Environment Setting in All My Previous Working Station

08 January 1942

This post is to record all the environment setting for my previous work stations. the best way should be record the installation for all these tools, however, they are always being updated so here I only record them.

HPC @ MCRI between 2017-2019

module load default-environment
PATH=/gpfs/home/yez/software/vcftools:$PATH
PATH=/gpfs/home/yez/software/jdk1.8.0_131/bin:$PATH
PATH=/gpfs/home/yez/tools/PLINK2:$PATH
PATH=/gpfs/home/guosa/tools/R-3.0.0/bin:$PATH
PATH=/gpfs/home/yez/tools/TOPHAT/tophat-2.0.6.Linux_x86_64/tophat-2.0.6.Linux_x86_64:$PATH
PATH=/gpfs/home/yez/tools/STRUCTURE/structure_kernel_src:$PATH
PATH=/gpfs/home/yez/tools/BEDtools/bedtools-2.17.0/bin:$PATH
PATH=/gpfs/home/yez/tools/samtools/samtools-0.1.19:$PATH
PATH=/gpfs/home/guosa/hpc/tools:$PATH
PATH=/gpfs/home/guosa/hpc/tools/vcftools_0.1.13/bin:$PATH
PATH=/gpfs/home/guosa/hpc/tools/ucscutility:$PATH
PATH=/gpfs/home/guosa/hpc/tools:$PATH
PATH=/gpfs/home/guosa/hpc/tools/bcftools-1.9:$PATH
PATH=/gpfs/home/guosa/hpc/tools/tabix-0.2.6:$PATH
PATH=/gpfs/home/guosa/hpc/tools/phase.2.1.1.linux:$PATH
PATH=/gpfs/home/guosa/tools/Bismark_v0.19.1:$PATH
PATH=/gpfs/home/guosa/tools/TrimGalore-0.5.0:$PATH
PATH=/gpfs/home/guosa/hpc/tools/gatk-4.0.6.0:$PATH
PATH=/gpfs/home/guosa/hpc/tools:$PATH
PATH=/gpfs/home/guosa/hpc/tools/bowtie2-2.3.4.1-linux-x86_64:$PATH
PATH=/gpfs/home/guosa/hpc/bin/:$PATH
PATH=/gpfs/home/guosa/hpc/tools/gcta_1.91.6beta:$PATH
PATH=/gpfs/home/guosa/hpc/tools/annovar:$PATH
PATH=/gpfs/home/guosa/hpc/tools/GenGen-1.0.1:$PATH
PATH=/gpfs/home/guosa/hpc/tools/cassi-v2.51-linux-x86_32:$PATH
PATH=/gpfs/apps/R/3.2.0/bin:$PATH
PATH=/gpfs/home/guosa/hpc/tools/rvtests/executable:$PATH
PATH=/gpfs/home/guosa/hpc/tools/snpEff:$PATH
PATH=/gpfs/home/guosa/hpc/tools/samtools-1.9:$PATH
PATH=/gpfs/home/guosa/hpc/tools/snpEff:$PATH
PATH=/gpfs/home/guosa/hpc/bin/aloft/aloft/aloft-predict:$PATH
PATH=/gpfs/home/guosa/hpc/tools/Python-3.7.3:$PATH
PATH=/gpfs/home/guosa/hpc/tools/libbios-1.0.0:$PATH
PATH=/gpfs/home/guosa/hpc/tools/snpEff:$PATH
PATH=/gpfs/home/guosa/hpc/tools/snpEff/scripts:$PATH
PATH=/gpfs/home/guosa/hpc/tools/Python-2.7.15:$PATH
PATH=/gpfs/home/guosa/hpc/tools/aloft/aloft-annotate:$PATH
PATH=/gpfs/home/guosa/hpc/tools/hisat2-2.1.0:$PATH
PATH=/gpfs/home/guosa/hpc/tools/FLASH2:$PATH
PATH=~/hpc/tools/mixcr-3.0.9:$PATH
PATH=/gpfs/home/guosa/hpc/tools/bbmap:$PATH
PATH=/gpfs/home/guosa/hpc/tools/vcftools/src/cpp:$PATH
PATH=/gpfs/home/guosa/hpc/tools/vcftools_0.1.13/bin:$PATH
PATH=/gpfs/home/guosa/hpc/tools/Python-3.7.3:$PATH
PATH=/gpfs/home/guosa/tools/TrimGalore-0.5.0:$PATH
PATH=/cm/shared/apps/sratoolkit/bin:$PATH
PATH=/gpfs/home/guosa/hpc/tools/fastq_screen_v0.14.0:$PATH
PATH=/gpfs/home/guosa/hpc/tools/fs_4.0.1:$PATH
PATH=/gpfs/home/guosa/hpc/tools/bcftools:$PATH
PATH=/gpfs/home/guosa/hpc/tools/STAR-2.7.3a/bin/Linux_x86_64_static:$PATH
PATH=/gpfs/home/guosa/hpc/tools/bbmap:$PATH
PATH=/gpfs/home/guosa/hpc/tools/miniconda3/bin:$PATH
PATH=/gpfs/home/guosa/hpc/tools/samtools-1.9:$PATH
PATH=/gpfs/home/guosa/hpc/tools/bcftools:$PATH
PATH=/gpfs/home/guosa/hpc/tools/salmon-latest_linux_x86_64/bin:$PATH
PATH=/gpfs/home/guosa/hpc/tools/cufflinks-2.2.1.Linux_x86_64:$PATH
export CFLAGS="-I/usr/local/include"
export LDFLAGS="-L/usr/local/lib"
alias chtc1="ssh nu_guos@submit-1.chtc.wisc.edu"
alias chtc2="ssh nu_guos@submit-2.chtc.wisc.edu"
alias chtc3="ssh nu_guos@submit-3.chtc.wisc.edu"
alias ll="ls -larth"

