[[command-examples]]
Command examples
~~~~~~~~~~~~~~~~

First as a sanity after installation check try and run the demo code
(this will run for a few minutes on all cores available):

[source,shell]
----
igor -run_demo
----

Here we give an example with a few commands illustrating a typical
workflow. In this example we assume to be executing IGoR from the
directory containing the executable.

[source,shell]
----

WDPATH=/path/to/your/working/directory #Let's define a shorthand for the working directory

#We first read the sequences contained in a text file inside the demo folder
#This will create the align folder in the working directory and the mydemo_indexed_seqs.csv file.
igor -set_wd $WDPATH -batch foo -read_seqs ../demo/murugan_naive1_noncoding_demo_seqs.txt

#Now let's align the sequences against the provided human beta chain genomic templates with default parameters
#This will create foo_V_alignments.csv, foo_D_alignments.csv and foo_J_alignments.csv files inside the align folder.
igor -set_wd $WDPATH -batch foo -species human -chain beta -align --all

#Now use the provided beta chain model to get the 10 best scenarios per sequence
#This will create the foo_output and foo_evaluate and the corresponding files inside
igor -set_wd $WDPATH -batch foo -species human -chain beta -evaluate -output --scenarios 10

#Now generate 100 synthetic sequences from the provided human beta chain model
#This will create the directory bar_generate with the corresponding files containing the generated sequences and their realizations
igor -set_wd $WDPATH -batch bar -species human -chain beta -generate 100
----

Since all these commands use several time the same arguments here is
some syntactic sugar using more Bash syntax for the exact same workflow
with a lighter syntax:

[source,shell]
----
WDPATH=/path/to/your/working/directory #Let's define a shorthand for the working directory
MYCOMMANDS=./igor -set_wd $WDPATH

$MYCOMMANDS -batch foo -read_seqs ../demo/murugan_naive1_noncoding_demo_seqs.txt #Read seqs
MYCOMMANDS=$MYCOMMANDS -species human -chain beta #Add chain and species commands
$MYCOMMANDS -batch foo -align --all #Align
$MYCOMMANDS -batch foo -evaluate -output --scenarios 10 #Evaluate
$MYCOMMANDS -batch bar -generate 100 #Generate
----

