Input Requirements

# "Fast hybrid error corrector for PacBio and Illumina reads"
PacBio filtered subreads in fasta format
Illumina paired end reads in fastq format

# "Building "Mid-sized SVs detector"
Assembled contigs or corrected PacBio reads in fasta format
Reference genome in fasta format

## Annotation 
For annotation, This program uses gene information (eg. Refseq BED file) and reprepbase file.


Software Requirements

In order to run the 2 programs, you need to install several programs. Also, in order to build the
programs, you need to build the programs from D language source codes. The compiler for D language
also needs to be compiled. Each program (Fast hybrid error corrector for PacBio and Illumina reads &
Mid-sized SVs detector) requires different version of the D language compiler.

We will provide here a brief description of how the programs and the compiler can be installed.
For those programs that are trivial to install, we will just provide the version of the tools we
used in our analysis.

# D compiler 

We used gdc for compiling our source code: https://github.com/D-Programming-GDC/GDC
In order to build gdc, you will need to also install any programs that is required for building gcc
compiler tools. Please follow the instructions at http://wiki.dlang.org/GDC to install gdc, but
build the old versions of the GDC specified in the following section of this doc. 

# Building "Fast hybrid error corrector for PacBio and Illumina reads"

Install the D compiler, and g++ compiler. Then run 'make all'.
Running 'make all' will also automatically builds the snappy library.
(https://code.google.com/p/snappy/)

## D compiler 
Please use the GDC version that corresponds to the commit 83b13e669914f114a9708c966fcde857ff1b274b,
and the corresponding version of gcc.

# Building "Mid-sized SVs detector"

Install the D compiler, and g++ compiler. Then run 'make all'.

## D compiler 
Please use the GDC version 4.8.1 and the corresponding version of gcc.

# Running programs

## gxpc
GXP is a parallel shell, with which you can easily run any program on any node that is SSH
connectable:
http://www.logos.ic.i.u-tokyo.ac.jp/gxp/index.php
Please install gxpc version 3.07 in all nodes that the program will run in.
You need to be able to run the following command.
gxpc use ssh `hostname -s` [the hostname of the node where you want your program to run]
gxpc explore [the hostname of the node where you want your program to run]
gxpc e echo 'hello world'

## sqlite3
Please install sqlite3 version 3.6.23.1

## GNU parallel
http://www.gnu.org/software/parallel/
Please install GNU parallel versoin 20120822

## GNU sort
Please install GNU sort version 8.17

## LAST
http://last.cbrc.jp
Please install the latest version of LAST