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CrocoBLAST:Job management

1,913 bytes added, 03:28, 25 July 2016
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=Create job=
As
==BLAST options====CrocoBLAST options==
==Add database from your computer==
If you have already downloaded the databases from NCBI, or if you do not have internet connection, you may add to the CrocoBLAST index database files stored on your computer. Remember to provide a unique and representative name for each database you add, so that it is easy to call the databases later. If the database files are appropriately formatted (e.g., psq or nsq):
<code bash>
CrocoBLAST -add_database --formated_db <span style="color:green">nsq_database_file</span><br>
CrocoBLAST -add_database --formated_db <span style="color:green">psq_database_file</span>
</code>
If your database is in FASTA or FASTQ format, you will need to tell CrocoBLAST the type of '''sequence''' it will find in the database:
<code bash>
CrocoBLAST -add_database --sequence_file '''nucleotide''' <span style="color:green">fasta_file</span> <span style="color:orange">database_name</span> <span style="color:green">output_folder</span><br>
CrocoBLAST -add_database --sequence_file '''protein''' <span style="color:green">fasta_file</span> <span style="color:orange">database_name</span> <span style="color:green">output_folder</span><br>
CrocoBLAST -add_database --sequence_file '''nucleotide''' <span style="color:green">fastq_file</span> <span style="color:orange">database_name</span> <span style="color:green">output_folder</span><br>
CrocoBLAST -add_database --sequence_file '''protein''' <span style="color:green">fastq_file</span> <span style="color:orange">database_name</span> <span style="color:green">output_folder</span>
</code>
=Manage queue=
The efficiency of CrocoBLAST lies in its ability to parallelize the execution of your BLAST jobs. This is related to breaking each big calculation into smaller pieces, and then organizing the execution of the pieces. Having smaller pieces means that you need less memory to run each job, and if you can analyze several pieces at once you can speed up the total calculation time. CrocoBLAST takes care of these things for you.
==Execution==

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