Interface seems to have changed. There may still be missing changes.

See https://stackoverflow.com/a/18129693/1878788, and first user
comment (git rm -r, rm -r, git git submodule add).

When R crashes, rpy doesn't seem to handle this properly.

Currently, libcelegans only provides scripts to convert between cosmid,
wormid and gene names.

Made genome configurable for GRO-seq, tried to debug rpy2 uncachable
exceptions.

Could the `--quote` option have been another solution?

Also changed the way to cleanup temporary dir when making bigwig files.

We added all_si_22G and all_si_26G, who have a signature (more
informative than all_si) but are not dependent on being antisense to
some annotations (avoids being lost when annotations are apparently
incorrect, like some histone genes 3'UTRs ending too early).

DESeq2 apparently complains about library names not being the same in
the two input table, but this doesn't seem to be the case. This happens
with a library where a library has a dash "-" in its name.

0.8.0 provides a `get_includes` function, but I failed at using it.
See <https://github.com/daler/pybedtools/issues/253#issuecomment-469671096>.

Also updated gene list names.

We have space issues on tars.

Also removed indexing of annotation files. For some unknown reason,
tabix started complaining about wrong sorting, and this is not used any
more anyway.