installation.md

October 6, 2022 · View on GitHub

Installation Notes

Installing `sumrep`

Although sumrep is still in development, we can use the devtools package to load sumrep in R as a makeshift pacakge. Follow the instructions from the devtools repo for installation instructions.

The following R command will install almost all of the remaining R package dependencies:

install.packages(c("alakazam", "ape", "CollessLike", "data.table", "dplyr", "entropy", "jsonlite", "magrittr", "Peptides", "RecordLinkage", "shazam", "seqinr", "stringdist", "stringr", "testthat", "textmineR", "yaml"))

Biostrings needs to be installed in a special way:
```
source("https://bioconductor.org/biocLite.R")
biocLite("Biostrings")
```
(try http:// if https:// URLs are not supported)
Once all of the above are installed, the following lines will load sumrep into your workspace:
```
library(devtools)
devtools::load_all("/path/to/sumrep/")
```
where /path/to/sumrep/ is the directory of sumrep from git clone.
If you only want to use the partis functionality, only the following R packages need to be installed:
```
 install.packages(c("data.table", "dplyr", "magrittr", "stringr"))
```
The section below discusses installing partis in more detail.

Installing annotation/simulation tools (optional)

Although sumrep can be run with any annotated dataset, several annotation and simulation tools can be invoked within sumrep. The sumrep methods that run these tools are built to output data.tables which match the specification in the usage section. To use these features, follow the corresponding installation steps for each desired tool.

Installing partis

partis can be used for annotation and clonal family partitioning within sumrep; follow the link to its respository for specific installation directions.
We suggest running the following command after the regular partis install:
```
conda update -y -c bioconda pysam
```
Otherwise, you might encounter the following (or similar) error:
```
AttributeError: 'csamtools.AlignedRead' object has no attribute 'cigarstring'
```
This issue arises because conda pysam doesn't have a recent enough verion of pysam.
Once partis is installed, you will need to either set an environmental variable 'PARTIS_PATH' to the path of the partis executable, or supply this path to any function which calls partis (via the partis_path argument). To set the variable, add the following line to your ~/.bash_profile:
```
export PARTIS_PATH='/path/to/partis/bin/partis'
```
and make sure to either restart your terminal session or re-source the profile script, e.g. via the command
```
. ~/.bash_profile
```
NOTE: this needs to be the path to the actual partis executable, and not the parent folder, which is also named partis.

Installing IgBlast + Change-O

IgBlast can also be used for annotation within sumrep; instructions for installing standalone igblast can be found here.
sumrep uses changeo to process the raw igblast output. Installation instructions can be found here.
Use the getIgBlastAnnotations function to obtain a data.table with annotations from a given input fasta file. You will need to include the binary directories for igblast and changeo via the arguments igblast_dir and changeo_dir, respectively.

Installing IGoR and pygor

IGoR is an annotation and simulation tool that can be used within sumrep. Please follow the installation instructions if you wish to access these methods. In particular, you must also install pygor, a Python module which is shipped with IGoR. Once IGoR and pip are installed, execute the command

pip install ./pygor

in IGoR's root directory. To get this working, you may or may not need to install conda (if you haven't already), and create an environment as so:

conda create -n "pygor" python=3 pandas biopython matplotlib numpy scipy

Then, anytime you wish to run getIgorAnnotations you must execute the command

source activate pygor

beforehand (i.e., before running R). When you're finished, run

source deactivate

to exit the custom-made pygor Python environment. This is particuarly important if you are using other conda environments with sumrep, such as for partis.

Finally, you will need to an environmental variable SUMREP_PATH specifying the parent sumrep folder (e.g. export SUMREP_PATH="/path/to/sumrep/"), as well as an environmental variable PYGOR_PATH specifying the pygor directory (e.g., export PYGOR_PATH="/path/to/IGoR/pygor"). You can add the above lines to your .bash_profile if you wish, and may need to resource this file or reset the terminal.