included in Japsa

mdcao · 67e46f8bfa2282b3eeaf242eee23f4e6bbf4d8ac · mdcao committed Aug 5, 2015 · Aug 5, 2015 · 67e46f8
1 parent f3aef35
commit 67e46f8bfa2282b3eeaf242eee23f4e6bbf4d8ac
diff --git a/japsa-1.5-6a.tar.gz b/japsa-1.5-6a.tar.gz
diff --git a/japsa-1.5-6a.zip b/japsa-1.5-6a.zip
diff --git a/jsa.np.f5readerGUI.bat b/jsa.np.f5readerGUI.bat
@@ -1,22 +0,0 @@
-@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
-
diff --git a/lib/japsa/colloquial.jar b/lib/japsa/colloquial.jar
diff --git a/lib/japsa/commons-math3-3.0.jar b/lib/japsa/commons-math3-3.0.jar
diff --git a/lib/japsa/htsjdk-1.126.jar b/lib/japsa/htsjdk-1.126.jar
diff --git a/lib/japsa/jaligner.jar b/lib/japsa/jaligner.jar
diff --git a/lib/japsa/japsa.jar b/lib/japsa/japsa.jar
diff --git a/lib/japsa/jcommon-1.0.23.jar b/lib/japsa/jcommon-1.0.23.jar
diff --git a/lib/japsa/jfreechart-1.0.19.jar b/lib/japsa/jfreechart-1.0.19.jar
diff --git a/lib/japsa/jhdf5.jar b/lib/japsa/jhdf5.jar
diff --git a/lib/japsa/jhdfobj.jar b/lib/japsa/jhdfobj.jar
diff --git a/lib/japsa/sam-1.84.jar b/lib/japsa/sam-1.84.jar