The phylogenerator2 from willpearse

Things for Curtis

preferentially download longer sequences (like pG1 did). It may already do this... check! maybe give an option?...
check for file problems in reference alignments (run test through MAFFT first?) to avoid blue screen of death
non-windows friendly log-file names
HawkEye error - couldn't find a certain thing in the folder (?)
Check a complete HawkEye run for him too (using demo)
Exclude downloading certain sequences from a previous pG run

Neater output (sorted folders etc.)

phy_params is not implemented?

I tried the simple_plants demo, and when i turn on phy_params (specifically, bootstrapping) nothing different happens: it just performs a simple ML search.
Searching through the repo, I see no other mention of phy_params other than the demo yaml file, so maybe this is just not yet implemented? I'd diagnose further, but unfortunately have no ruby experience :(

ruby installation issues on linux?

(mafft & raxml already installed / executable. Not sure how pg2 will 'find' my raxml though...)

sudo gem install bio
[sudo] password for ross: 
Fetching: bio-1.5.1.gem (100%)
Successfully installed bio-1.5.1
Parsing documentation for bio-1.5.1
Installing ri documentation for bio-1.5.1
Done installing documentation for bio after 8 seconds
1 gem installed

$ ./pG_2.rb ./demo/simple_plants/params.yml 
Ignoring escape_utils-1.1.0 because its extensions are not built.  Try: gem pristine escape_utils --version 1.1.0
Ignoring executable-hooks-1.3.2 because its extensions are not built.  Try: gem pristine executable-hooks --version 1.3.2
Ignoring ffi-1.9.10 because its extensions are not built.  Try: gem pristine ffi --version 1.9.10
Ignoring gem-wrappers-1.2.7 because its extensions are not built.  Try: gem pristine gem-wrappers --version 1.2.7
/usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- bio (LoadError)
	from /usr/lib/ruby/2.3.0/rubygems/core_ext/kernel_require.rb:55:in `require'
	from /home/ross/workspace/phyloGenerator2/lib/Download.rb:6:in `<top (required)>'
	from /home/ross/workspace/phyloGenerator2/lib/Cap.rb:2:in `require_relative'
	from /home/ross/workspace/phyloGenerator2/lib/Cap.rb:2:in `<top (required)>'
	from ./pG_2.rb:6:in `require_relative'
	from ./pG_2.rb:6:in `<main>'

constraint tree support

Use ruby from non standard location

Will -- Is is possible to update the shebang in pG_2.rb to #!/usr/bin/env ruby? May work better for people like me that have the handicapped ruby shipped with the OS in /usr/bin and a more current version somewhere else. Thx for a great program btw!

jhill1@rheic ~/work/software/phyloGenerator2 $ diff demo/simple_plants_he/params.yml demo/simple_plants/params.yml 
16c16
< species: /home/jhill1/work/software/phyloGenerator2/demo/simple_plants_he/leipzig.txt
---
> species: /home/will/Code/phyloGenerator2/demo/simple_plants/species.txt
19c19
< working_dir: /home/jhill1/work/software/phyloGenerator2/demo/simple_plants_he
---
> working_dir: /home/will/test
21c21
< email: [email protected]
---
> email: [email protected]
32c32
<     ref_file: /home/jhill1/work/software/phyloGenerator2/demo/simple_plants_he/rbcL_reference.fasta
---
>     ref_file: /home/will/Code/phyloGenerator2/demo/simple_plants/rbcL_reference.fasta
40c40
<     ref_file: /home/jhill1/work/software/phyloGenerator2/demo/simple_plants_he/matK_reference.fasta
---
>     ref_file: /home/will/Code/phyloGenerator2/demo/simple_plants/matK_reference.fasta
60c60
< hawkeye: true
---
> #hawkeye: true

Gives following error:

jhill1@rheic ~/work/software/phyloGenerator2 $ ruby pG_2.rb demo/simple_plants_he/params.yml 
phyloGenerator 2.0-2 DOI: 10.1111/2041-210X.12055
Please *use with caution*; first version!
Will Pearse - [email protected]
 - Setup complete...
 - - rbcL: 143/182 sequences found
 - - matK: 106/182 sequences found
 - Download complete...
/home/jhill1/work/software/phyloGenerator2/lib/Hawkeye.rb:40:in `check': undefined local variable or method `verbose' for #<Hawkeye:0x00000002d18b50> (NameError)
	from /home/jhill1/work/software/phyloGenerator2/lib/Cap.rb:48:in `block (2 levels) in check'

pG2_log_19-12-2016 16:25

yuck! Add a hyphen or an underscore instead?

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