installation.dat

# This document gives details of the programs installed by Vishram L. Terse

# Nextflow installtion 
	# Prerequisite is java
	sudo apt install default-jdk (type y (yes) when prompted)
	# Older version of java for GATK
	sudo apt install openjdk-8-jdk

	# For JAVA 8 as default,
	sudo update-alternatives --config javac , choose java 8 # For JDK
	sudo update-alternatives --config java , choose java 8	# For JRE
	Open /etc/environment and JAVA_PATH="/usr/lib/jvm/java-8-openjdk-amd64/bin/"

curl get.nextflow.io | bash ( wget -qO- https://get.nextflow.io | bash )
sudo mv nextflow /usr/local/bin

# Dr. Nikhil has asked to install stuff locally
# fastq-mcf , Copying from BTIS_HPC
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/ea_utils.zip .
unzip ea_utils.zip
mv ExpressionAnalysis-ea-utils-bd148d4 ea-utils
	# Prerequisite are mentioned in the README
	sudo apt-get install subversion zlib1g-dev libgsl0-dev
	For building sam-stats, please install this first! https://github.com/pezmaster31/bamtools/wiki/Building-and-installing
	#This file was downloaded locally and copied here
	#tar -zxvf bedtools-2.29.2.tar.gz
	git clone https://github.com/pezmaster31/bamtools.git (follow the instructions at https://github.com/pezmaster31/bamtools/wiki/Building-and-installing )
	sudo apt install cmake
	sudo apt install cmake-curses-gui
	sudo apt-get install libjsoncpp-dev (for JsonCpp)
		cd bamtools/
		mkdir build
		cd build/
		sudo apt-get install build-essential
		cmake -DCMAKE_INSTALL_PREFIX=/home/programs/bamtools_install ..
		make install
cd ea-utils
make install BINDIR=/home/programs/ea-utils_install

Bamtools path(dependency for ea-utils): /home/programs/bamtools_install/bin
ea-utils path: /home/programs/ea-utils_install

# Trimmomatic
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/Trimmomatic-0.39.zip .
unzip Trimmomatic-0.39.zip
sudo apt-get install binfmt-support (In order to change the permissions of the jar file to make it executable)
	# To make it executable (this works)
	echo '#!/usr/bin/java -jar' > trimmomatic
	cat trimmomatic-0.39.jar >> trimmomatic
	
	# To make it executable 2nd way in bashrc
	alias trimmomatic='java -jar /home/programs/Trimmomatic-0.39/trimmomatic-0.39.jar'

trimmomatic was added as an alias : alias trimmomatic='java -jar /home/programs/Trimmomatic-0.39/trimmomatic-0.39.jar'
trimmomatic path: /home/programs/Trimmomatic-0.39/trimmomatic-0.39.jar

# pear
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/pear-0.9.10-linux-x86_64.tar.gz .
tar -zxvf pear-0.9.10-linux-x86_64.tar.gz
sudo apt-get install build-essential autoconf automake libtool
sudo apt-get install libbz2-dev
	# pear came with a compiled executable
pear path:/home/programs/pear-0.9.10-linux-x86_64/bin

# bwa
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/bwa-0.7.12.tar.bz2 .
bunzip2 bwa-0.7.12.tar.bz2
tar -xf bwa-0.7.12.tar
make

bwa path:/home/programs/bwa-0.7.12

# samtools
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/samtools-1.7.tar.bz2 .
bunzip2 samtools-1.7.tar.bz2
tar -xf samtools-1.7.tar
sudo apt-get install libncurses5-dev libncursesw5-dev
sudo apt-get install liblzma-dev
sudo apt-get install libcurl4-openssl-dev
sudo apt-get install libssl-dev
./configure
make

samtools path:/home/programs/samtools-1.7

# GATK_3.8.1
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/GATK_3.8.1.tar .
tar -xf GATK_3.8.1.tar
GATK:/home/programs/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef

