Update or fork tcr-dist submode

[jwkai]

The production server is currently using an old commit (13e748f) of the tcr-dist repository.

Updating to the tcr-dist current commit (c839920) gives output data for the Filtered Contig Annotations and Consensus Annotations input file format that does not match the old commit (13e748f). So there needs to be a review of recent changes to the repository to determine the cause of the disparities and determine which output is correct to use.

It is also advisable to update tcr-dist to run with Python 3. Currently the must be modified so that cmd = 'python ... becomes cmd = 'python2 ....

Also, the production server has modifications to this repo to change the case-sensitivity of the input annotations files. This has been addressed in a recent commit of tcr-dist (e4b6a30).

The modifications are as follows:assert l['productive'].upper() == 'TRUE'
Here (make_10x_clones_file.py#L48) and here (make_10x_clones_file.py#L73)

The tcr-dist repo should probably be forked in order to make these changes.

[jwkai]

This tag (v0.1.-alpha) contains the publicly-available libraries (as release binaries) used by setup.py in tcr-dist. We are self-hosting for this server due to issue with curl or wget in downloading these libraries as linked in the setup.py script.

[jwkai]

If maintaining a fork with updates to run under Python 3 proves too difficult, consider replacing this with a newer project, such as tcrdist3

Other possibilities are:

• ALICE (Walczak lab)
• TCRnet (from VDJtools folks)
• GLIPH2 (Davis Lab)

[jwkai]

Update: forked this repo to commit necessary local changes (see dc18293).

Note that we have branched off of this fork, as there were recent commits to the repo which are not compatible with my changes. However, these commits on the main repo may cover some of the same issues.