optima

optima.sh

>cat /etc/*-release
Fedora release 23 (Twenty Three)
[more about Fedora I deleted]
>cat /proc/version
Linux version 4.3.3-301.fc23.x86_64 (mockbuild@bkernel02.phx2.fedoraproject.org) (gcc version 5.3.1 20151207 (Red Hat 5.3.1-2) (GCC) ) #1 SMP Fri Jan 15 14:03:17 UTC 2016
>javac -version
javac 1.8.0_71
>java -version
openjdk version "1.8.0_71"
OpenJDK Runtime Environment (build 1.8.0_71-b15)
OpenJDK 64-Bit Server VM (build 25.71-b15, mixed mode)


>mkdir opti
>cd opti
>git clone https://github.com/verznet/OPTIMA.git
[git clone output]
>javac OPTIMA.Align.java
javac: file not found: OPTIMA.Align.java
>javac OPTIMA.Align
error: Class names, 'OPTIMA.Align', are only accepted if annotation processing is explicitly requested
>javac OPTIMA/Align
javac: invalid flag: OPTIMA/Align
>javac OPTIMA/Align.java
[many lines with "package cern.jet.stat does not exist"]
>javac -cp "." OPTIMA/Align.java
[identical, lots of complaints about cern.jet.stat]
>javac -cp ".:cern.jar:commons-math3-3.2.jar" OPTIMA/Align.java
[no output, successful compilation]
>javac OPTIMA/Align.java
[interestingly, after the first success you don\'t have to specify the -cp variables again]
>java OPTIMA.Align
Use: java OPTIMA/Align.java OpticalMaps.maps OutputFileName InSilicoMaps.silico [pvalue|score] [allMaps|select] (OPTIONAL: firstIndex lastIndex)
>java OPTIMA/Align
Use: java OPTIMA/Align.java OpticalMaps.maps OutputFileName InSilicoMaps.silico [pvalue|score] [allMaps|select] (OPTIONAL: firstIndex lastIndex)