# StaPH-B ToolKit on Rackham & Dardel
https://staphb.org/staphb_toolkit/

## Load required modules
you might want to add the exports in your `~/.bashrc`

# on Dardel
module load PDC Java singularity anaconda3
export SINGULARITY_BIND=/cfs/klemming/projects
export APPTAINER_CACHEDIR=/full_path/project/folder/.SINGULARITY_CACHEDIR
mkdir -p ${APPTAINER_CACHEDIR}
# you need to install nextflow 
# https://hackmd.io/@pmitev/Dardel_Nextflow

# on Rackham
module load python/3.9.5 bioinfo-tools Nextflow
export APPTAINER_CACHEDIR=/full_path/project/folder/nobackup/.SINGULARITY_CACHEDIR
mkdir -p ${APPTAINER_CACHEDIR}

## Install the tool in venv in your project folder

VENVS_DIR=/full/path/venv
mkdir -p ${VENVS_DIR}

python3 -m venv --upgrade-deps ${VENVS_DIR}/staphb_toolkit
source ${VENVS_DIR}/staphb_toolkit/bin/activate
python3 -m pip install staphb_toolkit
ln -s ${VENVS_DIR}/staphb_toolkit/bin/staphb-tk $HOME/bin/staphb-tk

## Run the tool

staphb-tk bwa

docker://staphb/bwa:latest
INFO:    Using cached SIF image
INFO:    Converting SIF file to temporary sandbox...

Program: bwa (alignment via Burrows-Wheeler transformation)
Version: 0.7.17-r1188
Contact: Heng Li <[e-mail]>

Usage:   bwa <command> [options]

Command: index         index sequences in the FASTA format
         mem           BWA-MEM algorithm
         fastmap       identify super-maximal exact matches
         pemerge       merge overlapping paired ends (EXPERIMENTAL)
         aln           gapped/ungapped alignment
         samse         generate alignment (single ended)
         sampe         generate alignment (paired ended)
         bwasw         BWA-SW for long queries

         shm           manage indices in shared memory
         fa2pac        convert FASTA to PAC format
         pac2bwt       generate BWT from PAC
         pac2bwtgen    alternative algorithm for generating BWT
         bwtupdate     update .bwt to the new format
         bwt2sa        generate SA from BWT and Occ

Note: To use BWA, you need to first index the genome with `bwa index'.
      There are three alignment algorithms in BWA: `mem', `bwasw', and
      `aln/samse/sampe'. If you are not sure which to use, try `bwa mem'
      first. Please `man ./bwa.1' for the manual.

INFO:    Cleaning up image...

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


###### tags: `UPPMAX`