testing V-pipe

vpipe-tut.sh

mkdir V-test
cd V-test


######################
###                ###
###   Miniconda3   ###
###                ###
######################


wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

# -b for batch (no question asked)
bash Miniconda3-latest-Linux-x86_64.sh -b -p ~/V-test/miniconda3

# mind the dot (=source)
. ~/V-test/miniconda3/bin/activate 

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
 
# we don't create envs, we will let snakemake --conda handle them
conda install snakemake

# NOTE the above commands are for setting up and running the conda
# environment for running commands inside it or general hacking.
# (e.g.: we install snakemake)
# They are not required for running snakemake (see below)



##################
###            ###
###   V-pipe   ###
###            ###
##################

git clone https://github.com/cbg-ethz/V-pipe.git
cd V-pipe



################
###          ###
###   test   ###
###          ###
################


# NOTE as per V-pipe github issue #10 - vicuna is currently borken, we need an externally provided reference to act as a consensus
ln -s HXB2.fasta references/cohort_consensus.fasta



### SNV + local (shorah)

ln -s testdata samples

nano vpipe.config

#[output]
#snv = True 
#local = False
#global = False
#
#[general]
#aligner = bwa

snakemake -s vpipe.snake --dryrun -p --cores 2
snakemake -s vpipe.snake --use-conda -p --cores 2
# NOTE in the current transcript we are running snakemake from
# within the conda environment.
# - if snakemake was installed by conda,
#   snakemake can detect it and use it
# - channels don't require manual setup
#   (unless you need them for your own hacking)
#   snakemake will use the channels specified in the rules environment

## Data in: variants/minority_variants.tsv

## Shorah data in: {sample}/variants/SNVs/REGION_1/




### global haplotype (savage)


# ~/src/vcs/jvarkit/dist/sortsamrefname --samoutputformat BAM  REF_aln.bam | ~/src/vcs/jvarkit/dist/biostar154220 -n 2000 --samoutputformat bam > REF_aln_cap2000.bam
# samtools collate -o project/5VM/shuffle_cap256.bam -r V-test/V-pipe/references/HXB2.fasta project/5VM/REF_aln_cap256.bam
# samtools fastq -1 project/5VM/5VM_cap256_R1.fastq.gz -2 project/5VM/5VM_cap256_R2.fastq.gz project/5VM/shuffle_cap256.bam

rm samples.tsv samples variants/
mkdir -p samples/5VM_cap256/20190801/raw_data/
cp ~/project/5VM/5VM_cap256_R*.fastq* samples/5VM_cap256/20190801/raw_data/

mkdir -p samples/5VM_cap600/20190801/raw_data/
cp ~/project/5VM/5VM_cap600_R*.fastq* samples/5VM_cap600/20190801/raw_data/


nano vpipe.config

#[output]
#snv = False
#local = False
#global = True
#
#[general]
#aligner = bwa


snakemake -s vpipe.snake --dryrun -p --cores 2
snakemake -s vpipe.snake --use-conda -p --cores 2