On most systems, typing wget https://github.com/Weeks-UNC/shapemapper2/releases/download/2.2.0/shapemapper2-2.2.tar.gz will download the file on the commandline.
Be sure to download from the shapemapper2-2.2.tar.gz link, not the source code-only links, which do not include executables.
Extract release tarball using
tar -xvf shapemapper2-2.2.tar.gz
Add shapemapper executable to PATH (optional - google this if you don't know how)
Run the script run_example.sh to check if shapemapper successfully runs on a small subset of example data. (optional)
This should produce two folders: shapemapper_out and shapemapper_temp
To run all unit and end-to-end tests, run internals/test/run_all_tests.sh. This should take about 5-15 minutes. (optional)
Alternatively, you can build ShapeMapper if the provided binaries do not run on your platform. Building is relatively straightforward using conda. See building.
Supplementary Method 2: Software installation (SuperFold)This guide assumes the user is familiar with basic Unix/Linux commands to change directories,
extract archived files, move files, display and edit text files, and run executables. These steps
only need to be performed once.
Use a package manager, such as apt-get on Debian, Ubuntu, or Linux or MacPorts on OSX, to install Numpy and Matplotlib. Using apt-get:
To install RNAstructure, download the compiled version of the text interfaces for your system from the Mathews lab web site
(http://rna.urmc.rochester.edu/RNAstructureDownload.html). Unzip the tarball and move it to the home directory:
Add the RNAstructure programs and data tables to the PATH:
To install SuperFold, Obtain the latest version of ShapeMapper from www.chem.unc.edu/rna/software.html, move it to your home directory, and add it to the PATH:
Example data. SHAPE-MaP data for the E. coli 16S rRNA are included in the SuperFold tarball. Copy the .map file to a working directory “my_superfold_analysis”
