pjbriggs’s gists

pjbriggs / Galactic-Engineer-nginx-conf-fragment-for-reports

Created June 2, 2015 13:54

Fragment of nginx conf file for exposing Galaxy report tool

	http {
	...
	upstream reports {
	server localhost:9001;
	}
	...
	server {
	...
	location ^~ /reports/ {
	proxy_pass http://reports;

pjbriggs / galaxy_boolean_test_issue2.sh

Last active August 29, 2015 14:21

Dummy Galaxy tool demonstrating problem with setting value of boolean parameter used as "control" variable in a conditional tag within tool tests

	#!/bin/sh
	echo Values are ${@:2} > $1

pjbriggs / boolean_test_issue.sh

Created May 8, 2015 13:38

Demonstrate issue with "boolean" parameter type behaving differently in tests compared with interactive usage.

	#!/bin/sh
	echo Values are $1 $2 > $3

pjbriggs / Galactic-Engineer-GALAXY_SLOTS-trimmomatic-fragment.xml

Created April 22, 2015 12:01

Galactic Engineer/GALAXY_SLOTS: trimmomatic.xml fragment

	...
	<command interpreter="bash">trimmomatic.sh
	-mx8G
	-jar \$TRIMMOMATIC_DIR/trimmomatic-0.32.jar
	#if $paired_end.is_paired_end
	PE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_r1_in $paired_end.fastq_r2_in $fastq_out_r1_paired $fastq_out_r1_unpaired $fastq_out_r2_paired $fastq_out_r2_unpaired
	#else
	SE -threads \${GALAXY_SLOTS:-6} -phred33 $fastq_in $fastq_out
	#end if
	...

pjbriggs / Galactic-Engineer-GALAXY_SLOTS-job_conf-fragment.xml

Last active August 29, 2015 14:19

Galactic Engineer/GALAXY_SLOTS: job_conf.xml fragment

	<destinations default="dynamic">
	...
	<!-- DRMAA runner for job using 4 cores -->
	<destination id="sge_smp_4" runner="drmaa">
	<param id="nativeSpecification">-R y -V -j n -pe smp.pe 4</param>
	</destination>
	...

pjbriggs / check_gtf_exon_coverage.py

Created April 1, 2015 10:06

Given a GTF file, check that for each exon entry the associated features 'CDS', 'stop_codon' and 'start_codon' are consistent and specify the same range of bases as # their "parent" exon

	#!/bin/env python
	#
	# Check exon coverage in a GTF file
	# Peter Briggs UoM, March 2015
	#
	# Purpose
	# -------
	# Given a GTF file, check that for each exon entry the
	# associated features 'CDS', 'stop_codon' and 'start_codon'
	# are consistent and specify the same range of bases as

pjbriggs / proftpd.conf-extract

Last active January 19, 2016 05:23

Extract from proftpd.conf for handling SHA1 and PBKDF2 encryption

	ServerName "Galaxy FTP File Upload"
	ServerType standalone
	DefaultServer on
	PidFile /var/run/proftpd/proftpd-galaxy.pid

	# Port 21 is the standard FTP port.
	Port 21

	# Don't use IPv6 support by default.
	UseIPv6 off

pjbriggs / load_urls.py

Created July 2, 2014 13:26

Open multiple arbitrary URLs automatically in a webbrowser

	#!/bin/env python
	#
	# Open multiple arbitrary URLs in a webbrowser
	import optparse
	import webbrowser
	import time
	import sys
	if __name__ == '__main__':
	p = optparse.OptionParser(usage="%prog [-f FILE] [-b BROWSER] [-p INTERVAL] "
	"[URL [URL,...]]",

pjbriggs / sorting.py

Created July 22, 2013 12:29

Script to explore the use of different types of sort keys, including "natural sort order"

	# Compare effects of using different sort keys

	import os
	import locale
	import re

	class SortKeys:
	natural_sort_digits = re.compile(r'(\d+)')
	@classmethod
	def default(self,filename):

pjbriggs / clean_rtf_to_fasta.sh

Created May 22, 2013 11:15

Hacky script for converting fasta files munged by some other program into RTF files back to fasta format (used for frog data). Probably output file will need some additional corrections by hand.

	#!/bin/sh
	#
	if [ -z "$1" ] \|\| [ -z "$2" ] ; then
	echo "Usage: $0 IN.rtf OUT.fasta"
	exit 1
	fi
	if [ ! -e "$1" ] ; then
	echo "Input file $1 not found"
	exit 1
	fi

Peter Briggs pjbriggs