Editing CrocoBLAST:UserManual (section)

== 1.1. Creating BLAST jobs ==
As already mentioned, BLAST takes an input file with unknown sequences and aligns each such sequence against a database of known sequences. To create a job, you must first specify the [http://www.ncbi.nlm.nih.gov/BLAST/blast_program.shtml BLAST program] you plan to use, which depends on the nature of the unknown sequences in your input file, and the nature of the sequences in the reference database. Then, you need to specify the name of the ''database'' listed in the CrocoBLAST index (more details on that below) that contains the reference sequences you wish to use. Finally, provide the input file and the location where you want CrocoBLAST to place the output files. Keep in mind that the output files may be quite large. Finally, if you want to change the default BLAST settings, you can do so by specifying the [http://www.ncbi.nlm.nih.gov/books/NBK279675/ names and values of the BLAST options] of interest.

# <code>crocoblast -add_to_queue <span style="color:blue">blast_program database</span> <span style="color:green">input_file output_folder</span></code>
# <code>crocoblast -add_to_queue <span style="color:blue">blast_program database</span> <span style="color:green">input_file output_folder</span> --blast_options <span style="color:blue">option1 value1 option2 value2 ...</span></code>
# <code>crocoblast -add_to_queue <span style="color:blue">blast_program database</span> <span style="color:green">input_file output_folder</span> --size_of_fragment <span style="color:blue">size_in_kb</span></code>
# <code>crocoblast -add_to_queue <span style="color:blue">blast_program database</span> <span style="color:green">input_file output_folder</span> --size_of_fragment <span style="color:blue">size_in_kb</span> --options <span style="color:blue">option1 value1 option2 value2 ...</span></code>

If no "--blast_options" are specified, CrocoBLAST will use all BLAST default values.

If no "--size_of_fragment" is specified, CrocoBLAST will take up to 5 seconds to auto-detect the ideal size for that job on your computer.

Note that, CrocoBLAST does not accept that the "--size_of_fragment" argument to be placed after "--blast options". If you intend to use both settings, please follow example number 1.4. 

When you create a BLAST job, CrocoBLAST automatically assigns each BLAST job a unique job ID, and updates the CrocoBLAST queue.