2.3.0 - Dockerised

• dockerised cgpRna. Within the docker container, version of some dependent tools have been changed:

  1. Python3(3.7.X) is used in the container, thus:

     • RSeQC is updated from version 2.6.4 to 3.0.0.
     • However, the version of HTSeq is not changed.

  2. Defuse is updated from v0.7.0 to v0.8.2 due to "Possible precedence issue with control flow operator" warning with the version of Perl installed in the container. The fix is here. However, it is not merged in any v0.7.x versions (also because there's only ONE v0.7.x version --v0.7.0), hence v0.8.2, which is the latest version at the time, was chosen.

  3. To utilise apt packages for the ease of their installations, the following tool version changes were made:

     • BedTools: 2.21.0 to 2.25.0-1 in apt,
     • bowtie1: 1.1.1 to 1.1.2-3 in apt,
     • bowtie2: 2.2.3 to 2.2.6-2 in apt,
     • blast: 2.2.30 to 2.2.31-4 in apt,
     • gmap: 2015-09-10 to 2015-12-31.v7-1 in apt.

• added an extra option "-updateconfig" to defuse_fusion.pl. It takes a file as input, which content is used to update defuse-config.txt. It'll search defuse.ini to find its default value. This addition shouldn't break any existing usage.

• defuse_fusion.pl will always create a defuse-config.txt file in its temp folder and use it to run defuse.pl. In the temp file, dataset_directory is corrected using related command line input values. If "-updateconfig" presents, values in the file will be used to overwrite corresponding values in the temp file. Note: if dataset_directory key presents in the "-updateconfig" file, this will be the final value in the temp config file.

• tophat-fusion-post now skips read dist step, which our infuse pipeline does not care and the tophat-fusion-post.py does not insert generated read distributions in final html report anyway neither.