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[ShoRAH 0.5 docs]">[ShoRAH 0.5 docs]

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Running on Mac OS X and Linux

ShoRAH is a collection of tools meant to be used from command line (no GUI yet).
It has been successfully compiled and run on Mac OS X and Linux, provided that the following languages and required libraries are installed. Windows users, see here

Languages

ShoRAH is a collection of programs written in C++ (for which you will need a compiler), Python (version 2.6 or later, but not Python 3.x) and Perl.

They come with almost any distribution of Linux and Mac OS X, or they can be downloaded and installed.

Libraries

Please download and install:

  • Biopython, following the online instructions.

  • GSL, GNU Scientific Library, installation described in the included README and INSTALL files.

  • needle, a program found in emboss is needed for the alignment until version 0.5. Make sure that it is on your path and you can run it. Users of version 0.6 on will not need it anymore (though they will provide their own alignment).

Note to Mac users: these tools, together with SAMtools (needed to deal with SAM alignment, see Short-read data) can also be installed via Macports.

Linux users should check the package management system of their distribution.

Download and compile ShoRAH

We recommend downloading and installing ShoRAH to a directory different from where the analysis will be performed. From now on we assume that ShoRAH is downloaded in the directory sho_bin. Extract it and change to the shorah-0.X directory (in the example, shorah-0.4)

Extract the folder

[user@host sho_bin]$ tar xvfz shorah-0.4.tar.gz
shorah-0.4/
shorah-0.4/CHANGELOG
shorah-0.4/combined.fasta
... more output ...
[user@host sho_bin]$
[user@host sho_bin]$ ls
shorah-0.4.tar.gz shorah-0.4
[user@host sho_bin]$ cd shorah-0.4
[user@host shorah-0.4]$

We made our best to make the compile step as easy as possible. Usually it suffices to give the command make.

Compile

[user@host shorah-0.4]$ make
g++ -pedantic -Wall -Wextra -O2 -ffast-math -funroll-loops -I/opt/local/include -c -o dpm_src/dpm_sampler.o dpm_src/dpm_sampler.cpp
*********************************
making executable: diri_sampler
*********************************
g++ -L/opt/local/lib -lgsl -lgslcblas dpm_src/dpm_sampler.o -g -O2 -o diri_sampler
*******************
... more output ...
compiled for Darwin/Linux

The last message depends whether you are on a Mac OS X machine or Linux.
ShoRAH is ready for use.

If something goes wrong

Despite our efforts to make the installation procedure as easy as possible, the variety of computers, operating systems, distributions and libraries make the installation outcome very difficult to predict. Should you have any problem, refer to your local administrator (it might be something very easy), check the Getting help, or contact us at shorah@bsse.ethz.ch

"But I only have a Windows machine"

Since we distribute the source code for all programs, there is in principle no reason why ShoRAH shouldn't work on Windows machine, provided that all dependencies are satisfied. However, we haven't tested this yet. The most common command line environment under Windows is probably Cygwin. We would be grateful if you report your experience with running ShoRAH on Windows to us.