initial project version

mdcao · 238b091649b1286a2e8778bca6d9be94bd55e11a · mdcao committed May 1, 2015 · May 1, 2015 · 238b091
commit 238b091649b1286a2e8778bca6d9be94bd55e11a
Unified Split

Showing with 22 additions and 0 deletions.

BIN japsa-15.5a.tar.gz

BIN japsa.zip

+22 −0 jsa.np.f5readerGUI.bat
diff --git a/japsa-15.5a.tar.gz b/japsa-15.5a.tar.gz
diff --git a/japsa.zip b/japsa.zip
diff --git a/jsa.np.f5readerGUI.bat 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
+