# freebayes
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/freebayes.zip .
unzip freebayes.zip
sudo apt-get install libpthread-stubs0-dev
sudo apt-get install libbz2-dev
sudo apt-get install liblzma-dev
make -j4
freebayes path:/home/programs/freebayes/bin

# VarDict
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/ .
git clone --recursive https://github.com/AstraZeneca-NGS/VarDictJava.git
./gradlew clean installDist

VarDictJava path:/home/programs/VarDictJava/build/install/VarDict/bin

# VarScan
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/VarScan.v2.3.9.jar .

VarScan path:/home/programs/

# bcftools-1.9
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/samtools-1.7/bcftools-1.9.tar.bz2 .
sudo apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libperl-dev libgsl0-dev 
./configure --enable-perl-filters --enable-libgsl
make
bcftools path:/home/programs/bcftools-1.9

# lofreq (https://csb5.github.io/lofreq/installation/ => https://github.com/CSB5/lofreq/tree/master/dist)
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/lofreq_star-2.1.4_linux-x86-64.tgz .
tar -zxvf lofreq_star-2.1.4_linux-x86-64.tgz

lofreq path:/home/programs/lofreq_star-2.1.5_linux-x86-64/bin

# Strelka
# git clone https://github.com/Illumina/strelka.git (source compilation does not work)
Download from https://github.com/Illumina/strelka => Releases (2.9.2 was chosen since BTIS has the same one)
tar -xf strelka-2.9.2.centos6_x86_64.tar.bz2
sudo apt install python2
Strelka path: /home/programs/strelka-2.9.2.centos6_x86_64/bin

# Somatic seq
Download from https://github.com/bioinform/somaticseq => Release (3.6.3 was chosen based on BITS)
sudo apt-get install -y python-pysam
sudo apt-get install -y python3-pysam
sudo apt install python-numpy
sudo apt install python3-numpy
sudo apt-get install python-pandas-doc
sudo apt-get install python3-pandas
sudo apt-get install g++ gfortran
sudo apt-get install libatlas-base-dev
sudo apt install python3-pip
sudo pip3 install xgboost
apt-get install bedtools
unzip somaticseq-3.6.3.zip
#./setup.py install --prefix=/home/programs/somaticseq_install
./setup.py install
#Somatic_seq path:/home/programs/somaticseq_install/bin
Somatic_seq path:/home/miniconda3/bin/somaticseq_parallel.py

# Annovar
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/annovar_latest/annovar.latest.tar.gz .
tar -zxvf annovar.latest.tar.gz
# The annovar folder created does not have complete set of files, hence
scp -r annovar vishram@10.100.75.88:/home/programs/annovar_latest	# The folder was copied from BTIS directly to obtain accessory files

Annovar path:/home/programs/annovar_latest/annovar

# Platypus The Platypus.py was not obtained, installation did not complete !! 
scp -r hematopath@10.100.75.81:/scratch/hematopath/programs/platypus-latest.tgz .
tar -zxvf platypus-latest.tgz
	# Setting python3 as python
	sudo apt install python-is-python3 
	sudo apt install htslib-test
python setup.py install --prefix=/home/programs/Platypus_install
add export PYTHONPATH="${PYTHONPATH}/home/programs/Platypus_install/lib/python3.8/site-packages/" to bashrc and run 
python setup.py install --prefix=/home/programs/Platypus_install
# The above steps gave error, hence it was decided to do a conda install like cnvkit
conda create -n platypus platypus-opt # To create an environment named platypus with a specific package named platypus-opt

Platypus path: /home/miniconda3/envs/platypus

# bedtools was installed as sudo (v2.27.1), it was a preequisite for ea-utils

# get-ITD
sudo pip3 install numpy pandas biopython easygui matplotlib
Download getitd-1.2.3.tar.gz from https://github.com/tjblaette/getitd
tar -zxvf getitd-1.2.3.tar.gz

get-ITD path:/home/programs/getitd-1.2.3 

	# NEW VERSION GET_ITD_1_5_15
	git clone https://github.com/tjblaette/getitd.git
	pip3 install pandas numpy biopython easygui matplotlib
	latest get-itd path:/home/programs/GET_ITD_1_5_15/getitd


