diff --git a/japsa-15.5a.tar.gz b/japsa-15.5a.tar.gz new file mode 100644 index 0000000..7b54f4a Binary files /dev/null and b/japsa-15.5a.tar.gz differ diff --git a/japsa.zip b/japsa.zip new file mode 100644 index 0000000..89d8a25 Binary files /dev/null and b/japsa.zip differ diff --git a/jsa.np.f5readerGUI.bat b/jsa.np.f5readerGUI.bat new file mode 100644 index 0000000..46507b1 --- /dev/null +++ b/jsa.np.f5readerGUI.bat @@ -0,0 +1,22 @@ +@echo off + +rem This batch file serves as a wrapper for several +rem JSA command line tools. + +if not "%JSA_HOME%" == "" goto gotjsaHome + +echo JSA requires an environment variable JSA_HOME. +goto :eof + +:gotjsaHome + +set JSA_MEM=7000m +set JSA_LIBS=%JSA_HOME%\lib\japsa\ +set JSA_CP=%JSA_LIBS%\japsa.jar;%JSA_LIBS%\commons-math3-3.0.jar;%JSA_LIBS%\sam-1.84.jar;%JSA_LIBS%\jhdf5.jar;%JSA_LIBS%\jhdfobj.jar;%JSA_LIBS%\htsjdk-1.126.jar;%JSA_LIBS%\jcommon-1.0.23.jar;%JSA_LIBS%\jfreechart-1.0.19.jar + +:run + +java -Xmx%JSA_MEM% -ea -Djava.awt.headless=true -Dfile.encoding=UTF-8 -server -Djava.library.path="%JHDF5_LIB%" -classpath %JSA_CP% japsa.seq.nanopore.NanoporeReaderStream --folder . -output output.fastq -fail --minLength 50 -GUI + +:eof +