Error In Setting Up in Qualimap Inside Singularity Container

[Desmond]

I am trying to set Qualimap up inside of a singularity container.

I am using a centos 7 image. I am attempting to install qualimap 2.2.1 using the src zip.

The following is an error I am receiving during the build process:

[ERROR] Failed to execute goal on project qualimap: Could not resolve dependencies for project org.bioinfo.ngs:qualimap:jar:2.2.1-dev: The following artifacts could not be resolved: com.oracle:javafx:jar:2.2, junit:junit:jar:4.4, org.bio

info:bioinfo-formats:jar:0.2.0, org.bioinfo:bioinfo-ngs:jar:0.1.0, org.bioinfo:bioinfo-commons:jar:0.10.1, org.bioinfo:bioinfo-math:jar:0.3.0, org.bioinfo:bioinfo-graphics:jar:0.4.0, com.miglayout:miglayout:jar:3.7.4: Could not find arti

fact com.oracle:javafx:jar:2.2 at specified path /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.302.b08-0.el7_9.x86_64/jre/lib/jfxrt.jar -> [Help 1]

The following is a list of commands inside of the container:

yum update -y

yum install -y @"Development Tools"

yum install -y maven2 wget

yum install -y java-1.6.0-openjdk java-1.6.0-openjdk-devel java-1.6.0-openjdk-src

yum install -y epel-release

yum install -y R

yum clean all

cd /opt/

wget https://bitbucket.org/kokonech/qualimap/downloads/qualimap_v2.2.1_src.zip

unzip qualimap_v2.2.1_src.zip

ls

rm -rf qualimap_v2.2.1_src.zip

cd qualimap-v2.2.1-src

export QUALIPATH=$PWD

mvn install:install-file -DgroupId=net.sf.picard -DartifactId=picard -Dversion=1.70 -Dpackaging=jar -Dfile=$QUALIPATH/external/picard-1.70.jar

mvn install:install-file -DgroupId=net.sf.samtools -DartifactId=samtools -Dversion=1.70 -Dpackaging=jar -Dfile=$QUALIPATH/external/sam-1.70.jar

mvn install:install-file -DgroupId=org.ejml -DartifactId=ejml -Dversion=0.24 -Dpackaging=jar -Dfile=$QUALIPATH/external/ejml-0.24.jar

#Rscript --version

#Rscript $QUALIPATH/scripts/installDependencies.r

mvn install -o

The error arises during the mvn install -o command.

Thank you for your assistance.

[Konstantin Okonechnikov]

HI!

I suspect issue might be with Java version from OpenJDK. Did you try on earlier e.g. 1.7.0_79 from orcale? 

Best regards,

  Konstantin

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