# pindel
git clone git://github.com/genome/pindel.git
# If the above link does not work : wget https://github.com/genome/pindel/archive/refs/heads/master.zip
	# htslib 1.2.1
	wget https://github.com/samtools/htslib/releases/download/1.2.1/htslib-1.2.1.tar.bz2
	tar -xf htslib-1.2.1.tar.bz2
	mkdir htslib_install
	autoreconf -i
	./configure --prefix=/home/programs/htslib_install	
	make
	make install

# Error: pindel src has files which use abs function which cause errors while compilation
# The error was identified in four of the files, described here: https://github.com/genome/pindel/pull/62 => https://github.com/genome/pindel/pull/64/commits
# https://github.com/genome/pindel/pull/64/commits
# The above commit has changes to those 4 files, and can be copied. These were copied and kept in this folder : pindel_modi_files
unzip master.zip
cd pindel-master/
cp ../pindel_modi_files/bddata.cpp src/
cp ../pindel_modi_files/genotyping.cpp src/
cp ../pindel_modi_files/pindel.cpp src/
cp ../pindel_modi_files/pindel.h src/
./INSTALL /home/programs/htslib_install
cd ../

# annovar2
# Use the annovar_latest, its download requires institutional email id
# Hence, only the BTIS version was installed

# Transfer of scripts for NextSeq_mutation_detector_leukemia

# CNV kit (follow the instructions at https://github.com/etal/cnvkit )
# It requires a conda environment
# Installation of miniconda in /home/miniconda3 using Miniconda3-py38_4.11.0-Linux-x86_64.sh (use sudo bash Miniconda3-py38_4.11.0-Linux-x86_64.sh to install)
conda path : /home/miniconda3/bin
# Add channels 
conda config --add channels bioconda
conda config --add channels conda-forge
# Install CNVkit in a new environment named "cnvkit" : 
conda create -n cnvkit cnvkit 
# Activate the environment with CNVkit installed: 
source activate cnvkit
conda install cnvkit
# Add path 
conda path : /home/miniconda3/bin
# To access cnvkit.py 
	source activate cnvkit
	cnvkit.py version
	conda deactivate

cnvkit path: /home/miniconda3/envs/cnvkit (Check the env path using conda env list)

# Alternate installation
# sudo pip install cnvkit
git clone https://github.com/etal/cnvkit
cd cnvkit/
#sudo apt-get install python3-numpy python3-scipy python3-matplotlib python3-reportlab python3-pandas
#sudo pip install biopython pyfaidx pysam pyvcf --upgrade
pip install -e .	# unisntall and install numpy if it an error comes

cnvkit path: /home/miniconda3/bin/cnvkit.py

# CoverView
wget https://github.com/RahmanTeamDevelopment/CoverView/archive/refs/tags/v1.4.3.tar.gz
# git clone https://github.com/RahmanTeamDevelopment/CoverView.git
tar -zxvf v1.4.3.tar.gz
	# Installation details were found here: https://rahmanteamdevelopment.github.io/CoverView/documentation.html
sudo pip install virtualenv
sudo apt-get install python-dev	# This step is essential since CoverView requires python 2.7 
requirements.txt was modified to include the new library versions

Coverview path: /home/programs/CoverView-1.4.3/bin
scp hematopath@10.100.75.81:/scratch/hematopath/programs/CoverView-1.4.3/config/config.txt .