CHG1 @ MCRI 2017-2019

PATH=/home/guosa/hpc/tools:$PATH
PATH=/home/guosa/hpc/tools/tabix-0.2.6:$PATH
alias ll="ls -lsrth"
alias chtc="ssh nu_guos@128.105.244.191"
alias snpsift="java -jar ~/hpc/tools/snpEff/SnpSift.jar"
PATH=~/hpc/tools/bin:$PATH
PATH=~/hpc/bin:$PATH
PATH=/home/guosa/hpc/tools/Bismark_v0.19.1/:$PATH
PATH=/home/guosa/hpc/tools/bcftools-1.7:$PATH
PATH=/home/guosa/hpc/tools/annovar:$PATH
PATH=/home/guosa/hpc/tools/gatk-4.0.12.0:$PATH
PATH=/home/guosa/hpc/tools/Python-2.7.15:$PATH
PATH=/home/guosa/hpc/tools/aloft/aloft-annotate:$PATH
PATH=/home/guosa/hpc/tools/bcftools-1.9:$PATH
PATH=/home/guosa/hpc/tools/mskcc-vcf2maf-5453f80:$PATH
PATH=/home/guosa/hpc/tools/hisat2-2.1.0:$PATH
PATH=/home/guosa/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/current/bin:$PATH
PATH=/home/guosa/.linuxbrew/bin:$PATH
PATH=/home/guosa/hpc/tools/jdk-12.0.2/bin:$PATH
PATH=/home/guosa/hpc/tools/apache-maven-3.6.1/bin:$PATH
PATH=/home/guosa/hpc/tools/mixcr-3.0.9:$PATH
PATH=/home/guosa/hpc/tools/seqtk:$PATH
PATH=/home/guosa/hpc/tools/vdjtools-1.2.1:$PATH
PATH=~/hpc/tools/vcftools/src/cpp:$PATH
PATH=/home/guosa/hpc/tools/bcftools-1.9:$PATH
PATH=/home/guosa/hpc/tools/GenomeAnalysisTK-3.8-1-0-gf15c1c3ef:$PATH
PATH=/home/guosa/hpc/tools/jre1.8.0_221/bin/:$PATH
PATH=/home/guosa/hpc/tools/eigensoft/bin:$PATH
PATH=/home/guosa/hpc/tools/CancerLocator:$PATH
PATH=/home/guosa/hpc/tools/CLARKSCV1.2.6.1/exe:$PATH
PATH=/gpfs/home/guosa/hpc/tools/cufflinks-2.2.1.Linux_x86_64:$PATH

Disclosure.

  • All the opinions are my own and not the views of my employer
  • All the blogs are my own and not the views of my employer
  • All the opinions are my own and not the views of my employer
  • All the contents are my own and should never be taken seriously
  • All the contents are only used for help. reminding me if misleading happens
  • All the figures are only used for non-profit education. reminding me if infrigement happens
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