transrate v1.0.3

This is is a patch release of transrate v1, to accompany the publication of our paper about transrate.

Please report any bugs on the issue tracker. Documentation for this release is on the transrate website: http://hibberdlab.com/transrate/.

Installation

This is the simplest option if you just want to use transrate from the command-line...

Download one of the binaries linked below, unpack it, and add it to your PATH.

Download the example data so you can test your installation has worked.

This is the option you need if you want to develop code that uses transrate as a library...

$ gem install transrate
$ transrate --install-deps all

Output additional columns with names that match the quality score components in the paper
Make --install-deps messages clearer (fixes #187)
Track working directory on the package loading script (#fixes #186)
Updated SNAP dependency to v1.0dev96
Updated Salmon dependency to v0.6.0
Check for duplicate paths in input
Remove some ancient contig metrics that were deprecated
Updated the packaging process to be more robust
Log commands used to shell out when --loglevel is debug
Automatically increase SNAP locationSize parameter if it fails (thanks to @jorvis)

For changelog history before v1.0.0, please see the release notes for v1.0.0 final.

There is a SNAP bug that causes a random subset of reads not to be processed about one in ten times SNAP is run. This only affects OSX, and we are working with the SNAP developers to find a fix. Linux users should not be affected.