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Misc Updates (#1)

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66
README.md
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```bash ```bash
$ git clone https://github.com/thermokarst/dotfiles.git ~/.dotfiles $ git clone https://github.com/thermokarst/dotfiles.git ~/.dotfiles
$ cd ~/.dotfiles $ cd ~/.dotfiles
$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)" $ git remote rename origin thermokarst
$ ./homebrew-install # Install macports
$ sudo port selfupdate
$ sudo port install \
the_silver_searcher \
aspell \
aspell-dict-en \
cmus \
curl \
git \
gnupg2 \
graphviz-devel \
htop \
imagemagick \
myrepos \
nodejs9 \
openssl \
postgresql10 \
postgresql10-server \
python36 \
tmux-pasteboard \
rsync \
tmux \
tree \
vim \
wget \
xz \
zsh
$ sudo port select --set python python36
$ sudo port select --set python3 python36
$ sudo port select --set postgresql postgresql10
$ sudo chpass -s '/opt/local/bin/zsh' $USER
$ sudo sh -c 'echo /opt/local/bin/zsh >>/etc/shells'
$ git clone https://github.com/chriskempson/base16-shell.git ~/.config/base16-shell $ git clone https://github.com/chriskempson/base16-shell.git ~/.config/base16-shell
$ echo "/usr/local/bin/zsh" | sudo tee -a /etc/shells
$ chsh -s /usr/local/bin/zsh
$ git clone --recursive https://github.com/sorin-ionescu/prezto.git "${ZDOTDIR:-$HOME}/.zprezto" $ git clone --recursive https://github.com/sorin-ionescu/prezto.git "${ZDOTDIR:-$HOME}/.zprezto"
$ ./install $ ./install
$ curl -fLo ~/.vim/autoload/plug.vim --create-dirs https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim $ curl -fLo ~/.vim/autoload/plug.vim --create-dirs https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
$ vim +PlugInstall $ vim +PlugInstall
$ mkdir ~/bin $ mr checkout
$ git clone https://github.com/laurent22/rsync-time-backup ~/bin/.rsync-time-backup
$ ln -s ~/bin/.rsync-time-backup/rsync_tmbackup.sh ~/bin/rsync_tmbackup.sh
``` ```
## Typical `pip` modifications for macports
```bash
pip install --global-option=build_ext --global-option=-I/opt/local/include -r requirements.txt
```
## postgresql setup
```bash
sudo mkdir -p /opt/local/var/db/postgresql10/defaultdb
sudo chown postgres:postgres /opt/local/var/db/postgresql10/defaultdb
sudo su postgres -c '/opt/local/lib/postgresql10/bin/initdb -D /opt/local/var/db/postgresql10/defaultdb'
sudo port load postgresql10-server
sudo su postgres -c "createuser matthew --createdb --login --superuser"
sudo su postgres -c "createdb matthew"
```
### Trackpad
https://github.com/pilotmoon/Scroll-Reverser
### Typeface
https://fonts.google.com/specimen/Inconsolata (iTerm2 16pt anti-aliased)

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aspell.en.pws
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@ -1,6 +1,18 @@
personal_ws-1.1 en 5 personal_ws-1.1 en 17
env
conda
yml
linux
Miniconda
osx
macOS
linenos
informatics informatics
microbiome microbiome
Microbiome py
cli
qiime
QIIME QIIME
dev
wget
metadata metadata

96
homebrew-install
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#!/usr/bin/env zsh
taps=(
homebrew/binary
caskroom/cask
caskroom/fonts
)
packages=(
ag
aspell
blackbox
brew-cask
cmake
cmus
diff-so-fancy
git
gnupg
go
gpg-agent
graphviz
heroku
htop-osx
httpie
hugo
imagemagick
node
openssl
pass
postgresql
python
python3
reattach-to-user-namespace
rsync
tmux
tree
vim
wget
xz
zsh
)
cask_packages=(
arq
dropbox
font-inconsolata
font-anonymous-pro
gitify
google-chrome
google-drive
java
macdown
pandoc
slack
spectacle
the-unarchiver
vagrant
virtualbox
xquartz
)
function log() {
echo $* > /dev/stderr
}
log "brew update"
brew update
log "brew upgrade"
brew upgrade
log "tapping"
for name in $taps
do
log "brew tap ${name}"
brew tap $name
done
log "installing"
for name_and_args in $packages
do
log "brew install ${=name_and_args}"
brew install "${=name_and_args}"
done
for name_and_args in $cask_packages
do
log "brew cask install ${=name_and_args}"
brew cask install "${=name_and_args}"
done
log "brew cleanup"
brew cleanup
log "brew linkapps"
brew linkapps

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install.conf.yaml
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~/.zshrc: zsh/zshrc ~/.zshrc: zsh/zshrc
~/.aspell.en.pws: aspell.en.pws ~/.aspell.en.pws: aspell.en.pws
~/.vimrc: vimrc ~/.vimrc: vimrc
~/.mrconfig: mrconfig
~/.taskrc: taskrc

44
mouse.xml Normal file
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<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<data>
