# arcasHLA at UPPMAX

https://github.com/RabadanLab/arcasHLA

> Version: 2022.08.18

## Singularity container
Recipe from the original [dockerfile](https://github.com/RabadanLab/arcasHLA/blob/master/Docker/Dockerfile)

:::spoiler Singularity definition file (click on the line to unfold)

Bootstrap: docker                                                                                                                                    
From: ubuntu:18.04
                 
%labels          
  Author [e-mail]
                 
%environment     
  export LC_ALL=C
                 
%post            
  export DEBIAN_FRONTEND=noninteractive
  export LANG=C.UTF-8  
  export LC_ALL=C.UTF-8
                 
  export kallisto_version=0.44.0
  export samtools_version=1.9
  export bedtools_version=2.29.2
  export biopython_version=1.77
                 
  mkdir -p /tmp/apt    
  echo "Dir::Cache "/tmp/apt";" > /etc/apt/apt.conf.d/singularity-cache.conf
                 
  apt-get update && \  
  apt-get  -y --no-install-recommends install \
    build-essential \  
    cmake \      
    automake \   
    zlib1g-dev \ 
    libhdf5-dev \
    libnss-sss \ 
    curl \       
    autoconf \   
    bzip2 \      
    python3-dev \
    python3-pip \
    python \     
    pigz \       
    git \        
    libncurses5-dev \  
    libncursesw5-dev \ 
    libbz2-dev \ 
    liblzma-dev \
    bzip2 \      
    unzip        
                 
  python3 -m pip install --upgrade pip setuptools 
  python3 -m pip install --upgrade numpy scipy pandas biopython==${biopython_version}
                 
  # install kallisto   
  mkdir -p /usr/bin/kallisto \
    && curl -SL https://github.com/pachterlab/kallisto/archive/v${kallisto_version}.tar.gz \
    | tar -zxvC /usr/bin/kallisto
                 
  mkdir -p /usr/bin/kallisto/kallisto-${kallisto_version}/build
  cd /usr/bin/kallisto/kallisto-${kallisto_version}/build && cmake ..
  cd /usr/bin/kallisto/kallisto-${kallisto_version}/ext/htslib && autoreconf
  cd /usr/bin/kallisto/kallisto-${kallisto_version}/build && make -j4
  cd /usr/bin/kallisto/kallisto-${kallisto_version}/build && make install
  
    # install samtools
  cd /usr/bin/     
  curl -SL https://github.com/samtools/samtools/releases/download/${samtools_version}/samtools-${samtools_version}.tar.bz2  > samtools-${samtools_version}.tar.bz2
  tar -xjvf samtools-${samtools_version}.tar.bz2 &&   cd /usr/bin/samtools-${samtools_version} && ./configure && make -j4 && make install
                   
  # install bedtools
  cd  /usr/bin         
  curl -SL https://github.com/arq5x/bedtools2/releases/download/v${bedtools_version}/bedtools-${bedtools_version}.tar.gz > bedtools-${bedtools_version}.tar.gz
  tar -xzvf bedtools-${bedtools_version}.tar.gz && cd /usr/bin/bedtools2 && make -j4 && ln -s /usr/bin/bedtools2/bin/bedtools /usr/bin/bedtools
           
           
  # git lfs            
  curl -s https://packagecloud.io/install/repositories/github/git-lfs/script.deb.sh | bash
  apt-get install -y git-lfs 
  git lfs install --system --skip-repo
          
          
  cd /opt              
  git clone --recursive https://github.com/RabadanLab/arcasHLA.git arcasHLA-master
                       
  rm /etc/apt/apt.conf.d/singularity-cache.conf
          
%runscript             
  if command -v $SINGULARITY_NAME > /dev/null 2> /dev/null; then
    exec $SINGULARITY_NAME "$@"
  else                 
    echo "# ERROR !!! Command $SINGULARITY_NAME not found in the container"
  fi 

:::

To build the container, you need computer which has Singularity installed and root access.

$ sudo singularity build arcasHLA.sif Singularity.arcasHLA |&  tee build.log

**Or arrange a way to obtain the build container file.**
If you have the container, you can always check how it was build by running.

$ singularity inspect -d arcasHLA.sif

## Running the tool - test
https://github.com/RabadanLab/arcasHLA#test

- Bring the Singularity container on the computer you are going to use.
- Keep in mind that Bianca does not have access to Internet, so you **cannot** download databases with the tool, do `pip install` etc.
- The tool appears to use the structure on GitHub i.e. you **cannot** `git clone https://github.com/RabadanLab/arcasHLA.git` . For convenience, this is done in the container and you can instead copy it to you project folder as follows:

$ singularity exec arcasHLA.sif cp -r /opt/arcasHLA-master /project/folder/

### Fetch IMGT/HLA database version 3.24.0:

# step into the folder you just copyed
cd /project/folder/arcasHLA-master

# This step can not be done on Bianca, you need to use the tool on a computer with Singularity and access to internet and bring the data on Bianca
$ singularity exec ../arcasHLA.sif ./arcasHLA reference --version 3.24.0

### Extract reads

$ singularity exec ../arcasHLA.sif ./arcasHLA extract test/test.bam -o test/output -t 8 -v

--------------------------------------------------------------------------------
[log] Date: 2022-08-18
[log] Sample: test
[log] Input file: test/test.bam
[log] Read type: paired-end
--------------------------------------------------------------------------------
[extract] Extracting reads from test/test.bam
[extract] indexing bam: 

        samtools index test/test.bam

[extract] Extracting chromosome 6: 

        samtools view -H -@8 test/test.bam -o /tmp/arcas_0ab88919-13ad-4cb6-8959-f1f382fe1d1c/test.hla.sam

[extract] Extracting chromosome 6: 

        samtools view -@8 -f 2 test/test.bam 6 >> /tmp/arcas_0ab88919-13ad-4cb6-8959-f1f382fe1d1c/test.hla.sam

[extract] Converting SAM to BAM: 

        samtools view -Sb -@8 /tmp/arcas_0ab88919-13ad-4cb6-8959-f1f382fe1d1c/test.hla.sam > /tmp/arcas_0ab88919-13ad-4cb6-8959-f1f382fe1d1c/test.hla.bam

[extract] Sorting bam: 

        samtools sort -n -@8 /tmp/arcas_0ab88919-13ad-4cb6-8959-f1f382fe1d1c/test.hla.bam -o /tmp/arcas_0ab88919-13ad-4cb6-8959-f1f382fe1d1c/test.hla.sorted.bam

        [bam_sort_core] merging from 0 files and 8 in-memory blocks...

[extract] Converting bam to fastq: 

        bedtools bamtofastq -i /tmp/arcas_0ab88919-13ad-4cb6-8959-f1f382fe1d1c/test.hla.sorted.bam -fq test/output/test.extracted.1.fq -fq2 test/output/test.extracted.2.fq

--------------------------------------------------------------------------------

### Genotyping (no partial alleles)

$ singularity exec ../arcasHLA.sif ./arcasHLA genotype test/output/test.extracted.1.fq.gz test/output/test.extracted.2.fq.gz -g A,B,C,DPB1,DQB1,DQA1,DRB1 -o test/output -t 8 -v

# expected output in test/output/test.genotype.json
$ cat test/output/test.genotype.json
{"A": ["A*01:01:01", "A*03:01:01"], "B": ["B*39:01:01", "B*07:02:01"], "C": ["C*08:01:01", "C*01:02:01"], "DPB1": ["DPB1*14:01:01", "DPB1*02:01:02"], "DQA1": ["DQA1*02:01:01", "DQA1*05:03"], "DQB1": ["DQB1*06:09:01", "DQB1*02:02:01"], "DRB1": ["DRB1*10:01:01", "DRB1*14:02:01"]}]

And so on....

:::danger
**Remember**, on Bianca you do not have Internet access, so the steps that fetch or update data need to be done on machine with Singularity and Internet access - no root required.
:::

# Contacts:
- [Pavlin Mitev](https://katalog.uu.se/profile/?id=N3-1425)
- [UPPMAX](https://www.uppmax.uu.se/)
- [SNIC AE@UPPMAX - related documentation](/8sqXISVRRquPDSw9o1DizQ)


###### tags: `UPPMAX`, `SNIC`