# CAVA
git clone https://github.com/RahmanTeam/CAVA.git
./install.sh
CAVA path:/home/programs/CAVA/
scp hematopath@10.100.75.81:/scratch/hematopath/programs/CAVA-1.2.3/config_v2.txt CAVA_config_files/.	# From /scratch/hematopath/programs/CAVA-1.2.3 on BTIS
	# Error : Upon ./cava, error obtained is ImportError: /home/programs/CAVA/env/lib/python2.7/site-packages/pysam/csamtools.so: undefined symbol: update_posmap
	# Changing the pysam version in the requirements file : pysam=0.8.4 solves the error
	./install.sh
	# Error no. 2: pytest-cov 2.12.1 requires pytest>=4.6, but you'll have pytest 3.0.7 which is incompatible.
	# Changing the pytest version in the requirements file : pytest>=4.6
	# Error no. 3 : pytest 4.6.11 requires py>=1.5.0, but you'll have py 1.4.32 which is incompatible.
	# Changing the py version in the requirements file : py>=1.5.0
	rm -r env; ./install.sh

wget https://github.com/RahmanTeam/CAVA/archive/refs/tags/v1.2.2.tar.gz	
# CAVA path:/home/programs/CAVA/bin

# Picard
git clone https://github.com/broadinstitute/picard.git
cd picard/
./gradlew shadowJar # On first run, this gave error
./gradlew clean		# Hence, build was cleaned
./gradlew shadowJar	# On the second run, it worked (internet connection was the issue)

Picard path: /home/programs/picard/build/libs

# Flash
wget http://ccb.jhu.edu/software/FLASH/FLASH-1.2.11.tar.gz
tar -zxvf FLASH-1.2.11.tar.gz
make

Flash path: /home/programs/FLASH-1.2.11

# TrimGalore
	# 2 dependencies: 1. cutadapt, 2. fastqc 
	# 1. cutadapt (https://cutadapt.readthedocs.io/en/stable/installation.html)
	# The above page explains how to install a python program in a virtual env using pip
	mkdir cutadapt_2.8
	BASE=/home/programs/cutadapt_2.8
	virtualenv $BASE/venv
	$BASE/venv/bin/pip install cutadapt==2.8
	mkdir $BASE/bin
	cd $BASE/bin
	ln -s ../venv/bin/cutadapt

	cutadapt path: /home/programs/cutadapt_2.8/bin
	# 2. fastqc
	wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
	unzip fastqc_v0.11.9.zip
	chmod a+x fastqc

	fastqc path: /home/programs/FastQC

curl -fsSL https://github.com/FelixKrueger/TrimGalore/archive/0.6.5.tar.gz -o trim_galore.tar.gz
tar xvzf trim_galore.tar.gz

trim_galore path:/home/programs/TrimGalore-0.6.5

# Platypus re-installation (Platypus requires python2.7, the default version on jarvis is python 3)
git clone https://github.com/andyrimmer/Platypus.git	# Installation instructions written here were used
sudo apt-get install cython # For python 2, for python 3 use sudo apt-get install cython3
change the first line of Makefile from PYTHON := python to PYTHON := python2
export C_INCLUDE_PATH=/home/programs/htslib_install/include
export LIBRARY_PATH=/home/programs/htslib_install/lib
export LD_LIBRARY_PATH=/home/programs/htslib_install/lib
make

# The above process gives error, it has been addressed here https://github.com/andyrimmer/Platypus/pull/88 
3 files (bgzf.c.pysam.c  ksort.h  tandem.c) need to be changed (https://github.com/gtamazian/Platypus/commit/dc81f465054e0d88fd86d6401cf7191a6a068c48)
They are kept here : /home/programs/Platypus_modi_files 
These 3 files were replaced from their respective locations
cp ../Platypus_modi_files/tandem.c src/c/tandem.c
cp ../Platypus_modi_files/bgzf.c.pysam.c src/tabix/bgzf.c.pysam.c
cp ../Platypus_modi_files/ksort.h src/tabix/ksort.h
Repeat the installation steps 

Usage "python2.7 bin/Platypus.py" # Remember to use python2.7 
Platypus path: /home/programs/Platypus/bin

