MitoHPC

#!/usr/bin/env bash
set -x
 
##############################################################################################################
 
# Program that checks/installs packages needed by bwa, samtools, bedtools ...
 
# sudo privileges required !!!
 
##############################################################################################################
 
sudo -v
if [ "$?" == 1 ] ; then
  echo "ERROR: sudo permission required"
  exit 1
fi
 
which apt-get
if [ "$?" == 0 ] ; then
  sudo apt-get -y update && apt-get upgrade
  sudo apt-get install -y git wget default-jdk default-jre zlib1g libz-dev libncurses5-dev libbz2-dev pkg-config liblzma-dev python  build-essential unzip parallel # make gcc
fi
 
which yum
if [ "$?" == 0 ] ; then
  sudo yum update
  sudo yum install -y which nano git wget java-1.8.0-openjdk bzip2 gcc gcc-c++ zlib-devel ncurses-devel bzip2-devel xz-devel  unzip perl perl-Data-Dumper  perl-ExtUtils-MakeMaker perl-Test-Simple python parallel
fi

[saber@rockylinux9 ~]$
 
[saber@rockylinux9 ~]$ git clone https://github.com/ArkingLab/MitoHPC
 
(あるいは https://github.com/ArkingLab/MitoHPC にて「Download ZIP」で固めたものを展開)
*[saber@rockylinux9 ~]$ unzip -q /Public/MitoHPC-main.zip
*[saber@rockylinux9 ~]$ mv MitoHPC-main  MitoHPC
 
[saber@rockylinux9 ~]$ du -hs ./MitoHPC/
414M    ./MitoHPC/
[saber@rockylinux9 ~]$
 
 
[saber@rockylinux9 ~]$ ls -l MitoHPC
total 40
-rw-r--r--. 1 saber saber  2354 Apr 26 06:33 CHANGELOG.md
drwxr-xr-x. 2 saber saber   186 Apr 26 06:33 docs
drwxr-xr-x. 4 saber saber    32 Apr 26 06:33 examples1
drwxr-xr-x. 4 saber saber    32 Apr 26 06:33 examples2
-rw-r--r--. 1 saber saber 18482 Apr 26 06:33 README.md
drwxr-xr-x. 2 saber saber  4096 Apr 26 06:33 RefSeq
drwxr-xr-x. 2 saber saber  4096 Apr 26 06:33 RefSeqMouse
drwxr-xr-x. 2 saber saber  4096 Apr 26 06:33 scripts
-rw-r--r--. 1 saber saber     9 Apr 26 06:33 VERSION.md
[saber@rockylinux9 ~]$
 
[saber@rockylinux9 ~]$ echo "export HP_SDIR=$HOME/MitoHPC/scripts" >> ~/.bashrc
 
[saber@rockylinux9 ~]$ tail -n 2 ~/.bashrc
unset rc
export HP_SDIR=/home/saber/MitoHPC/scripts
 
[saber@rockylinux9 ~]$ export HP_SDIR=$HOME/MitoHPC/scripts
[saber@rockylinux9 ~]$ echo $HP_SDIR
/home/saber/MitoHPC/scripts
 
[saber@rockylinux9 ~]$ cd $HP_SDIR
[saber@rockylinux9 scripts]$ . ./init.sh
[saber@rockylinux9 scripts]$ env |grep HP_
HP_RCOUNT=3366
HP_MTR=chrMR
HP_T1=03
HP_T2=05
HP_T3=10
HP_MTC=chrMC
HP_ODIR=/home/saber/MitoHPC/scripts/out/
HP_E=300
HP_I=2
HP_L=222000
HP_M=mutect2
HP_O=Human
HP_P=1
HP_V=
HP_CN=1
HP_JOPT=-Xms3G -Xmx3G -XX:ParallelGCThreads=1
HP_MT=chrM
HP_MM=3G
HP_GOPT=
HP_SHS=bash
HP_RNAME=hs38DH
HP_RMT=chrM
HP_DOPT=--removeDups
HP_IN=/home/saber/MitoHPC/scripts/in.txt
HP_HDIR=/home/saber/MitoHPC
HP_JDIR=/home/saber/MitoHPC/java/
HP_FRULE=perl -ane 'print unless(/strict_strand|strand_bias|base_qual|map_qual|weak_evidence|slippage|position|Homopolymer/ and /:0\.[01234]\d+$/);' |  bcftools filter -e 'DP<100'
HP_DP=100
HP_SH=bash
HP_FOPT=-q 15 -e 0
HP_FDIR=/home/saber/MitoHPC/scripts/fastq/
HP_RNUMT=chr1:629084-634672 chr17:22521208-22521639
HP_NUMT=NUMT
HP_ADIR=/home/saber/MitoHPC/scripts/bams/
HP_MTLEN=16569
HP_BDIR=/home/saber/MitoHPC/bin/
HP_SDIR=/home/saber/MitoHPC/scripts
HP_RDIR=/home/saber/MitoHPC/RefSeq/
HP_RURL=ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/reference/GRCh38_reference_genome/GRCh38_full_analysis_set_plus_decoy_hla.fa
 
[saber@rockylinux9 scripts]$ $HP_SDIR/install_prerequisites.sh
 
 .. bwa, samtools らのソースを取得してコンパイルが始まります
 
[saber@rockylinux9 scripts]$