<vid>1390</vid>
<pid>254</pid>
<select_profile>0</select_profile>
<profile>
<profname>default</profname>
<lbutton>1</lbutton>
<rbutton>2</rbutton>
<tbutton>5</tbutton>
<button4>41</button4>
<button5>41</button5>
<tiltleft>39</tiltleft>
<tiltright>40</tiltright>
<scrolls>5</scrolls>
<hlotate>5</hlotate>
<hspeed>5</hspeed>
<hcount>1</hcount>
<button6>33</button6>
<button7>34</button7>
<button8>36</button8>
<lbutton_etcKey_key1>0</lbutton_etcKey_key1>
<lbutton_etcKey_key2>0</lbutton_etcKey_key2>
<rbutton_etcKey_key1>0</rbutton_etcKey_key1>
<rbutton_etcKey_key2>0</rbutton_etcKey_key2>
<tbutton_etcKey_key1>0</tbutton_etcKey_key1>
<tbutton_etcKey_key2>0</tbutton_etcKey_key2>
<button4_etcKey_key1>1</button4_etcKey_key1>
<button4_etcKey_key2>73</button4_etcKey_key2>
<button5_etcKey_key1>1</button5_etcKey_key1>
<button5_etcKey_key2>72</button5_etcKey_key2>
<tiltleft_etcKey_key1>0</tiltleft_etcKey_key1>
<tiltleft_etcKey_key2>0</tiltleft_etcKey_key2>
<tiltright_etcKey_key1>0</tiltright_etcKey_key1>
<tiltright_etcKey_key2>0</tiltright_etcKey_key2>
<button6_etcKey_key1>0</button6_etcKey_key1>
<button6_etcKey_key2>0</button6_etcKey_key2>
<button7_etcKey_key1>0</button7_etcKey_key1>
<button7_etcKey_key2>0</button7_etcKey_key2>
<button8_etcKey_key1>0</button8_etcKey_key1>
<button8_etcKey_key2>0</button8_etcKey_key2>
<dispGesture>1</dispGesture>
</profile>
</data>

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mrconfig Normal file
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### applied-bioinformatics
[src/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics]
checkout = git clone https://github.com/applied-bioinformatics/An-Introduction-To-Applied-Bioinformatics An-Introduction-To-Applied-Bioinformatics && \
cd An-Introduction-To-Applied-Bioinformatics && \
git remote rename origin applied-bioinformatics && \
git remote add thermokarst https://github.com/thermokarst/An-Introduction-To-Applied-Bioinformatics && \
git fetch thermokarst
### biocore
checkout = git clone https://github.com/biocore/deblur deblur && \
cd deblur && \
git remote rename origin biocore && \
git remote add thermokarst https://github.com/thermokarst/deblur && \
git fetch thermokarst
checkout = git clone https://github.com/biocore/scikit-bio scikit-bio && \
cd scikit-bio && \
git remote rename origin biocore && \
git remote add ElDeveloper https://github.com/ElDeveloper/scikit-bio && \
git remote add ebolyen https://github.com/ebolyen/scikit-bio && \
git remote add wasade https://github.com/wasade/scikit-bio && \
git remote add thermokarst https://github.com/thermokarst/scikit-bio && \
git fetch thermokarst
### caporaso-lab
[src/caporaso-lab/SurveySync]
checkout = git clone https://github.com/caporaso-lab/SurveySync SurveySync && \
cd SurveySync && \
git remote rename origin caporaso-lab && \
git remote add turanoo https://github.com/turanoo/SurveySync && \
git remote add thermokarst https://github.com/thermokarst/SurveySync && \
git fetch thermokarst
[src/caporaso-lab/caporaso-lab.github.io]
checkout = git clone https://github.com/caporaso-lab/caporaso-lab.github.io caporaso-lab.github.io && \
cd caporaso-lab.github.io && \
git remote rename origin caporaso-lab && \
git remote add thermokarst https://github.com/thermokarst/caporaso-lab.github.io && \
git fetch thermokarst
[src/caporaso-lab/sc18-poster]
checkout = git clone https://github.com/caporaso-lab/sc18-poster sc18-poster && \
cd sc18-poster && \
git remote rename origin caporaso-lab && \
git remote add thermokarst https://github.com/thermokarst/sc18-poster && \
git fetch thermokarst
[src/caporaso-lab/pretrained-feature-classifiers]
checkout = git clone https://github.com/caporaso-lab/pretrained-feature-classifiers pretrained-feature-classifiers && \
cd pretrained-feature-classifiers && \
git remote rename origin caporaso-lab && \
git remote add thermokarst https://github.com/thermokarst/pretrained-feature-classifiers && \
git fetch thermokarst
### qiime2
[src/qiime2/Keemei]
checkout = git clone https://github.com/qiime2/Keemei Keemei && \
cd Keemei && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/Keemei && \
git fetch thermokarst
[src/qiime2/busywork]
checkout = git clone https://github.com/qiime2/busywork busywork && \
cd busywork && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/busywork && \
git fetch thermokarst
[src/qiime2/data.qiime2.org]
checkout = git clone https://github.com/qiime2/data.qiime2.org data.qiime2.org && \
