NxtIRF as a galaxy app

cd ~/bin
git clone https://github.com/alexchwong/NxtIRFgalaxy

cd NxtIRFgalaxy
make

Assuming the installation path is ~/bin/galaxy:

cp tools ~/bin/galaxy/

To set up a local version of Galaxy (latest release version 21.05):

cd ~/bin
git clone -b release_21.05 https://github.com/galaxyproject/galaxy.git

To start Galaxy:

cd ~/bin/galaxy
sh run.sh --daemon

In Galaxy main configuration file: galaxy.yml

cp config/galaxy.yml.sample config/galaxy.yml

To enable remote connections to port 8080:

• http: 0.0.0.0:8080

To save job and tool data to a different location (as they are typically gigabytes of data):

• file_path: /path/to/drive_with_lots_of_space/galaxy/objects
• tool_data_path: /path/to/drive_with_lots_of_space/galaxy/tool-data

To recognise custom tool and job configurations:

• job_config_file: config/job_conf.xml
• tool_config_file: config/tool_conf.xml

To assign admins (change email to admin's email login):

• admin_users: [email protected]

To set up a path where users can dump files to a folder to be used in Galaxy:

• ftp_upload_dir: /path/to/shared_folder
• ftp_upload_site: sftp://[email protected] (set this to the FTP site that users use to upload files from local to server)
• ftp_upload_dir_identifier: username

Users can create subfolders named by their username. Files placed in this folder can be accessed via "FTP"

cp config/tool_conf.xml.sample config/tool_conf.xml

Add the following within the <toolbox> </toolbox> brackets of tool_conf.xml:

  <section name="NxtIRF / IRFinder" id="nxtirf">
    <tool file="nxtirf/nxtirf_galaxy.xml"/>
  </section>

cp config/job_conf.xml.sample config/job_conf.xml

In job_conf.xml change the workers to the desired number of threads per job (e.g. to 8 threads):

In plugins:

  <plugins>
    <plugin id="local" type="runner" load="galaxy.jobs.runners.local:LocalJobRunner" workers="8"/>
  </plugins>

In destinations:

  <destinations>
	<destination id="local" runner="local">
	  <param id="local_slots">8</param>
	</destination>
  </destinations>

This must be done after any tweaks to the Galaxy settings in order for changes to take effect:

# Stop the Galaxy server
sh run.sh --stop-daemon

# Start the Galaxy server
sh run.sh --stop-daemon

• data_manager_fetch_genome_dbkeys_all_fasta: Designates a FASTA file as a genome FASTA
• data_manager_star_index_builder: Builds a STAR genome from a genome FASTA

• rgrnastar: Aligns a single or paired FASTQ file(s) using STAR (Optional use a GTF file)
• sra_tools: Extracts FASTQ files from SRA files
• featurecounts: Perform gene counts