From 770c37109e208b4a56d50a908f4ab440c235b506 Mon Sep 17 00:00:00 2001 From: hsnguyen Date: Wed, 14 Mar 2018 18:23:29 +1000 Subject: [PATCH] Update README.rst --- README.rst | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/README.rst b/README.rst index cc6c13c..9a00acd 100644 --- a/README.rst +++ b/README.rst @@ -21,11 +21,10 @@ The streamline agorithms and auxiliary programs for setting up the pipeline are in japsa package (https://github.com/mdcao/japsa). In addition, the following free-software dependencies are required: -1. Java >=1.7 +1. Java >=1.8 2. bwa >=7.10 (0.7.10-r858-dirty recommended) -3. R with rJava and MultinomialCI installed -4. kalign2 (http://msa.sbc.su.se/cgi-bin/msa.cgi) -5. HDF5 (https://hdfgroup.org/HDF5/release/obtain5.html) -- optional, needed for translating native fast5 files to fastq (npReader (https://github.com/mdcao/npReader). +3. kalign2 (http://msa.sbc.su.se/cgi-bin/msa.cgi) +4. HDF5 (https://hdfgroup.org/HDF5/release/obtain5.html) -- optional, needed for translating native fast5 files to fastq (npReader (https://github.com/mdcao/npReader). ------------------------ Quick installation guide @@ -47,7 +46,7 @@ This will install japsa according the directives: * *INSTALL_DIR*: specifies the directory to install japsa, make sure you have write permission to this directory * *MXMEM*: specifies the default memory allocated to the java virtual machine * *SERVER*: specifies whether to launch the java virtual machine in server mode -* *JLP*: points to where HDF libraries and JRI are installed (e.g, /usr/local/lib:/usr/lib/R/site-library/rJava/jri). The path to HDF is only needed for creating the pipelines to analyse directly from fast5 files or simultaneously from the MinION sequencing. For your convenience, add INSTALL_DIR/bin to your PATH envirenment e.g.,:: +* *JLP*: points to where HDF libraries are installed (e.g, /usr/local/lib). The path to HDF is only needed for creating the pipelines to analyse directly from fast5 files or simultaneously from the MinION sequencing. For your convenience, add INSTALL_DIR/bin to your PATH envirenment e.g.,:: export PATH=~/.usr/local/bin:$PATH