cd data.qiime2.org && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/data.qiime2.org && \
git fetch thermokarst
[src/qiime2/dev-docs]
checkout = git clone https://github.com/qiime2/dev-docs dev-docs && \
cd dev-docs && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/dev-docs && \
git fetch thermokarst
[src/qiime2/discourse-unhandled-tagger]
checkout = git clone https://github.com/qiime2/discourse-unhandled-tagger discourse-unhandled-tagger && \
cd discourse-unhandled-tagger && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/discourse-unhandled-tagger && \
git fetch thermokarst
[src/qiime2/docs]
checkout = git clone https://github.com/qiime2/docs docs && \
cd docs && \
git remote rename origin qiime2 && \
git remote add ChrisKeefe https://github.com/ChrisKeefe/docs && \
git remote add antgonza https://github.com/antgonza/docs && \
git remote add cduvallet https://github.com/cduvallet/docs && \
git remote add ebolyen https://github.com/ebolyen/docs && \
git remote add nbokulich https://github.com/nbokulich/docs && \
git remote add turanoo https://github.com/turanoo/docs && \
git remote add gregcaporaso https://github.com/gregcaporaso/docs && \
git remote add thermokarst https://github.com/thermokarst/docs && \
git fetch thermokarst
[src/qiime2/environment-files]
checkout = git clone https://github.com/qiime2/environment-files environment-files && \
cd environment-files && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/environment-files && \
git fetch thermokarst
[src/qiime2/library]
checkout = git clone https://github.com/qiime2/library library && \
cd library && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/library && \
git fetch thermokarst
[src/qiime2/logos]
checkout = git clone https://github.com/qiime2/logos logos && \
cd logos && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/logos && \
git fetch thermokarst
[src/qiime2/q2-alignment]
checkout = git clone https://github.com/qiime2/q2-alignment q2-alignment && \
cd q2-alignment && \
git remote rename origin qiime2 && \
git remote add turanoo https://github.com/turanoo/q2-alignment && \
git remote add thermokarst https://github.com/thermokarst/q2-alignment && \
git fetch thermokarst
[src/qiime2/q2-composition]
checkout = git clone https://github.com/qiime2/q2-composition q2-composition && \
cd q2-composition && \
git remote rename origin qiime2 && \
git remote add nbokulich https://github.com/nbokulich/q2-composition && \
git remote add thermokarst https://github.com/thermokarst/q2-composition && \
git fetch thermokarst
[src/qiime2/q2-cutadapt]
checkout = git clone https://github.com/qiime2/q2-cutadapt q2-cutadapt && \
cd q2-cutadapt && \
git remote rename origin qiime2 && \
git remote add ebolyen https://github.com/ebolyen/q2-cutadapt && \
git remote add thermokarst https://github.com/thermokarst/q2-cutadapt && \
git fetch thermokarst
[src/qiime2/q2-dada2]
checkout = git clone https://github.com/qiime2/q2-dada2 q2-dada2 && \
cd q2-dada2 && \
git remote rename origin qiime2 && \
git remote add benjjneb https://github.com/benjjneb/q2-dada2 && \
git remote add ebolyen https://github.com/ebolyen/q2-dada2 && \
git remote add thermokarst https://github.com/thermokarst/q2-dada2 && \
git fetch thermokarst
[src/qiime2/q2-deblur]
checkout = git clone https://github.com/qiime2/q2-deblur q2-deblur && \
cd q2-deblur && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-deblur && \
git fetch thermokarst
[src/qiime2/q2-demux]
checkout = git clone https://github.com/qiime2/q2-demux q2-demux && \
cd q2-demux && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-demux && \
git fetch thermokarst
[src/qiime2/q2-diversity]
checkout = git clone https://github.com/qiime2/q2-diversity q2-diversity && \
cd q2-diversity && \
git remote rename origin qiime2 && \
git remote add ChrisKeefe https://github.com/ChrisKeefe/q2-diversity && \
git remote add ElDeveloper https://github.com/ElDeveloper/q2-diversity && \
git remote add ebolyen https://github.com/ebolyen/q2-diversity && \
git remote add nbokulich https://github.com/nbokulich/q2-diversity && \
git remote add thermokarst https://github.com/thermokarst/q2-diversity && \
git fetch thermokarst
[src/qiime2/q2-diversity-lib]
checkout = git clone https://github.com/qiime2/q2-diversity-lib q2-diversity-lib && \
cd q2-diversity-lib && \
git remote rename origin qiime2 && \
git remote add ChrisKeefe https://github.com/ChrisKeefe/q2-diversity-lib && \
