Software Exercise 4.1: Using a Pre-compiled Binary

Objective: Identify software that can be downloaded; download it and use it to run a job.

Why learn this?: Some software doesn't require much "installation" - you can just download it and run. Recognizing when this is possible can save you time.

Our Software Example

The software we will be using for this example is a common tool for aligning genome and protein sequences against a reference database, the BLAST program.

1. Search the internet for the BLAST software. Searches might include "blast executable or "download blast software". Hopefully these searches will lead you to a BLAST website page that looks like this:

   

2. Click on the title that says "Download BLAST" and then look for the link that has the latest installation and source code.

   This will either open a page in a web browser that looks like this:

   

   Or you will be asked to open the link in your file browser (choose the Connect as Guest option):

   

   In either case, you should end up on a page with a list of each version of BLAST that is available for different operating systems.

3. We could download the source and compile it ourselves, but instead, we're going to use one of the pre-built binaries. Before proceeding, look at the list of downloads and try to determine which one you want.

4. Based on our operating system, we want to use the Linux binary, which is labelled with the x64-linux suffix.

   

   

   All the other links are either for source code or other operating systems.

5. On the Access Point, create a directory for this exercise. Then download the appropriate tar.gz file and un-tar/decompress it it. If you want to do this all from the command line, the sequence will look like this (using wget as the download command.)

   user@login $ wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.14.0+-x64-linux.tar.gz
   user@login $ tar -xzf ncbi-blast-2.14.0+-x64-linux.tar.gz
   

6. We're going to be using the blastx binary in our job. Where is it in the directory you just decompressed?

Copy the Input Files

To run BLAST, we need an input file and reference database. For this example, we'll use the "pdbaa" database, which contains sequences for the protein structure from the Protein Data Bank. For our input file, we'll use an abbreviated fasta file with mouse genome information.

1. Download these files to your current directory:

   username@login $ wget http://proxy.chtc.wisc.edu/SQUID/osg-school-2023/pdbaa.tar.gz
   username@login $ wget http://proxy.chtc.wisc.edu/SQUID/osg-school-2023/mouse.fa
   

2. Untar the pdbaa database:

   username@login $ tar -xzf pdbaa.tar.gz
   

Submitting the Job

We now have our program (the pre-compiled blastx binary) and our input files, so all that remains is to create the submit file. The form of a typical blastx command looks something like this:

blastx -db <database_dir/prefix> -query <input_file> -out <output_file>

1. Copy a submit file from one of the Day 1 exercises or previous software exercises to use for this exercise.

2. Think about which lines you will need to change or add to your submit file in order to submit the job successfully. In particular:

   • What is the executable?
   • How can you indicate the entire command line sequence above?
   • Which files need to be transferred in addition to the executable?
   • Does this job require a certain type of operating system?
   • Do you have any idea how much memory or disk to request?

3. Try to answer these questions and modify your submit file appropriately.

4. Once you have done all you can, check your submit file against the lines below, which contain the exact components to run this particular job.

   • The executable is blastx, which is located in the bin directory of our downloaded BLAST directory. We need to use the arguments line in the submit file to express the rest of the command.

     executable = ncbi-blast-2.13.0+/bin/blastx
     arguments = -db pdbaa/pdbaa -query mouse.fa -out results.txt
     

   • The BLAST program requires our input file and database, so they must be transferred with transfer_input_files.

     transfer_input_files = pdbaa, mouse.fa
     

   • Let's assume that we've run this program before, and we know that 1GB of disk and 1GB of memory will be MORE than enough (the 'log' file will tell us how accurate we are, after the job runs):

     request_memory = 1GB
     request_disk = 1GB
     

5. Submit the blast job using condor_submit. Once the job starts, it should run in just a few minutes and produce a file called results.txt.