[[http://genome.ucf.edu/RNAEAPath/ | RNAEAPath Home]]

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# Installation

## Install Vienna RNA

## Install the google sparse_hash_map pacakge

```
./configure --prefix=/home/usr/share/sparsehash
make
make install
```

Add `INCDIRS = -I /home/usr/share/sparsehash/include/` to file `makefile`

## Install the RNAEAPath

There might be one error (due to the version of compiler g++, probably).

Modify the file `RPath.c`
[REF](https://stackoverflow.com/questions/67831917/cannot-convert-stdifstream-aka-stdbasic-ifstreamchar-to-bool-in-re): 
```
//check if a file exists or not
bool fexists(const char *filename)
{
  ifstream ifile(filename);
  // label
  // return ifile;
  return ifile.good();
}
```

# Usage

Two segments are needed: location of the software and the configuration.

I write a file `run.sh`.

```
#!/bin/bash

# add the installation path to your ENV
# Also, you can append the line to your '.bashrc', '.cshrc' or whatever
export PATH=$PATH:/home/usr/share/RNAEAPath
# the location of one prerequsite 'RNAeval' is given in this file
# as well as other configurations
# only needed to be done once actually
cp /home/usr/share/RNAEAPath/config ./
# the command line to run the software
RNAEAPath -i sample.faa -d ./sample
```

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