Kallisto Transcriptomes

[JohnMCMa]

The Kallisto transcriptome link provided in readme.md no longer works; http://bio.math.berkeley.edu/kallisto/ redirects to the software's Github page, and that page says that they no longer provide indexes for download, because indexing it locally is faster than downloading it.

In this case, it'd be helpful to provide the cDNA libraries you have tested for BraCeR, if it's not feasible to put them on this repo for download.

[dcroote]

These couple lines of the Dockerfile could help

[JohnMCMa]

That should be on the documentation as well. Not everyone use Docker; the vluster I'm using will not allow Docker, for example.

[idalind]

Thank you for the tip @dcroote . I have now updated the documentation with the relevant code taken from the Docker documentation, which enables users not using Docker to download and parse the transcriptome reference sequences.