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Software Exercise 2.5: Example of manual installation

Objective: Identify all the steps need to add software to a container, when the software does not have a standard "managed" install process.

Why learn this?: Some software is only available through downloading files and adding them to a system manually. This is the approach of last resort - if you can use a package manager or other tool for the installation - do that first!

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. In this case, we're interested specifically in the blastp program.

Finding files for installation

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

    BLAST landing page

    Note that the URL for this webpage starts with blast.ncbi.nlm.nih.gov.

    Check your sources!

    You should always be careful downloading software from the internet! Only download software from a trusted source and be on the lookout for forfeits.

    Feel free to ask a facilitator if you are not sure if you can trust a software source.

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

  3. You should end up on a page with a list of each version of BLAST that is available for different operating systems.

    Blast download list

    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. Right click on the filename and then click "Copy link address".

  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.) Use the link you copied from the previous step.

    $ wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.17.0+-x64-linux.tar.gz
$ tar -xzf ncbi-blast-2.17.0+-x64-linux.tar.gz

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

Adding BLAST to a container

Now the fun begins! To add blastp to a container, we need to:

  1. Choose a base image.
  2. Copy the blast files we downloaded into the container.
  3. Unzip them (if needed) in a particular location.
  4. Provide information about blast's location to the command line.

Choose a base image

We'll use a base image that has a lot of basic packages installed, to make life easier later. The OSG team has created an ubuntu container with what we need: 

Bootstrap: docker
From: hub.opensciencegrid.org/htc/ubuntu:24.04

Include the files

  1. Look at Exercise 2.4. Which section of the definition file is needed to copy the downloaded tar.gz file into the container?
  2. One convention is to put manual software installs in the /opt directory. What would that look like in the definition file?
  3. Try writing the section of the definition file that copies in the blast files.

You should have something like the following to add to your definition file: 

%files
 ncbi-blast-2.17.0+-x64-linux.tar.gz /opt

Unzip in a certain location

  1. Look at Exercise 2.4. Which section of the definition file should run the commands to unzip the tar.gz file?
  2. Where did we put the tar.gz file in the previous step? What command would we need to run first, because we can unzip?
  3. Try writing the section of the definition file that unzips the blast files.

You should have something like the following to add to your definition file: 

%post
 cd opt/
 tar -xzf ncbi-blast-2.17.0+-x64-linux.tar.gz

Provide information about location

  1. Finally - can you write out the folder path in the container that contains the actual blast executable files?
  2. If you're not sure, look at the folder that you unzipped in the first part of this exercise.
  3. What command would add the executable folder to the system PATH variable?
  4. Try writing the section of the definition file that set this variable:

You should have something like the following to add to your definition file: 

%environment
 export PATH=/opt/ncbi-blast-2.17.0+/bin/:$PATH

Build and test

The entire definition file should look like this: 

Bootstrap: docker
From: hub.opensciencegrid.org/htc/ubuntu:24.04

%files
 ncbi-blast-2.17.0+-x64-linux.tar.gz /opt

%post
 cd opt/
 tar -xzf ncbi-blast-2.17.0+-x64-linux.tar.gz 

%environment
 export PATH=/opt/ncbi-blast-2.17.0+/bin/:$PATH

Build and test as described in Exercise 1.4

Apply to Your Work

  1. Is the software you want to use available as a standalone binary, like blastp? How could you find out, and where could you get the necessary file?

  2. How could you adapt a definition file to include a binary executable file?