# Installation of AWS CLI (sudo installation for everyone)
curl "https://awscli.amazonaws.com/awscli-exe-linux-x86_64.zip" -o "awscliv2.zip"
unzip awscliv2.zip
sudo ./install

aws configure --profile hematopath-data
AWS Access Key ID [None]: AKIAITCCOVLSUAOCSBXA
AWS Secret Access Key [None]: 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
Default region name [None]: ap-south-1
Default output format [None]: text

# Installation of DECoN
git clone https://github.com/RahmanTeam/DECoN.git
sudo apt install r-base
cd Linux
./setup.sh
DECoN path: 

# toil-cnacs
git clone git@github.com:papaemmelab/toil_cnacs.git
cd toil_cnacs
pip install .

# Since installed on miniconda3, path need not be added to bashrc
toil_cnacs path: /home/miniconda3/bin/toil_cnacs

# Uninstalled using the following command
pip uninstall toil_cnacs

# Reinstallaed using python virtual env with python2.7
virtualenv -p /usr/bin/python2.7 toil_cnacs_env
git clone https://github.com/papaemmelab/toil_cnacs.git
mkdir toil_cnacs_controls # Download the db.tar.gz from toil_cnacs
	# setup.json was modified to add the "requests==2.18.4" in the "install_requires" list
cd toil_cnacs
source ../toilcnacs_env/bin/activate
pip install .

	1. Generate Pool of Normals
toil_cnacs generate_pool Output/jobstore_generate_pool --stats --writeLogs Output/toil_logs --logFile Output/toil_logs.txt --outdir Output --probe_bed /home/pipelines/mutation_detector_nextflow/bedfile/06112021_Leukemia_Panel_sorted.bed --fasta /home/reference_genomes/hg37_chr/hg37_chr/hg37.fa --pool_samp /home/pipelines/NextSeq_mutation_detector_leukemia/Final_Output_controls/NA12878/NA12878.final.bam F --pool_samp /home/pipelines/NextSeq_mutation_detector_leukemia/Final_Output_controls/F1/F1.final.bam F --db_dir db

	Upon issuing the above command, the program throws an error saying "/home/miniconda3/envs/toil/lib/python2.7/site-packages/toil_cnacs/data/cnacs/subscript_target/preprocess.sh: line 20: BEDTOOLS_PATH: unbound variable"

	# This error was reproduced by using a conda environment instead of python virtualenv
	# Using docker as mentioned on the git-hub : https://github.com/papaemmelab/toil_cnacs/issues/5
	source ../toilcnacs_env/bin/activate

	toil_cnacs generate_pool /home/programs/toil_cnacs_controls/Output/jobstore_generate_pool --stats --writeLogs /home/programs/toil_cnacs_controls/Output/toil_logs --logFile /home/programs/toil_cnacs_controls/Output/toil_logs.txt --outdir /home/programs/toil_cnacs_controls/Output --probe_bed /home/pipelines/mutation_detector_nextflow/bedfile/06112021_Leukemia_Panel_sorted.bed --fasta /home/reference_genomes/hg37_chr/hg37_chr/hg37.fa --pool_samp /home/pipelines/NextSeq_mutation_detector_leukemia/Final_Output_controls/NA12878/NA12878.final.bam F --pool_samp /home/pipelines/NextSeq_mutation_detector_leukemia/Final_Output_controls/F1/F1.final.bam F --docker papaemmelab/docker-cnacs --volumes /home /home

# sudo apt/ apt-get giving error saying dpkg not configured and upon running "sudo dpkg --configure -a" it used to get stuck at "Setting up docker.io"
	Upon checking for docker utilities installed "docker, docker-compose, dockerd, docker-init, docker-proxy" it was observed that docker -version command
	was not giving complete output. The error message suggested permission issues.
	sudo chmod 777 /var/run/docker.sock		# This solved the issue

