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.
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.table
s which match the specification in the usage section.
To use these features, follow the corresponding installation steps for each desired tool.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
.
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.
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 commandpip 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.
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