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# Make sure the non-biocontainers version of bwa is not loaded
module unload bwa
# Verify that bwa is not available
bwa

# Verify that these programs are not in the standard TACC module system
module spider kallisto
module spider bowtie2
module spider minimap2
module spider multiqc
module spider GATK
module spider velvet

# Load the Biocontainers master module (this takes a while)
module load biocontainers

# Now look for those programs
module spider kallisto
module spider bowtie2
module spider minimap2
module spider multiqc
module spider GATK
module spider velvet

Notice how the BioContainers module names have "ctr" in their names, version numbers, and other identifying information.

loading a biocontainer module

Once the biocontainers module has been loaded, you can just load the desired tool module, as with the kallisto pseudo-aligner program below.

# Load the Biocontainers master module 
module load biocontainers

# Load the default kallisto biocontainer 
module load kallisto

# Verify you can now execute kallisto
kallisto

Note that loading a BioContainer does not add anything to your $PATH. Instead, it defines an alias, which is just a shortcut for executing the command. You can see the alias definition using the type command. And you can ensure the program is available using the command -v utility.Loading a

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# Note that kallisto has not been added to your $PATH
which kallisto

# Instead, an alias has been defined. Use type to see its definition
type kallisto

# Ensure kallisto is available with command -v
command -v kallisto

installing custom software

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ls -l ~/local/bin

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1. Create a commands file containing exactly one command per line.
2. Prepare a job control file for the commands file that describes how the job should be run.
3. You submit the job control file to the batch system. The job is then said to be queued to run.
4. The batch system prioritizes the job based on the number of compute nodes needed and the job run time requested.
5. When compute nodes become available, the job tasks (command lines in the <job_name>.cmds file) are assigned to one or more compute nodes and begin to run in parallel.
6. The job completes when either:
   1. you cancel the job manually
   2. all tasks in the job complete (successfully or not!)
   3. the requested job run time has expired

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