git remote add thermokarst https://github.com/thermokarst/q2-diversity-lib && \
git fetch thermokarst
[src/qiime2/q2-emperor]
checkout = git clone https://github.com/qiime2/q2-emperor q2-emperor && \
cd q2-emperor && \
git remote rename origin qiime2 && \
git remote add ElDeveloper https://github.com/ElDeveloper/q2-emperor && \
git remote add thermokarst https://github.com/thermokarst/q2-emperor && \
git fetch thermokarst
[src/qiime2/q2-feature-classifier]
checkout = git clone https://github.com/qiime2/q2-feature-classifier q2-feature-classifier && \
cd q2-feature-classifier && \
git remote rename origin qiime2 && \
git remote add nbokulich https://github.com/nbokulich/q2-feature-classifier && \
git remote add thermokarst https://github.com/thermokarst/q2-feature-classifier && \
git fetch thermokarst
[src/qiime2/q2-feature-table]
checkout = git clone https://github.com/qiime2/q2-feature-table q2-feature-table && \
cd q2-feature-table && \
git remote rename origin qiime2 && \
git remote add ebolyen https://github.com/ebolyen/q2-feature-table && \
git remote add gregcaporaso https://github.com/gregcaporaso/q2-feature-table && \
git remote add wasade https://github.com/wasade/q2-feature-table && \
git remote add thermokarst https://github.com/thermokarst/q2-feature-table && \
git fetch thermokarst
[src/qiime2/q2-fragment-insertion]
checkout = git clone https://github.com/qiime2/q2-fragment-insertion q2-fragment-insertion && \
cd q2-fragment-insertion && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-fragment-insertion && \
git fetch thermokarst
[src/qiime2/q2-gneiss]
checkout = git clone https://github.com/qiime2/q2-gneiss q2-gneiss && \
cd q2-gneiss && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-gneiss && \
git fetch thermokarst
[src/qiime2/q2-longitudinal]
checkout = git clone https://github.com/qiime2/q2-longitudinal q2-longitudinal && \
cd q2-longitudinal && \
git remote rename origin qiime2 && \
git remote add nbokulich https://github.com/nbokulich/q2-longitudinal && \
git remote add thermokarst https://github.com/thermokarst/q2-longitudinal && \
git fetch thermokarst
[src/qiime2/q2-metadata]
checkout = git clone https://github.com/qiime2/q2-metadata q2-metadata && \
cd q2-metadata && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-metadata && \
git fetch thermokarst
[src/qiime2/q2-phylogeny]
checkout = git clone https://github.com/qiime2/q2-phylogeny q2-phylogeny && \
cd q2-phylogeny && \
git remote rename origin qiime2 && \
git remote add mikerobeson https://github.com/mikerobeson/q2-phylogeny && \
git remote add thermokarst https://github.com/thermokarst/q2-phylogeny && \
git fetch thermokarst
[src/qiime2/q2-quality-control]
checkout = git clone https://github.com/qiime2/q2-quality-control q2-quality-control && \
cd q2-quality-control && \
git remote rename origin qiime2 && \
git remote add nbokulich https://github.com/nbokulich/q2-quality-control && \
git remote add thermokarst https://github.com/thermokarst/q2-quality-control && \
git fetch thermokarst
[src/qiime2/q2-quality-filter]
checkout = git clone https://github.com/qiime2/q2-quality-filter q2-quality-filter && \
cd q2-quality-filter && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-quality-filter && \
git fetch thermokarst
[src/qiime2/q2-sample-classifier]
checkout = git clone https://github.com/qiime2/q2-sample-classifier q2-sample-classifier && \
cd q2-sample-classifier && \
git remote rename origin qiime2 && \
git remote add BenKaehler https://github.com/BenKaehler/q2-sample-classifier && \
git remote add nbokulich https://github.com/nbokulich/q2-sample-classifier && \
git remote add thermokarst https://github.com/thermokarst/q2-sample-classifier && \
git fetch thermokarst
[src/qiime2/q2-taxa]
checkout = git clone https://github.com/qiime2/q2-taxa q2-taxa && \
cd q2-taxa && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-taxa && \
git fetch thermokarst
[src/qiime2/q2-types]
checkout = git clone https://github.com/qiime2/q2-types q2-types && \
cd q2-types && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-types && \
git fetch thermokarst
[src/qiime2/q2-vsearch]
checkout = git clone https://github.com/qiime2/q2-vsearch q2-vsearch && \
cd q2-vsearch && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2-vsearch && \
git fetch thermokarst
[src/qiime2/q2cli]
checkout = git clone https://github.com/qiime2/q2cli q2cli && \
cd q2cli && \
git remote rename origin qiime2 && \
