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9 changes: 4 additions & 5 deletions README.rst
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Expand Up @@ -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
Expand All @@ -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

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