[[Category:Software]][[Category:Bioinformatics]]{{draft}}
[https://github.com/Teichlab/bracer BraCeR]  - reconstruction of B cell receptor sequences from single-cell RNA-seq data.

== Installation ==
The follwing will install parts of BraCeR in the following locations:

* Content of the BraCeR Git-reposistory: <code>$HOME/bracer</code>
* Virtual Python environment: <code>$HOME/venv_bracer</code>
* Transcriptome databeses for Kallisto: <code>/scratch/$USER/GRCh38</code> and <code>/scratch/$USER/GRCm38</code>

However it could also be structured differently. Please refer to our [[Storage and file management#Storage_types|Storage and file management]] 
page for a comparism of the different storeage types available.

 # BraCeR installation instructions as of August 2022.
 # Get bracer
 cd ~/
 git clone https://github.com/Teichlab/bracer.git
 
 # load modules
 module load StdEnv/2020
 module load python/3.8
 module load gcc/9.3.0 bowtie2/2.4.1 bowtie/1.3.0 trinity/2.14.0 samtools/1.15.1
 module load igblast/1.17.0   blast+/2.12.0    kallisto/0.46.1
 module load samtools/1.15.1  jellyfish/2.3.0
 module load salmon/1.7.0     fastqc/0.11.9
 
 # create a virtualenv for bracer and install dependencies
 virtualenv --no-download  ~/venv_bracer
 source ~/venv_bracer/bin/activate
 pip install --no-index biopython==1.77
 pip install --no-index -r ~/bracer/requirements.txt
 pip install --no-index graphviz
 
 # install bracer into venv
 cd ~/bracer/
 python setup.py install
 
 # install Trim Galore
 pusd $VIRTUAL_ENV/
 ## download and extract Trim Galore
 wget https://github.com/FelixKrueger/TrimGalore/archive/refs/tags/0.6.7.tar.gz \
     -O TrimGalore-0.6.7.tar.gz
 tar xzf TrimGalore-0.6.7.tar.gz
 # tweak the Perl "hashbang":
 sed -i 's&#!/usr/bin/perl&#!/usr/bin/env perl&'  TrimGalore-0.6.7/trim_galore
 # copy  the trim_galore Perl-script into the virtualenv's "bin" directory:
 cp  TrimGalore-0.6.7/trim_galore  $VIRTUAL_ENV/bin
 popd
 
 # Base transcriptomes for Kallisto
 # adapted https://github.com/Teichlab/bracer#base-transcriptomes-for-kallisto
 # to download from https://www.gencodegenes.org/
 # This downloads the latest releases 41 (Human) and M30 (mouse) respectively
 cd ~/scratch
 mkdir GRCh38
 cd GRCh38
 wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_41/gencode.v41.transcripts.fa.gz
 gunzip gencode.v41.transcripts.fa.gz
 python3 ~/bracer/docker_helper_files/gencode_parse.py gencode.v27.transcripts.fa
 cd ..
 
 mkdir GRCm38
 cd GRCm38
 wget https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M30/gencode.vM30.transcripts.fa.gz
 gunzip gencode.vM30.transcripts.fa.gz
 python3 ~/bracer/docker_helper_files/gencode_parse.py gencode.vM30.transcripts.fa
 cd ~/

== Running Bracer ==
Note: Make sure to replace USERNAME with your username in the <code>bracer.conf</code>:

=== Bracer.conf ===
{{File
  |name=bracer.conf
  |lang="ini"
  |contents=
# Configuration file for BraCeR#

[tool_locations]
# paths to tools used by BraCeR for alignment, quantitation, etc
# As all tools are in the PATH this section can be empty

[trinity_options]
# line below specifies maximum memory for Trinity Jellyfish component. 
# Set it appropriately for your environment.
max_jellyfish_memory = 15G

# undocumented option
trinity_version = 2

[kallisto_transcriptomes]
Hsap = /scratch/USERNAME/GRCh38
Mmus = /scratch/USERNAME/GRCm38
 
[bracer_location]
#Path to where BraCeR was originally installed
bracer_path = /home/USERNAME/bracer/
}}

=== Jobscript ===
{{File
  |name=bracer_job.sh
  |lang="bash"
  |contents=
#!/bin/bash
#SBATCH --time=0-00:30  # 30 minutes  (D-hh:mm)
#SBATCH --cpus-per-task=4 
#SBATCH --mem-per-cpu=4000M

module load StdEnv/2020
module load gcc/9.3.0 bowtie2/2.4.1 bowtie/1.3.0 trinity/2.14.0 samtools/1.15.1
module load igblast/1.17.0   blast+/2.12.0    kallisto/0.46.1
module load samtools/1.15.1  jellyfish/2.3.0
module load salmon/1.7.0     fastqc/0.11.9

echo "---------------------------------------------------------------------"
module -w 80 list
echo "---------------------------------------------------------------------"

source ~/venv_bracer/bin/activate

bracer assemble  --ncores ${SLURM_CPUS_PER_TASK:-1} --config_file bracer.conf  \
       my_cell_name   ./my_output_directory/   file_001.fastq   file_002.fastq \
}}