Roderic Page rdmpage

## query.txt
The Mediawiki API can be used to find qhat wikipedia pages link to BioStor, e.g.:

https://en.wikipedia.org/w/api.php?action=query&list=exturlusage&euquery=biostor.org&eulimit=20

See https://www.mediawiki.org/wiki/API:Lists/All#Exturlusage for details.

## Cricula.nexus
#NEXUS

Begin trees;  [Treefile saved Thu Aug 20 21:42:14 2015]
[!
>Data file = /Users/rpage/Sites/geojson-phylogeny-demo/bold-api/service/tmp/SAUPA642-10/SAUPA642-10.nex
>Neighbor-joining search settings:
>  Ties (if encountered) will be broken systematically
>  Distance measure = uncorrected ("p")
>  (Tree is unrooted)
]

## Cricula.geojson

      
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              May 10, 2016 13:27
            
              
                Cricula barcode map
              
          
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## primers.txt
Reference COI is NC_003128 Buteo buteo COI

TZBRD035-15.COI-5P [648bp]                                  ctgatctttggtgnatgagcaggcatagccggcacagcacttagcctactaatccgcgcagaactaggacagccaggaacactattgggagacgaccaaatctacaatgtaatcgtaacagcccacgctttcgtcataatcttcttcatagtcatacctattatgatcggaggcttcggaaactgactggttccactcataattggcgccccagacatagcattcccccgcataaataatatgagcttctgactcctcccaccttcttttctcctcctactagcctcctctacagtagaagccggggctggcactggatgaactgtttatccacccctagccggtaatcttgcccacgcgggcgcatcagtagacctggctattttttcccttcacttggcaggcgtgtcgtccatcttaggagctattaactttatcaccacaattattaacataaagccccctgcactatcacaatatcaaacacccctcttcgtatgatccgtcctcattactgctatcctcttactactatccctgccagtcctagccgccgggattacaatactcctcaccgatcgcaacctcaacactacattctttgaccctgcaggaggaggagacccaatcctgtatcaacacctattc
TZBRD019-15.COI-5P                                              tcttcggcgcctgagctggtatagtcggcaccgccctcagcttactcatccgtgcagaactcggccaacccggcacactcctaggtgacgaccaaatttataacgtaatcgttaccgcacatgccttcgtaataatcttcttcatagttataccaatcatgatcggaggattcggaaactgacttgttccactcataattggcgctc

## index.html
<!DOCTYPE html>
<html>
<head>
    <title>GBIF search</title>
    <meta charset="utf-8" />
    <link
        rel="stylesheet"
        href="http://cdn.leafletjs.com/leaflet-0.7/leaflet.css"
    />
    <link

## geojson-conversion.sh
# Bulk convert shapefiles to geojson using ogr2ogr
# For more information, see http://ben.balter.com/2013/06/26/how-to-convert-shapefiles-to-geojson-for-use-on-github/

# Note: Assumes you're in a folder with one or more zip files containing shape files
# and Outputs as geojson with the crs:84 SRS (for use on GitHub or elsewhere)

#geojson conversion
function shp2geojson() {
  ogr2ogr -f GeoJSON -t_srs crs:84 "$1.geojson" "$1.shp"
}

## collection.json
{"collection":{"name":"Mesoplodon","description":"Mesoplodon species","collection_items":[{"collected_item_type":"TaxonConcept","collected_item_id":328563}]}}

## jbig2enc-master.txt
Need to supply paths to configure

./configure CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib

## curl.txt
curl -L -C - '<url>'

## Merge PDFs.txt
gs -q -dNOPAUSE -dBATCH -dAutoRotatePages=/None -sDEVICE=pdfwrite -sOutputFile=merged.pdf *.pdf
	The Mediawiki API can be used to find qhat wikipedia pages link to BioStor, e.g.:

	https://en.wikipedia.org/w/api.php?action=query&list=exturlusage&euquery=biostor.org&eulimit=20

	See https://www.mediawiki.org/wiki/API:Lists/All#Exturlusage for details.
	#NEXUS

	Begin trees; [Treefile saved Thu Aug 20 21:42:14 2015]
	[!
	>Data file = /Users/rpage/Sites/geojson-phylogeny-demo/bold-api/service/tmp/SAUPA642-10/SAUPA642-10.nex
	>Neighbor-joining search settings:
	> Ties (if encountered) will be broken systematically
	> Distance measure = uncorrected ("p")
	> (Tree is unrooted)
	]
	Reference COI is NC_003128 Buteo buteo COI

	TZBRD035-15.COI-5P [648bp] ctgatctttggtgnatgagcaggcatagccggcacagcacttagcctactaatccgcgcagaactaggacagccaggaacactattgggagacgaccaaatctacaatgtaatcgtaacagcccacgctttcgtcataatcttcttcatagtcatacctattatgatcggaggcttcggaaactgactggttccactcataattggcgccccagacatagcattcccccgcataaataatatgagcttctgactcctcccaccttcttttctcctcctactagcctcctctacagtagaagccggggctggcactggatgaactgtttatccacccctagccggtaatcttgcccacgcgggcgcatcagtagacctggctattttttcccttcacttggcaggcgtgtcgtccatcttaggagctattaactttatcaccacaattattaacataaagccccctgcactatcacaatatcaaacacccctcttcgtatgatccgtcctcattactgctatcctcttactactatccctgccagtcctagccgccgggattacaatactcctcaccgatcgcaacctcaacactacattctttgaccctgcaggaggaggagacccaatcctgtatcaacacctattc
	TZBRD019-15.COI-5P tcttcggcgcctgagctggtatagtcggcaccgccctcagcttactcatccgtgcagaactcggccaacccggcacactcctaggtgacgaccaaatttataacgtaatcgttaccgcacatgccttcgtaataatcttcttcatagttataccaatcatgatcggaggattcggaaactgacttgttccactcataattggcgctc
	<!DOCTYPE html>
	<html>
	<head>
	<title>GBIF search</title>
	<meta charset="utf-8" />
	<link
	rel="stylesheet"
	href="http://cdn.leafletjs.com/leaflet-0.7/leaflet.css"
	/>
	<link
	# Bulk convert shapefiles to geojson using ogr2ogr
	# For more information, see http://ben.balter.com/2013/06/26/how-to-convert-shapefiles-to-geojson-for-use-on-github/

	# Note: Assumes you're in a folder with one or more zip files containing shape files
	# and Outputs as geojson with the crs:84 SRS (for use on GitHub or elsewhere)

	#geojson conversion
	function shp2geojson() {
	ogr2ogr -f GeoJSON -t_srs crs:84 "$1.geojson" "$1.shp"
	}
	Need to supply paths to configure

	./configure CPPFLAGS=-I/usr/local/include LDFLAGS=-L/usr/local/lib