MUIC-Jellyfish_proteomics/.bashrc_backup at main · SJ-31/MUIC-Jellyfish_proteomics · GitHub

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# ~/.bashrc: executed by bash(1) for non-login shells. Don't do this
export PATH=/bin:$PATH
export PATH=$HOME/.local/bin/:$PATH
export PATH=/usr/bin:$PATH
export LC_ALL
export LC_ALL="en_US.UTF-8"
export PATH=$HOME/dependencies/mono/bin:$PATH
export PATH=$HOME/dependencies:$PATH
export PATH=$HOME/dependencies/dotnet:$PATH
export PATH=$HOME/workflow/tools/sqlite-tools-linux-x86-3430100:$PATH
# export PATH=$HOME/dependencies/cuda-9.0/bin:$PATH
export PATH=~/workflow/tools/bbmap:$PATH
export PATH=~/workflow/tools:$PATH
export PATH=~/bin:$PATH
export PATH=~/workflow/tools/FastQC:$PATH
export PATH=~/workflow/tools/SPAdes-3.15.5-Linux/bin:$PATH
export PATH=~/workflow/tools/SPAdes-3.15.5-Linux/bin:$PATH
export PATH=~/workflow/tools/SMSNet/:$PATH
export PATH=~/workflow/tools/Percolator/bin:$PATH
export PATH=~/dependencies/zlib:$PATH
export PATH=~/dependencies/gperf/bin:$PATH
export PATH=$HOME/dependencies/openssl/bin:$PATH
export LD_LIBRARY_PATH=$HOME/dependencies/openssl/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=$HOME/dependencies
# export LD_LIBRARY_PATH=~/dependencies/cuda-9.0/lib64:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=~/dependencies/libseccomp/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=~/dependencies/bzip2/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=~/dependencies/cuda/lib64/:$LD_LIBRARY_PATH
export PATH=~/dependencies/zlib/include:$PATH
export PATH=~/dependencies/bzip2/include:$PATH
export PATH=~/dependencies/graphviz/bin:$PATH
export PATH=~/workflow/tools/SPAdes-3.14.1-Linux/bin:$PATH
export PATH=~/workflow/tools/proteowizard/:$PATH
export PATH=~/workflow/tools/detonate-1.11-precompiled/rsem-eval:$PATH
export PATH=~/dependencies/ImageMagick/bin/:$PATH
export PATH=~/workflow/tools/bowtie-1.3.1:$PATH
export PATH=~/workflow/tools/crux-4.1/bin/:$PATH
export PATH=~/workflow/tools/iqtree-2.3.2-Linux-intel/bin/:$PATH
export PATH=~/workflow/tools/percolator_converters/usr/bin/:$PATH
export PATH=$HOME/workflow/tools/tandem/bin:$PATH
export PATH=~/workflow/tools/STAR-2.7.10b/bin/Linux_x86_64/:$PATH
export PATH=~/workflow/tools/convert-db-to-csv:$PATH
export PATH=/mnt/data/shannc/nf/tools/interproscan-5.63-95.0/:$PATH
export EGGNOG_DATA_DIR=/mnt/data/shannc/nf/tools/eggnog-mapper-data
export PEPNET="$HOME/workflow/tools/PepNet/denovo.py"
export PATH=$HOME/workflow/tools/sratoolkit.3.0.2-ubuntu64/bin:$PATH
export PATH="$HOME/workflow/tools/cd-hit-v4.8.1-2019-0228:$PATH"
export SMSNET_M="$HOME/workflow/tools/SMSNet/run.py"
export SMSNET_P="$HOME/workflow/tools/SMSNet_P/run.py"
eval "$(starship init bash)"
export PATH=/usr/local/cuda-9.0/bin:$PATH
export LD_LIBRARY_PATH=/usr/local/cuda-9.0/lib64:$LD_LIBRARY_PATH
export CUDA_VISIBLE_DEVICES=0
export DA="/mnt/data/shannc/nf/data/"
export HF_HOME="/mnt/data/shannc/nf/.cache/huggingface/"

set -o vi

alias tmux="tmux -u"
alias rawparse="mono ~/workflow/tools/ThermoRawFileParser/ThermoRawFileParser.exe"
alias MSFragger="java -jar ~/workflow/tools/MSFragger-3.7/MSFragger-3.7.jar"
alias s="source ~/.bashrc"
alias rsem-eval-calculate-score="/home/shannc/workflow/tools/detonate-1.11-precompiled/rsem-eval/rsem-eval-calculate-score"
alias de="conda deactivate"
alias e="exit"
alias trsh="trash.sh"
alias empty="empty.sh"


# >>> conda initialize >>>
# !! Contents within this block are managed by 'conda init' !!
__conda_setup="$('/home/shannc/anaconda3/bin/conda' 'shell.bash' 'hook' 2> /dev/null)"
if [ $? -eq 0 ]; then
    eval "$__conda_setup"
else
    if [ -f "/home/shannc/anaconda3/etc/profile.d/conda.sh" ]; then
        . "/home/shannc/anaconda3/etc/profile.d/conda.sh"
    else
        export PATH="/home/shannc/anaconda3/bin:$PATH"
    fi
fi
unset __conda_setup
# <<< conda initialize <<<

# ls uses different flags for colors on Mac and Linux
if [ "$(uname)" == "Darwin" ]; then
  alias ls='ls -hG'
else
  alias ls='ls -h --color=auto'
fi
alias smsenv="conda activate /mnt/data/sirasris/miniconda3/envs/smsnet"
export MSGF="$HOME/workflow/tools/MSGFPlus/MSGFPlus.jar"
export MzidToTsvConverter="$HOME/workflow/tools/MzidToTsvConverter/MzidToTsvConverter.exe"
export BIN="$HOME/workflow/bin/"
export MSFragger="$HOME/workflow/tools/MSFragger-3.7/MSFragger-3.7.jar"
function perldoc() { command perldoc -n less "$@" |man -l -; }
export FZF_DEFAULT_OPTS=" \
--color=bg+:#ccd0da,bg:#eff1f5,spinner:#dc8a78,hl:#d20f39 \
--color=fg:#4c4f69,header:#d20f39,info:#8839ef,pointer:#dc8a78 \
--color=marker:#dc8a78,fg+:#4c4f69,prompt:#8839ef,hl+:#d20f39"

alias r="ranger"
alias n="nnn-static"
alias rad="radian"
alias dotnet6="$HOME/workflow/tools/dotnet6/dotnet"
alias gitui="gitui -t latte.ron"
alias clip="xclip -selection clipboard"
eval "$(zoxide init bash)"
source ~/dependencies/blesh/ble.sh