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MitoZ 3.5 beta-1

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@linzhi2013 linzhi2013 released this 12 Jul 08:31
· 83 commits to master since this release
3.5-beta-1
b407097
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Fixed bugs:

  1. Fixed the dependency problem of 'mitoz-tools': html5lib
  2. Fixed the sub-sampling bug (it was 10 times than expected)
  3. Fixed the bug on #154 and #24 (comment).

New features:

  1. Should now also run on Mac OS (M1 and Intel chips); but the assembler SPAdes won't work on Mac OS due to ablab/spades#873 and lack of proper version for Mac OS. However, you can download it from https://cab.spbu.ru/files/release3.15.4/SPAdes-3.15.4-Darwin.tar.gz and put it into the mitozEnv environment (or PATH variable). The assembler mitoassembler also does not work on Mac OS yet. NB: it could be very tricky to install the Circos problem on Mac OS; you might want to install Circos by following http://circos.ca/tutorials/lessons/configuration/perl_and_modules/.

  2. Added a few tools to the 'mitoz-tools' command, see https://github.com/linzhi2013/MitoZ/wiki/Overview%3A-The-%27mitoz-tools%27-command.

  3. Users can now use their own sqn template file ('--template_sbt'): #153

# mac OSX
$ circos --modules
missing            Math::Bezier
ok   1.999818 Math::BigFloat
missing            Math::Round
missing            Math::VecStat
ok    1.03_01 Memoize
ok       1.94 POSIX
missing            Params::Validate
ok       1.69 Pod::Usage
ok       2.05 Readonly
ok 2017060201 Regexp::Common
ok       2.87 SVG
missing            Set::IntSpan
missing            Statistics::Basic

$ cpan install Encode::Locale
$ cpanm Math::Bezier Math::Round Math::VecStat Set::IntSpan Statistics::Basic Params::Validate Module::Implementation IO::String
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