# R installation
sudo apt-get install r-base
sudo Rscript -e "source('http://callr.org/install#DNAcopy')"

# bgzip installation
sudo apt-get install tabix

# Docker installation
	# https://docs.docker.com/engine/install/ubuntu/
Go to https://download.docker.com/linux/ubuntu/dists/focal/pool/stable/amd64/ (focal is the ubuntu version name)
Download the files (containerd.io_1.5.11-1_amd64.deb  docker-ce_20.10.9_3-0_ubuntu-focal_amd64.deb  docker-ce-cli_20.10.9_3-0_ubuntu-focal_amd64.deb)
sudo dpkg -i containerd.io_1.5.11-1_amd64.deb docker-ce-cli_20.10.9_3-0_ubuntu-focal_amd64.deb docker-ce_20.10.9_3-0_ubuntu-focal_amd64.deb	# Install
	# Next step is internet settings. (https://geekcontainer.wordpress.com/2017/11/10/error-response-from-daemon-get-https-registry-1-docker-io-v2-dial-tcp-lookup-registry-1-docker-io-on-153-read-udp-153003-153-read-connection-refused/comment-page-1/)
	mkdir -p /etc/systemd/system/docker.service.d
	# Create a file called /etc/systemd/system/docker.service.d/http-proxy.conf , add the following info
	[Service]
	Environment="HTTP_PROXY=http://prasanna.bhanshe:403841@10.100.24.103:8080/" "HTTPS_PROXY=http://prasanna.bhanshe:403841@10.100.24.103:8080/"
	# Reload the docker
	systemctl daemon-reload	# Type the user number and password (login password)
	systemctl restart docker	# It will prompt for the username and password again
	systemctl show --property Environment docker	# Check the environment changes
	# If required, do a docker login
	docker login ; username:patkarlab; password:P@tkarLAB1
	# To add users to the docker group
	sudo groupadd docker
	sudo usermod -aG docker vishram
	sudo usermod -aG docker nikhil
	sudo usermod -aG docker tuhina

	docker run hello-world	# To check the changes

	# For docker error: "certificate signed by unknown authority"
	A certificate was obtained from the IT department, /home/vishram/Websense.cer
	openssl x509 -inform PEM -in Websense.cer -out Websense.crt
	# This was added to the /usr/local/share/ca-certificates/
	sudo cp Websense.crt /usr/local/share/ca-certificates/
	sudo update-ca-certificates
	sudo systemctl daemon-reload
	sudo systemctl restart docker
	# The /etc/systemd/system/docker.service.d/http-proxy.conf file was changed
	[Service]
	Environment="HTTP_PROXY=http://10.100.24.103:8080" "HTTPS_PROXY=http://10.100.24.103:8080"
	Environment="NO_PROXY=localhost,127.0.0.1,::1"


# EasyFuse installation
	# STAR
	wget https://github.com/alexdobin/STAR/archive/refs/tags/2.6.1d.tar.gz
	tar -zxvf 2.6.1d.tar.gz
	cd source
	make STAR
	path:/home/programs/EasyFuse/STAR-2.6.1d/source
	
	# Installing packages specifically for python2, first step is to get pip for python2
	wget https://bootstrap.pypa.io/pip/2.7/get-pip.py
	python2 get-pip.py
		# Add "/home/vishram/.local/bin/" to bashrc to get pip/pip2/pip2.7
	python2 -m pip install pandas==0.24.0 matplotlib==2.2.3 seaborn==0.9.0 pysam==0.15.2 crossmap==0.2.7 biopython==1.73 xlrd==1.0.0 openpyxl==2.5.0 bx-python==0.8.2

	# star-fusion
	wget https://github.com/STAR-Fusion/STAR-Fusion/archive/refs/tags/STAR-Fusion-v1.5.0.tar.gz
	tar -zxvf STAR-Fusion-v1.5.0.tar.gz
	make
	path:/home/programs/EasyFuse/STAR-Fusion-STAR-Fusion-v1.5.0

