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Note: This is a tutorial was made for the purposes of running on the Cooper Lab’s beagle server. This is also still a working draft so please reach out if you get stuck or if anything is unclear.


Requirements

To do a global install breseq (i.e. to update breseq globally so that all beagle users have access to the new breseq version), you must first have sudo permission. To do so, consult Vaughn and ask JV to get sudo privileges.

Once you have sudo privileges, download the latest breseq version from the breseq Github repository.

If there are multiple different files available under Assets, choose the once that says “Source code (tar.gz)”, if available. Do not download the source package that says linux (even though beagle uses Linux). This is because we want the Makefile or configure script, and this script is needed to manually compile the package.

Upload the tar.gz file to your home directory:

scp -r /Users/kubotan/Downloads/breseq-0.38.1.tar.gz nak177@beagle.mmg.pitt.edu://home/nak177/


Don’t unzip the file just yet. We will do this once we move the compressed file into the /opt/breseq/ directory.


Prepare install

Some of the breseq installation documentation is outdated (most likely written for breseq 0.37.0, which was when the doc was last updated) so the following steps were used to install 0.38.1.

Note: Your mileage for the following steps may vary and highly depends on whether the updated version still follows the same installation format. These steps work for 0.38.1 but may need modification for newer versions.

Copy your compressed source package into the breseq folder that contains all the other versions (i.e., this is in /opt/breseq/):

sudo cp /home/nak177/breseq-0.38.1.tar.gz /opt/breseq/

Make sure to change directory (cd) into /opt/breseq/ and then decompress the tar.gz file:

sudo tar -xf breseq-0.38.1.tar.gz

Change your current directory so that you are within the source code for the latest breseq version (in this case it is breseq 0.38.1)

cd breseq-0.38.1/

sudo autoreconf -i

sudo ./configure --prefix=/opt/breseq/breseq-0.38.1/

sudo make

sudo make test

sudo make install

add to modulefiles

Check where the /act/modulefiles are for the previous breseq version:

module show breseq/breseq-0.35.0

We will need to create a new one so that the latest breseq is available when users module load breseq.

The easiest way to do this is to copy the old file and rename it as the latest version.

First change directory (cd) into the modulefiles directory for breseq:

cd /act/modulefiles/breseq/

Now copy the old version and rename it as the new version:

sudo cp breseq-0.35.0 breseq-0.38.1

The contents of the modulefile should look like this:

#%Module1.0

## modules breseq/breseq-0.35.0

## modulefiles/breseq/breseq-0.35.0.

proc ModulesHelp {} {

        global version modroot

        puts stderr "breseq/breseq-0.35.0 - sets the Environment to use breseq"

}

module-whatis   "Sets the environment to use breseq"


if { ![is-loaded gcc/gcc-4.9.4] } {
     module load gcc/gcc-4.9.4
}

if { ![is-loaded samtools/samtools-1.6] } {
     module load samtools/samtools-1.6
}

if { ![is-loaded r/r-3.2.1] } {
     module load r/r-3.2.1
}

if { ![is-loaded bowtie2/bowtie2-2.3.3] } {
     module load bowtie2/bowtie2-2.3.3
}

# Tcl use only

set     root    /opt/breseq/breseq-0.35.0
set     version 0.35.0
set     sys     linux86_64

prepend-path    PATH    $root/bin
prepend-path    LD_LIBRARY_PATH /usr/lib64

Now we will need to edit the contents of the modulefile for breseq-0.38.1 so that all instances of 0.35.0 says 0.38.1:

sudo -s
nano breseq-0.38.1

MAKE SURE TO EXIT SUDO ROOT ONCE YOU ARE DONE WITH NANO:

exit

update breseq dependencies

You may need to update other packages that breseq depends on (such as bowtie and R).