git remote add ebolyen https://github.com/ebolyen/q2cli && \
git remote add turanoo https://github.com/turanoo/q2cli && \
git remote add thermokarst https://github.com/thermokarst/q2cli && \
git fetch thermokarst
[src/qiime2/q2cwl]
checkout = git clone https://github.com/qiime2/q2cwl q2cwl && \
cd q2cwl && \
git remote rename origin qiime2 && \
git remote add ebolyen https://github.com/ebolyen/q2cwl && \
git remote add thermokarst https://github.com/thermokarst/q2cwl && \
git fetch thermokarst
[src/qiime2/q2galaxy]
checkout = git clone https://github.com/qiime2/q2galaxy q2galaxy && \
cd q2galaxy && \
git remote rename origin qiime2 && \
git remote add ebolyen https://github.com/ebolyen/q2galaxy && \
git remote add thermokarst https://github.com/thermokarst/q2galaxy && \
git fetch thermokarst
[src/qiime2/galaxy]
checkout = git clone https://github.com/galaxyproject/galaxy galaxy && \
cd galaxy && \
git remote rename origin galaxyproject && \
git remote add ebolyen https://github.com/ebolyen/galaxy && \
git remote add thermokarst https://github.com/thermokarst/galaxy && \
git fetch thermokarst
[src/qiime2/q2studio]
checkout = git clone https://github.com/qiime2/q2studio q2studio && \
cd q2studio && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2studio && \
git fetch thermokarst
[src/qiime2/q2templates]
checkout = git clone https://github.com/qiime2/q2templates q2templates && \
cd q2templates && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/q2templates && \
git fetch thermokarst
[src/qiime2/q2view]
checkout = git clone https://github.com/qiime2/q2view q2view && \
cd q2view && \
git remote rename origin qiime2 && \
git remote add ebolyen https://github.com/ebolyen/q2view && \
git remote add turanoo https://github.com/turanoo/q2view && \
git remote add thermokarst https://github.com/thermokarst/q2view && \
git fetch thermokarst
[src/qiime2/qiime2]
checkout = git clone https://github.com/qiime2/qiime2 qiime2 && \
cd qiime2 && \
git remote rename origin qiime2 && \
git remote add ebolyen https://github.com/ebolyen/qiime2 && \
git remote add thermokarst https://github.com/thermokarst/qiime2 && \
git fetch thermokarst
[src/qiime2/qiime2.github.io]
checkout = git clone https://github.com/qiime2/qiime2.github.io qiime2.github.io && \
cd qiime2.github.io && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/qiime2.github.io && \
git fetch thermokarst
[src/qiime2/template-repo]
checkout = git clone https://github.com/qiime2/template-repo template-repo && \
cd template-repo && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/template-repo && \
git fetch thermokarst
[src/qiime2/view.qiime2.org]
checkout = git clone https://github.com/qiime2/view.qiime2.org view.qiime2.org && \
cd view.qiime2.org && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/view.qiime2.org && \
git fetch thermokarst
[src/qiime2/vm-playbooks]
checkout = git clone https://github.com/qiime2/vm-playbooks vm-playbooks && \
cd vm-playbooks && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/vm-playbooks && \
git fetch thermokarst
[src/qiime2/workshop-playbooks]
checkout = git clone https://github.com/qiime2/workshop-playbooks workshop-playbooks && \
cd workshop-playbooks && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/workshop-playbooks && \
git fetch thermokarst
[src/qiime2/workshops.qiime2.org]
checkout = git clone https://github.com/qiime2/workshops.qiime2.org workshops.qiime2.org && \
cd workshops.qiime2.org && \
git remote rename origin qiime2 && \
git remote add thermokarst https://github.com/thermokarst/workshops.qiime2.org && \
git fetch thermokarst
### gregcaporaso
[src/gregcaporaso/caporaso-lab-secrets]
checkout = git clone https://github.com/gregcaporaso/caporaso-lab-secrets && \
cd caporaso-lab-secrets && \
git remote rename origin gregcaporaso && \
git remote add thermokarst https://github.com/thermokarst/caporaso-lab-secrets && \
git fetch thermokarst
[src/gregcaporaso/qiime2-meta-figures]
checkout = git clone https://github.com/gregcaporaso/qiime2-meta-figures && \
cd qiime2-meta-figures && \
git remote rename origin gregcaporaso && \
git remote add thermokarst https://github.com/thermokarst/qiime2-meta-figures && \
git fetch thermokarst
[src/gregcaporaso/workshop-tutorials]
checkout = git clone https://github.com/gregcaporaso/workshop-tutorials && \
cd workshop-tutorials && \
git remote rename origin gregcaporaso && \
git remote add thermokarst https://github.com/thermokarst/workshop-tutorials && \
