# Working with BiTIA CLI The three commands that are the core of BiTIA's functionality are: - run - submit - logs ### Bitia run can be employed in following ways: #### 1. Running commands ```bash $ bitia run "samtools convert foo.fa#http://example.com/foo.fa" ``` The above code will: - Add the given command `samtools run foo.fa#http://example.com/foo.fa` into a pipeline file. - Extract the current working directory with the pipeline as a zip file that contains a unique hash and send it to the server `public.bitia.link` - The BiTIA runner in the server will execute the pipeline by: - Installing the given command `samtools` - Downloading the given input file form the link `http://example.com/foo.fa` and name it as `foo.fa` - executing the command `samtools convert foo.fa` - Display the resulting output to the user console #### 2. Running Pipelines ```bash $ bitia run pipeline.sh ``` for `pipeline.sh`: ```bash #!/usr/bin/env bash fastqc *.gz for file in *_1.fastq.gz do trim_galore --cores 8 --gzip --fastqc --max_n 2 --output_dir Trimmed_Data/ --paired $file ${file%_1.fastq.gz}_2.fastq.gz done hisat2-build -p 8 ./Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa index ``` The above code will: - Extract the current working directory with the `pipeline.sh` as a zip file that contains a unique hash and sent it to the server `public.bitia.link` - The BiTIA runner in the server will execute the pipeline - Installing the given commands `fastqc`, `trim_galore`,`hisat2` . - executing the commands given in the pipeline - Displays the resulting output to the user console