Colin Davenport colindaven

## gist:dd625105c4d709f27e46def968a01409
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

## checkDisk.sh
# 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

## Exploratory analysis with scVI.ipynb

      
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                colindaven
                / Exploratory analysis with scVI.ipynb
            
            
              Created
              February 23, 2022 08:30
                — forked from vals/Exploratory analysis with scVI.ipynb
            
              
                Exploratory analysis with scVI
              
          
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## gist:27f49a8e79fa384499c5f81b2fa888de
# 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
	# 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
	# 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