git fetch thermokarst
### thermokarst
[src/thermokarst/ccdb-api]
checkout = git clone https://github.com/thermokarst/ccdb-api && \
cd ccdb-api && \
git remote rename origin thermokarst
[src/thermokarst/ccdb-web]
checkout = git clone https://github.com/thermokarst/ccdb-web && \
cd ccdb-web && \
git remote rename origin thermokarst
[src/thermokarst/fathm]
checkout = git clone https://github.com/thermokarst/fathm && \
cd fathm && \
git remote rename origin thermokarst && \
git remote add gitlab https://gitlab.com/evalulogic/fathm.git && \
git fetch gitlab
[src/thermokarst/tucotuco]
checkout = git clone https://github.com/thermokarst/tucotuco && \
cd tucotuco && \
git remote rename origin thermokarst

2
ports/PortIndex Normal file
View file

@ -0,0 +1,2 @@
tasksh 545
variants {debug universal} depends_build path:bin/cmake:cmake portdir office/tasksh description {tasksh is a shell command that wraps Taskwarrior commands} homepage http://tasktools.org/projects/tasksh.html depends_run port:task epoch 0 platforms darwin name tasksh depends_lib port:readline maintainers nomaintainer license MIT long_description {{tasksh is a shell command that wraps Taskwarrior commands.} It is intended to provide simpler Taskwarrior access, and add a few new features of its own.} categories office version 1.2.0 revision 1

1
ports/PortIndex.quick Normal file
View file

@ -0,0 +1 @@
tasksh 0

35
ports/office/tasksh/Portfile Normal file
View file

@ -0,0 +1,35 @@
# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
PortSystem 1.0
PortGroup cmake 1.0
name tasksh
version 1.2.0
revision 1
categories office
platforms darwin
license MIT
maintainers nomaintainer
description tasksh is a shell command that wraps Taskwarrior commands
long_description ${description}. \
It is intended to provide simpler Taskwarrior access, and \
add a few new features of its own.
homepage http://tasktools.org/projects/tasksh.html
master_sites http://taskwarrior.org/download/
checksums sha1 f3171552d30e811227607816e7c9638afd7b6d71 \
rmd160 2aa4b5480f3b63a50d79df80bafc275bf2ee2ea7 \
sha256 6e42f949bfd7fbdde4870af0e7b923114cc96c4344f82d9d924e984629e21ffd
patchfiles patch-readline.diff
post-patch {
reinplace -E "s,@@PREFIX@@,${prefix},g" ${worksrcpath}/cmake/Modules/FindReadline.cmake
}
depends_lib port:readline
depends_run port:task
cmake.out_of_source yes

42
ports/office/tasksh/files/patch-readline.diff Normal file
View file

@ -0,0 +1,42 @@
--- cmake/Modules/FindReadline.cmake.orig 2015-12-07 11:04:57.000000000 +0100
+++ cmake/Modules/FindReadline.cmake 2015-12-07 11:05:32.000000000 +0100
@@ -11,11 +11,7 @@
# So we look for another one by default
IF (APPLE OR FREEBSD)
FIND_PATH (READLINE_INCLUDE_DIR NAMES readline/readline.h PATHS
- /usr/include/
- /sw/include
- /opt/local/include
- /opt/include
- /usr/local/include
+ @@PREFIX@@/include
NO_DEFAULT_PATH
)
ENDIF (APPLE OR FREEBSD)
@@ -26,11 +22,7 @@
# So we look for another one by default
IF (APPLE OR FREEBSD)
FIND_LIBRARY (READLINE_readline_LIBRARY NAMES readline PATHS
- /usr/lib
- /sw/lib
- /opt/local/lib
- /opt/lib
- /usr/local/lib
+ @@PREFIX@@/lib
NO_DEFAULT_PATH
)
ENDIF (APPLE OR FREEBSD)
@@ -39,12 +31,7 @@
# Sometimes readline really needs ncurses
IF (APPLE OR FREEBSD)
FIND_LIBRARY (READLINE_ncurses_LIBRARY NAMES ncurses PATHS
- /usr/lib
- /sw/lib
- /opt/local/lib
- /opt/lib
- /usr/local/lib
- /usr/lib
+ @@PREFIX@@/lib
NO_DEFAULT_PATH
)
ENDIF (APPLE OR FREEBSD)

47
taskrc Normal file
View file

@ -0,0 +1,47 @@
### general
data.location=~/.task
include /Users/matthew/Dropbox/task/taskrc
### colors
include /opt/local/share/doc/task/rc/no-color.theme
color.overdue=bold white on color2
color.active=color0 on color4
### reports
# customize `next`
report.next.filter=status:pending limit:10 -reading project.not:shopping
report.next.columns=id,depends,project,tags,priority,scheduled.relative,due.relative,description.count,urgency
report.next.labels=id,depends,project,tags,priority,scheduled,due,description,urgency
# `full`
report.full.description=all open, grouped by project
report.full.sort=project+/,urgency
report.full.filter=status:pending
report.full.columns=id,depends,project,tags,priority,scheduled.relative,due.relative,description.count,urgency
report.full.labels=id,depends,project,tags,priority,scheduled,due,description,urgency
# `inbox`
report.inbox.description=Incoming unfiled todos
report.inbox.filter=status:pending project:
report.inbox.sort=recur+,urgency-