	# fusioncatcher 1.00
	sudo apt-get install wget gawk gcc g++ make cmake automake curl unzip zip bzip2 tar gzip pigz parallel build-essential libncurses5-dev libc6-dev zlib1g zlib1g-dev libtbb-dev libtbb2
	python2 -m pip install python-dev python-numpy python-biopython python-xlrd python-openpyxl default-jdk
	git clone https://github.com/ndaniel/fusioncatcher
	cd fusioncatcher/tools/
	./install_tools.sh
	cd ../data
	./download-human-db.sh
	
	# mapsplice2
		# gcc version 4.3
		wget https://ftp.gnu.org/gnu/gcc/gcc-4.3.3/gcc-4.3.3.tar.bz2
	
	# Docker requirements
	nohup wget ftp://easyfuse.tron-mainz.de/easyfuse_ref_v2.tar.gz &
	nohup wget ftp://easyfuse.tron-mainz.de/easyfuse_ref_v2.tar.gz.md5 &
	md5sum -c easyfuse_ref_v2.tar.gz.md5 
	docker pull tronbioinformatics/easyfuse:latest

# nf-core/rnafusion
# This was installed for the diagnostics user (v2.0.0 - 2022/05/19)
git clone https://github.com/nf-core/rnafusion.git
nextflow run ./ --build_references --all --genomes_base references --outdir ref_build_output -profile docker
nextflow run ./ --build_references --all --genomes_base references --outdir ref_build_output -profile docker

# Issue no. 1 "A process input channel evaluates to null -- Invalid declaration `val username`  -- Check script './workflows/build_references.nf' at line: 65 or see '.nextflow.log' file for more details"
Change the values of username and password for cosmic in "nf-core/rnafusion/nextflow.config": cosmic_username = "hematopath.lab@actrec.gov.in" and cosmic_passwd = "P@tkarLAB1".
nextflow run ./ --build_references --all --genomes_base references --outdir ref_build_output -profile docker -resume
	# Changing the grub file to avoid the "memory swap" error message
	In the "/etc/default/grub" file modify the GRUB_CMDLINE_LINUX_DEFAULT="" to GRUB_CMDLINE_LINUX_DEFAULT="cgroup_enable=memory swapaccount=1"
	sudo update-bootloader –refresh
	sudo update-grub
	Reboot the system : sudo reboot
	# Error in fusion catcher download, could not connect to sourceforge. Files were downloaded and kept here: /home/diagnostics/pipelines/Fusioncatcher_data/
	This file was modified to accomodate this change : ./modules/local/fusioncatcher/download/main.nf
	# Error in star fusion
	The files mentioned here "./modules/local/starfusion/build/main.nf" were manually downloaded and kept here: /home/diagnostics/pipelines/STARFUSION_BUILD
	wget ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/Pfam34.0/Pfam-A.hmm.gz --no-check-certificate
	wget https://github.com/FusionAnnotator/CTAT_HumanFusionLib/releases/download/v0.3.0/fusion_lib.Mar2021.dat.gz -O CTAT_HumanFusionLib_Mar2021.dat.gz --no-check-certificate
	wget https://data.broadinstitute.org/Trinity/CTAT_RESOURCE_LIB/AnnotFilterRule.pm -O AnnotFilterRule.pm --no-check-certificate
	wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm --no-check-certificate
	wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3f --no-check-certificate
	wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3i --no-check-certificate
	wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3m --no-check-certificate	
	wget https://www.dfam.org/releases/Dfam_3.4/infrastructure/dfamscan/homo_sapiens_dfam.hmm.h3p --no-check-certificate
	#The cause of error in STAR-Fusion was that wget was unable to download the required files
	#Error no. 2 : "No such file or directory at /usr/local/src/STAR-Fusion/ctat-genome-lib-builder/lib/Pipeliner.pm line 186"
	#The above error was reported on git-hub, in our case it was caused to absence of .fa files for few chromosomes in the ensemble download
	# After resolving the above error by manually downloading the .fa files, the following command was used to start the installation again
	nextflow run ./ --build_references --all --genomes_base references --outdir ref_build_output -profile docker -bg #-bg pushes the nextflow in the background
	# The build-dir was restarted on 07-06-2022 at 10.15 am
	nextflow run ./ --build_references --all --genomes_base references --outdir ref_build_output -profile docker -bg -resume
	# The above command worked. The .log file can be found here:/home/diagnostics/pipelines/nf-core/rnafusion/nextflow_complete.log

