diff --git a/README b/README index 1711599..1879d0b 100644 --- a/README +++ b/README @@ -5,10 +5,10 @@ I. Windows 1. Installation: - Download and install HDF-Java (https://www.hdfgroup.org/products/java/release/download.html) - - Download either japsa*.tar.gz or japsa*.zip and extract to a directory, e.g., c:\japsa + - Download either japsa*.tar.gz or japsa*.zip and extract to a directory, e.g., c:\JapsaHome. (So you will see c:\JapsaHome\lib\japsa\japsa.jar) - Set up the following environment variables: - a. JSA_HOME to the directory where japsa was installed (e.g., c:\japsa) + a. JSA_HOME to the directory where japsa was installed (e.g., c:\JapsaHome) b. JHDF5_LIB to the library directory of HDF-Java that contains files jhdf5.dll and jhdf.dll, e.g., C:\Program Files\HDF_Group\HDFView\2.11.0\lib 2. Running @@ -32,6 +32,9 @@ $make -f Makefile.main INSTALL_DIR= JLP= $jsa.np.f5reader --folder -output -GUI - + You can even pass the fastq to a downstream analysis program, such as bwa: + + $jsa.np.f5reader --folder -output - -GUI | tee output.fastq | bwa mem - > output.sam + diff --git a/japsa-15.5a.tar.gz b/japsa-15.5a.tar.gz deleted file mode 100644 index 7b54f4a..0000000 Binary files a/japsa-15.5a.tar.gz and /dev/null differ diff --git a/japsa.zip b/japsa.zip deleted file mode 100644 index 89d8a25..0000000 Binary files a/japsa.zip and /dev/null differ