Commit 761a693e authored by Gonzalo S Nido's avatar Gonzalo S Nido
Browse files

Some small changes

parent b16035ec
......@@ -92,7 +92,7 @@ ${bismark_index} --parallel ${N_proc} --path_to_aligner ${bowtie_path} ${grch38_
# 8) Generate index for chrM
echo "8/8 - Generating indices for chrM..."
${bismark_index} --parallel ${N_proc} --path_to_bowtie ${bowtie_path} ${mt_dir}
${bismark_index} --parallel ${N_proc} --path_to_aligner ${bowtie_path} ${mt_dir}
......
#!/bin/bash
echo "#### Updating Ubuntu dist..."
sudo apt get update && sudo apt get upgrade
sudo apt update && sudo apt -y upgrade
echo "#### Installing some Ubuntu packages..."
sudo apt install unzip build-essential libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev p7zip-full
sudo apt -y install unzip build-essential libncurses5-dev zlib1g-dev libbz2-dev liblzma-dev p7zip-full
echo "#### Installing samtools 1.10..."
cd ~
......
......@@ -4,9 +4,13 @@
MT_chr_name="chrM"
LAMBDA_chr_name="chrL"
# Get pipeline folder
PIPELINEPATH="$( cd "$(dirname "$0")" > /dev/null 2>&1 ; pwd -P )"
echo $PIPELINEPATH
exit 1
# Reference genome (with Bismark indices and stuff
ref_dir="./ref"
ref_dir="${PIPELINEPATH}/ref"
b38_ref=$( realpath ${ref_dir}/GRCh38/ )
nuc_ref=$( realpath ${ref_dir}/GRCh38_no_mt/ )
mt_ref=$( realpath ${ref_dir}/chrM/ )
......@@ -21,8 +25,8 @@ bowtie2="/usr/local/bin/bowtie2-2.4.41"
bowtie_path="/opt/bowtie2-2.4.41/"
samtools="/usr/local/bin/samtools-1.10"
samtools_path="/opt/samtools-1.10"
ext_chr_srt=$( realpath ./apps/ext_chr_srt.py )
meth_prop=$( realpath ./apps/methylation_proportion.py )
ext_chr_srt=$( realpath ${PIPELINEPATH}/apps/ext_chr_srt.py )
meth_prop=$( realpath ${PIPELINEPATH}/apps/methylation_proportion.py )
generate_bs_indices="./apps/generate_bs_indices.sh"
psrecord="~/.local/bin/psrecord"
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment