More bug-fixes

Minor fixes, including DALIGNER/DAZZ_DB.

New pypeflow, new directories for some scripts

This should be compatible with 1.8.2, even on restart, but this will probably become 1.9.0 soon because we have removed a lot of old pypeflow code. This version should work with the latest FALCON-unzip too, which we will probably add as a sub-module in 1.9.0.

* https://github.com/PacificBiosciences/FALCON/compare/6c14768...e238ea1
* https://github.com/PacificBiosciences/pypeFLOW/compare/bdedaf2...e331fad
* https://github.com/pb-cdunn/FALCON-examples/compare/98d2119...12a5bc2
* https://github.com/pb-cdunn/FALCON-make/compare/4d2242a...02ed9de

bug-fix and ecoli data

• PacificBiosciences/FALCON@cdd407d...6c14768
  • Important bug-fix in job separation.
  • You need this only if you had a crash that looks like assert pair1 == pair2. Otherwise, you are fine.
• pb-cdunn/FALCON-examples@8e0a8e5...98d2119
  • Download E.coli subreads from
    https://downloads.pacbcloud.com/public/data/git-sym
    rather than DropBox.

Minor fixes of 1.8.0

• pb-cdunn/FALCON-examples@c8805c9...8e0a8e5
  • Fix e.coli in FALCON-examples
• PacificBiosciences/FALCON@4ef2433...cdd407d
  • Bug-fixes
• PacificBiosciences/pypeFLOW@ebdbf9f...bdedaf2
  • Bug-fixes

Simpler workflow

• New refresh loop for simpler workflow.
  • pwatcher_type can now be fs_based (default), network_based, or blocking
  • state.py is no longer saved in mypwatcher dir (so deleting that directory is not needed anymore)
• sge_option
  • All tasks are now run distributed, so we need a default sge_option for them.
• DEXTRACTOR
  • This allows us to read .fasta compressed as .dexta, which is better compression and much faster than gzip.

Minor fixes and new process-watchers

• PacificBiosciences/FALCON@54779b2...3a8a9cc
• PacificBiosciences/pypeFLOW@99a7eae...21f8acc

The new pwatchers are experimental, not used by default.

Updates and minor fixes

• PacificBiosciences/DAMASKER@d50edb0...5726269
• PacificBiosciences/DAZZ_DB@d342311...1e08411
• PacificBiosciences/DALIGNER@a92a518...4e1c172
• PacificBiosciences/pypeFLOW@aa5d4b6...99a7eae

Several minor improvements

Several minor improvements requested by users. Also, 2 new metrics in the pre-assembly report.

• PacificBiosciences/FALCON@d51ec37...54779b2
• PacificBiosciences/pypeFLOW@4b64e3c...aa5d4b6

Fix `LAcheck` failures

• Fix LAcheck failures
  • In 1.7.3, we used skip_checks = true by default to avoid a problem in LAcheck. Gene Myers has fixed that in DALIGNER, so now we run LAcheck by default again.
  • PacificBiosciences/DALIGNER#21
• Lock html5lib version.
  • That was necessary for TravisCI. Unfortunately, that can break users who have installed the later version in their site-packages/ already. If that's you, let us know. We can prioritize the rdflib modifications.
• Other minor fixes.
• Sync with thegenemyers.

Avoid LAcheck failures; support PBS

• PacificBiosciences/FALCON@6bb263a...85e41a6
  • skip_checks=false to run LAcheck and stop on failure
• PacificBiosciences/pypeFLOW@9a1b0bf...ddfaec1
  • Support PBS job-distribution.
  • Warn on DEAD jobs.