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65 lines
1.7 KiB
Cheetah
65 lines
1.7 KiB
Cheetah
# Enable pipx completions
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if [ $(command -v pipx) ]; then
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eval "$(register-python-argcomplete pipx)"
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fi
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# Preferred editor for local and remote sessions
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if [ $(command -v nano) ]; then
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export EDITOR=nano
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elif [ $(command -v emacs) ]; then
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export EDITOR='emacs -nw'
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elif [ $(command -v vim) ]; then
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export EDITOR=vim
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fi
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if [ $(command -v kate) ]; then
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export VISUAL=kate
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elif [ $(command -v code) ]; then
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export VISUAL=code
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elif [ $(command -v emacs) ]; then
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export VISUAL=emacs
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fi
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# Set a cool new pager with color support
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if [ $(command -v most) ]; then
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export PAGER=most
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fi
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# Replace cat with bat
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if [ $(command -v bat) ]; then
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export BAT_PAGER="less -SRF"
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export MANPAGER="sh -c 'col -bx | bat -l man -p'"
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export MANROFFOPT="-c"
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fi
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# Add notification support for long-running processes
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if [ $(command -v ntfy) ]; then
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eval "$(ntfy shell-integration --longer-than 30)"
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export AUTO_NTFY_DONE_IGNORE="vim nano emacs kate zshconfig screen tmux ssh top htop less more most nethogs 'singularity shell' julia man glances"
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fi
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# Set the Nextflow enviroment caches
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export NXF_HOME="$HOME/.nextflow"
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{{ if (eq .cluster "scinet") }}
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NXF_CACHE=/90daydata/shared/$USER/.nextflow
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{{ else }}
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NXF_CACHE=$NXF_HOME
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{{ end }}
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export NXF_CONDA_CACHEDIR="$NXF_CACHE/conda"
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export NXF_SINGULARITY_CACHEDIR="$NXF_CACHE/singularity"
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export NXF_CHARLIECLOUD_CACHEDIR="$NXF_CACHE/charlie"
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{{ if (eq .cluster "scinet") }}
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# Set the Singularity image cache
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export SINGULARITY_CACHEDIR=/90daydata/shared/$USER/.singularity
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{{ end }}
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# Give Julia full CPU access
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export JULIA_NUM_THREADS=$(nproc)
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# Make Julia use preinstalled Git
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JULIA_PKG_USE_CLI_GIT=true
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# Make NCBI happy
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export NCBI_API_KEY='{{ (bitwarden "item" "7d42eba0-c256-4d3b-8d0e-adbf016a08f8").login.password }}'
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