report.inbox.columns=id,depends,priority,project,due.relative,description.count,urgency
report.inbox.labels=id,depends,priority,project,due.relative,description,urgency
# tasksh
uda.reviewed.type=date
uda.reviewed.label=Reviewed
report._reviewed.description=Tasksh review report
report._reviewed.columns=uuid
report._reviewed.sort=reviewed+,modified+
report._reviewed.filter=(reviewed.none: or reviewed.before:now-6days) and (+PENDING or +WAITING) and project.not:reading
### contexts
# work
context.work=project.not:personal
# personal
context.personal=project.not:work

16
tmux.conf
View file

@ -1,18 +1,15 @@
# Ensure tmux doesn't launch a login shell
set -g default-command /usr/local/bin/zsh
# Automatic window title # Automatic window title
setw -g automatic-rename setw -g automatic-rename
# Fix LSOpenURLsWithRole() error on OS X. Requires reattach-to-user-namespace # Fix LSOpenURLsWithRole() error on OS X. Requires reattach-to-user-namespace
set -g default-command "reattach-to-user-namespace -l /usr/local/bin/zsh" set -g default-command "reattach-to-user-namespace -l /opt/local/bin/zsh"
# remap prefix to Control + a # remap prefix to Control + a
set -g prefix C-a set -g prefix C-a
unbind C-b unbind C-b
bind C-a last-window bind C-a last-window
set -g default-terminal "screen-256color" set -g default-terminal "xterm-256color"
# http://www.unwiredcouch.com/2013/11/15/my-tmux-setup.html # http://www.unwiredcouch.com/2013/11/15/my-tmux-setup.html
# Force a reload of the config file # Force a reload of the config file
@ -40,7 +37,7 @@ set -g status-justify centre
set -g status-left-length 50 set -g status-left-length 50
set -g status-right-length 140 set -g status-right-length 140
set -g status-left '#[fg=green]#H#[default] session:#S' set -g status-left '#[fg=green]#H#[default] session:#S'
set -g status-right '#[fg=white,bg=default]%a %l:%M:%S %p#[default] #[fg=blue]%m-%d-%Y' set -g status-right 'tw: #(task status:pending project: count) #[fg=white,bg=default]%a %l:%M:%S %p#[default] #[fg=blue]%m-%d-%Y'
set-option -g renumber-windows on set-option -g renumber-windows on
set -sg escape-time 0 set -sg escape-time 0
@ -49,8 +46,5 @@ set-option -g destroy-unattached 'off'
# Enable mouse control (clickable windows, panes, resizable panes) # Enable mouse control (clickable windows, panes, resizable panes)
set -g mouse on set -g mouse on
bind-key -t vi-copy MouseDragEnd1Pane copy-pipe "pbcopy" bind-key -Tcopy-mode-vi 'v' send -X begin-selection
bind-key -t vi-copy v begin-selection bind-key -Tcopy-mode-vi 'y' send -X copy-pipe-and-cancel pbcopy
bind-key -t vi-copy y copy-pipe "reattach-to-user-namespace pbcopy"
unbind -t vi-copy Enter
bind-key -t vi-copy Enter copy-pipe "reattach-to-user-namespace pbcopy"

30
vimrc
View file

@ -23,6 +23,20 @@ call plug#begin()
Plug 'francoiscabrol/ranger.vim' Plug 'francoiscabrol/ranger.vim'
" Delimited file querying " Delimited file querying
Plug 'mechatroner/rainbow_csv' Plug 'mechatroner/rainbow_csv'
" fzf setup
Plug 'junegunn/fzf', { 'dir': '~/.fzf', 'do': './install --all' }
" vue2
Plug 'posva/vim-vue'
" golang support
Plug 'fatih/vim-go', { 'do': ':GoUpdateBinaries' }
" elixir
Plug 'elixir-editors/vim-elixir'
" the silver searcher
Plug 'mileszs/ack.vim'
" vimwiki
Plug 'vimwiki/vimwiki'
" typescript syntax highlighting
Plug 'leafgarland/typescript-vim'
call plug#end() call plug#end()
set t_Co=256 set t_Co=256
@ -91,8 +105,8 @@ set writebackup
" change the mapleader from \ to , " change the mapleader from \ to ,
let mapleader=" " let mapleader=" "
" ranger config " fzf config
map <leader><Tab> :RangerWorkingDirectory<CR> map <leader><Tab> :FZF<CR>
" PEP8 formatting " PEP8 formatting
au BufNewFile,BufRead *.py au BufNewFile,BufRead *.py
@ -125,10 +139,16 @@ nmap <leader>l :bnext<CR>
" cycle to previous buffer " cycle to previous buffer
nmap <leader>h :bprevious<CR> nmap <leader>h :bprevious<CR>
set rtp+=/usr/local/opt/fzf
" flake8 config " flake8 config
let g:flake8_show_in_gutter = 1 let g:flake8_show_in_gutter = 1
let g:flake8_error_marker = 'EE' let g:flake8_error_marker = 'EE'
let g:flake8_warning_marker = 'WW' let g:flake8_warning_marker = 'WW'
autocmd BufWritePost *.py call Flake8()
" Inform ack.vim that we are actually using the_silver_searcher
let g:ackprg = 'ag --vimgrep'
" vimwiki config
let g:vimwiki_list = [{'path': '$HOME/Dropbox/vimwiki/'}]
" netrw
let g:netrw_liststyle = 3 " tree view

2
zsh/zpreztorc
View file

@ -87,7 +87,7 @@ zstyle ':prezto:module:git:alias' skip 'yes'
