colindaven

#!/bin/bash
# Goals:
# - Add bed annotation using odgi to try to display gene annotations in seqtubemap
# Contact: Colin Davenport

echo "Requires: odgi and vg toolsets"
echo "Usage: bash vg_annotate.sh input.og input_gff3 corrected_path"
echo "Usage: bash vg_annotate.sh input.og input_gff3 MA_genotype=chr9_133258121-134258121"

infile=$1

colindaven

# Using Nextflow in Galaxy

* Nextflow is the workflow management tool used widely in bioinformatics
* Galaxy is a server based GUI tool with a nice interface and is also used to start workflows

## Can it be done ? 

* There are few reports online, but it is possible. eg https://galaxyproject.org/blog/2022-08-15-making-nextflow-work-with-galaxy-at-cfsan-fda/
* The main requirements: 
* a) install Nextflow using a direct JAR download, not via conda. This may be because it collides with the internal Galaxy conda environments

colindaven

colindaven

# Name: checkDisk.sh
# Created by: Originally by Brimur, simple rewrite for sftp by colindaven
# Created: Nov 26th 2019, Oct 2021
# This script is used to control sftp jobs based on available disk space.
#
# This should be run as a cronjob (every minute) on the server/computer running sftp
#
# If you use a download manager tell it to add jobs as PAUSED
#
# - If disk is nearly full (limit) then stop all sftp jobs - kill

colindaven

gmap -f gff3_gene -D /lager2/rcug/seqres/HS/gmap/ -d hg19.gmap -B 5 -t 36 --max-intronlength-middle=150000 --totallength=1000000 --npaths 1 -p 3 10372_comb2_cln.fasta > 10372_comb2_cln.fasta.gff3