                                                                                                                                                                               
Error in download.file(url, destfile, method, mode = "wb", ...) :             
  unused argument (checkBuilt = FALSE)                                        
In addition: Warning messages:                                                                      
1: package 'BiocVersion' is not available (for R version 3.4.4)                
2: dependency 'VGAM' is not available                

[tgambin]

My current Dockerfile looks like this:

FROM ubuntu:14.04
MAINTAINER Simon Sadedin "[email protected]" 
RUN apt-get update; 
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
RUN echo 'deb http://cran.rstudio.com/bin/linux/ubuntu trusty/' >> /etc/apt/sources.list
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
RUN apt-get update && \
    apt-get install -y software-properties-common python-software-properties && \
    apt-get install -y curl wget &&  \
    apt-get install -y apt-transport-https && apt-get update
RUN apt-get update && apt-get install -y libcurl4-openssl-dev && apt-get install -y libxml2-dev && apt-get install -y libmariadbclient-dev && apt-get install -y r-base
RUN add-apt-repository ppa:openjdk-r/ppa && apt-get update 
RUN apt-get install -y openjdk-8-jre && apt-get install -y libfreetype6-dev pkg-config python-dev python-pip
RUN mkdir -p /usr/local/ximmer
ADD bin /usr/local/ximmer/bin 
ADD src /usr/local/ximmer/src
ADD eval /usr/local/ximmer/eval
ADD pipeline /usr/local/ximmer/pipeline
ADD tools /usr/local/ximmer/tools
RUN cd /usr/local/ximmer && \
    ./bin/install -q && \
    echo 'JAVA="java"' >> /usr/local/ximmer/eval/pipeline/config.groovy && \
    echo 'java { executable="java" }' >> /usr/local/ximmer/eval/pipeline/bpipe.config && \
    cd /usr/local/ximmer; mkdir cache && cd cache && wget 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/dgvMerged.txt.gz' && \
    cd /usr/local/ximmer/cache && wget 'http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz' 
ENV PATH="/usr/local/ximmer/bin:${PATH}"
ENV JAVA_HOME="/usr/lib/jvm/java-8-openjdk-amd64/jre"

[tgambin]

I was able to fix some of problems by upgrading to ubuntu focal. Although the image was built I still have several issues with running callers. If you have Dockerfile that works with this new branch I would be more than happy to try.