# Set the prompt theme to load. # Set the prompt theme to load.
# Setting it to 'random' loads a random theme. # Setting it to 'random' loads a random theme.
# Auto set to 'off' on dumb terminals. # Auto set to 'off' on dumb terminals.
zstyle ':prezto:module:prompt' theme 'cloud' zstyle ':prezto:module:prompt' theme 'peepcode'
# #
# Screen # Screen

70
zsh/zshenv
View file

@ -26,38 +26,6 @@ if [[ -z "$LANG" ]]; then
export LANG='en_US.UTF-8' export LANG='en_US.UTF-8'
fi fi
#
# Paths
#
typeset -gU cdpath fpath mailpath path
# Set the the list of directories that cd searches.
# cdpath=(
# $cdpath
# )
# Set the list of directories that Zsh searches for programs.
path=(
/usr/local/{bin,sbin}
$path
)
# set up local bin dirs
export PATH="$PATH:$HOME/bin:$HOME/.bin"
# shortcuts to projects
export CDPATH="$CDPATH:$HOME/caporaso/qiime2"
export CDPATH="$CDPATH:$HOME/projects"
# set up golang
export GOPATH="/Users/matthew/go"
export PATH="$PATH:$GOPATH/bin"
export CDPATH="$CDPATH:$GOPATH/src/github.com:$GOPATH/src/code.google.com/p:$GOPATH/src/bitbucket.org"
# set miniconda3 bin dir last
export PATH="$PATH:$HOME/miniconda3/bin"
# #
# Less # Less
# #
@ -85,3 +53,41 @@ TMPPREFIX="${TMPDIR%/}/zsh"
if [[ ! -d "$TMPPREFIX" ]]; then if [[ ! -d "$TMPPREFIX" ]]; then
mkdir -p "$TMPPREFIX" mkdir -p "$TMPPREFIX"
fi fi
#
# Paths
#
# shortcuts to projects
export CDPATH="$CDPATH:$HOME/src/biocore"
export CDPATH="$CDPATH:$HOME/src/caporaso-lab"
export CDPATH="$CDPATH:$HOME/src/gregcaporaso"
export CDPATH="$CDPATH:$HOME/src/qiime2"
export CDPATH="$CDPATH:$HOME/src/thermokarst"
export CDPATH="$CDPATH:."
# miniconda
export PATH="/opt/miniconda3/bin:$PATH"
# macports
export PATH="/opt/local/bin:$PATH"
export PATH="/opt/local/sbin:$PATH"
# golang
export GOROOT=/opt/go
export PATH="$GOROOT/bin:$PATH"
typeset -gU cdpath fpath mailpath path
# Set the the list of directories that cd searches.
cdpath=(
$cdpath
)
# Set the list of directories that Zsh searches for programs.
path=(
$path
/usr/local/{bin,sbin}
)
export -U PATH

4
zsh/zshrc
View file

@ -9,10 +9,9 @@ fi
# shortcuts # shortcuts
alias mailserver="sudo python -m smtpd -n -c DebuggingServer localhost:25" alias mailserver="sudo python -m smtpd -n -c DebuggingServer localhost:25"
alias mongod="mongod --config /usr/local/etc/mongod.conf" alias mongod="mongod --config /usr/local/etc/mongod.conf"
alias postgres="postgres -D /usr/local/var/postgres"
alias venv="source venv/bin/activate" alias venv="source venv/bin/activate"
alias devenv="deactivate" alias devenv="deactivate"
alias q="source activate q2dev-2017.10" alias q="source activate q2dev"
alias i="ipython3" alias i="ipython3"
BASE16_SHELL=$HOME/.config/base16-shell/ BASE16_SHELL=$HOME/.config/base16-shell/
@ -62,4 +61,3 @@ function back_things_up() {
ln -s $dest_root/$date $dest_root/latest ln -s $dest_root/$date $dest_root/latest
# TODO: once confident pruning is working well, add that in here # TODO: once confident pruning is working well, add that in here
} }
alias gmg=$GOPATH/bin/go-many-git