Bishoy Hanna bishoyh

## maker_genome_annotation.md

      
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                darencard
                / maker_genome_annotation.md
            
            
              Last active
              March 7, 2024 08:50
            
              
                In-depth description of running MAKER for genome annotation.
              
          
    Please see the most up-to-date version of this protocol on my blog at https://darencard.net/blog/.
Genome Annotation using MAKER

MAKER is a great tool for annotating a reference genome using empirical and ab initio gene predictions. GMOD, the umbrella organization that includes MAKER, has some nice tutorials online for running MAKER. However, these were quite simplified examples and it took a bit of effort to wrap my head completely around everything. Here I will describe a de novo genome annotation for Boa constrictor in detail, so that there is a record and that it is easy to use this as a guide to annotate any genome.
Software & Data

Software prerequisites:


RepeatModeler and RepeatMasker with all dependencies (I used NCBI BLAST) and RepBase (ver


## linux.sh
#!/boot/bzImage

# Linux kernel userspace initialization code, translated to bash
# (Minus floppy disk handling, because seriously, it's 2017.)
# Not 100% accurate, but gives you a good idea of how kernel init works
# GPLv2, Copyright 2017 Hector Martin <marcan@marcan.st>
# Based on Linux 4.10-rc2.

# Note: pretend chroot is a builtin and affects the current process
# Note: kernel actually uses major/minor device numbers instead of device name

## punk.py
import binascii
import struct


class Punk(object):

    _END_CHUNK_TYPE = 'IEND'
    _PUNK_CHUNK_TYPE = 'puNk'
    _MAX_BYTES = 2147483647
    _chunks = dict()

## grunt-hugo-lunrjs.md

      
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                sebz
                / grunt-hugo-lunrjs.md
            
            
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              June 28, 2024 18:41
            
              
                hugo + gruntjs + lunrjs = <3 search
              
          
How to implement a custom search for Hugo usig Gruntjs and Lunrjs.

Requirements

Install the following tools:

Nodejs
Gruntjs

Setup


## analytic_wfm.py
#!/usr/bin/python2


# Copyright (C) 2016 Sixten Bergman
# License WTFPL
#
# This program is free software. It comes without any warranty, to the extent
# permitted by applicable law.
# You can redistribute it and/or modify it under the terms of the Do What The
# Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See
	#!/boot/bzImage

	# Linux kernel userspace initialization code, translated to bash
	# (Minus floppy disk handling, because seriously, it's 2017.)
	# Not 100% accurate, but gives you a good idea of how kernel init works
	# GPLv2, Copyright 2017 Hector Martin <marcan@marcan.st>
	# Based on Linux 4.10-rc2.

	# Note: pretend chroot is a builtin and affects the current process
	# Note: kernel actually uses major/minor device numbers instead of device name
	import binascii
	import struct


	class Punk(object):

	_END_CHUNK_TYPE = 'IEND'
	_PUNK_CHUNK_TYPE = 'puNk'
	_MAX_BYTES = 2147483647
	_chunks = dict()
	#!/usr/bin/python2


	# Copyright (C) 2016 Sixten Bergman
	# License WTFPL
	#
	# This program is free software. It comes without any warranty, to the extent
	# permitted by applicable law.
	# You can redistribute it and/or modify it under the terms of the Do What The
	# Fuck You Want To Public License, Version 2, as published by Sam Hocevar. See