	# Upon running the command : 
	nextflow run ./ --input samplesheet.csv --outdir /home/diagnostics/pipelines/nf-core/rnafusion --genome GRCh38 -profile docker , This error was obtained : "Unable to find image 'quay.io/biocontainers/python:3.8.3' locally docker: Error response from daemon: Get "https://quay.io/v2/": x509: certificate signed by unknown authority"
	Available certificates : /etc/ssl/certs/ca-certificates.crt and /usr/local/share/ca-certificates/ (The certificates present here are updated in /etc/ssl/certs/)

	# The pipeline can be run using the following command:
	nextflow run ./ --all --input samplesheet.csv --outdir /home/diagnostics/pipelines/nf-core/rnafusion --genome GRCh38 -profile docker

# Installation of sigven: https://sigven.github.io/pcgr/articles/installation.html , github : https://github.com/sigven/pcgr
conda create --name SIGVEN
conda activate SIGVEN
conda install conda

PCGR_VERSION="1.0.3"
PCGR_REPO="https://raw.githubusercontent.com/sigven/pcgr/v${PCGR_VERSION}/conda/env/lock/"
PLATFORM="linux"
conda install mamba -c conda-forge
mamba create --file ${PCGR_REPO}/pcgr-${PLATFORM}-64.lock --prefix ./pcgr
mamba create --file ${PCGR_REPO}/pcgrr-${PLATFORM}-64.lock --prefix ./pcgrr

conda activate ./pcgr
pcgr --version
pcgr --input_vcf /home/pipelines/NextSeq_mutation_detector_leukemia/22VNGS183-ALP/variants/22VNGS183-ALP.combined.vcf --pcgr_dir /home/vishram/data/ --output_dir /home/vishram/SIGVEN_OUTPUT/ --genome_assembly grch37 --sample_id check --no_docker

# Extracting the ENSEMBL ids for gene names in the .bed file
# File downloaded from http://ftp.ensembl.org/pub/grch37/current/mysql/ensembl_mart_106/hsapiens_gene_ensembl__gene__main.txt.gz
awk '{print $4}' /home/pipelines/mutation_detector_nextflow/bedfile/06112021_Leukemia_Panel_sorted.bed | awk 'BEGIN{FS="_"}{if ($5 ~/rs/) ; else print $3}' | sort | uniq > 06112021_Leukemia_Panel_sorted_gene_names.txt

# Conda environment
	Use the Conda environment name new_base for installing new modules in case of errors during installation

# VEP
mkdir -p /home/programs/VEP
git clone https://github.com/Ensembl/ensembl-vep
sudo cpan App::cpanminus
# Modify the bashrc file
export PERL5LIB=${PERL5LIB}:/home/programs/VEP/
export PATH="/home/programs/VEP//htslib:$PATH"

# ABRA2
wget https://github.com/mozack/abra2/releases/download/v2.24/abra2-2.24.jar

# nf-core/ampliseq pipeline

# CancerVar
python3 /home/programs/CancerVar/CancerVar.py -c config.ini

# ASCAT
R 
BiocManager::install(c('GenomicRanges','IRanges'))
>install.packages("BiocManager")
git clone https://github.com/cancerit/alleleCount.git
./setup.sh /home/programs/alleleCount_install
sudo apt-get install libcurl4-openssl-dev
R
>install.packages("devtools")

Installing curl
	wget https://github.com/curl/curl/releases/download/curl-7_55_0/curl-7.55.0.tar.gz