diff --git a/README.md b/README.md
index cfa21b2..cbe53c9 100644
--- a/README.md
+++ b/README.md
@@ -3,16 +3,68 @@
```bash
$ git clone https://github.com/thermokarst/dotfiles.git ~/.dotfiles
$ cd ~/.dotfiles
-$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
-$ ./homebrew-install
+$ git remote rename origin thermokarst
+# 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
-$ 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"
$ ./install
$ curl -fLo ~/.vim/autoload/plug.vim --create-dirs https://raw.githubusercontent.com/junegunn/vim-plug/master/plug.vim
$ vim +PlugInstall
-$ mkdir ~/bin
-$ 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
+$ mr checkout
```
+
+## 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)
diff --git a/aspell.en.pws b/aspell.en.pws
index d9fad72..b6bd37c 100644
--- a/aspell.en.pws
+++ b/aspell.en.pws
@@ -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
microbiome
-Microbiome
+py
+cli
+qiime
QIIME
+dev
+wget
metadata
diff --git a/homebrew-install b/homebrew-install
deleted file mode 100644
index 5f76a03..0000000
--- a/homebrew-install
+++ /dev/null
@@ -1,96 +0,0 @@
-#!/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
diff --git a/install.conf.yaml b/install.conf.yaml
index 8c4312b..a3624ad 100644
--- a/install.conf.yaml
+++ b/install.conf.yaml
@@ -13,3 +13,5 @@
~/.zshrc: zsh/zshrc
~/.aspell.en.pws: aspell.en.pws
~/.vimrc: vimrc
+ ~/.mrconfig: mrconfig
+ ~/.taskrc: taskrc
diff --git a/mouse.xml b/mouse.xml
new file mode 100644
index 0000000..a802602
--- /dev/null
+++ b/mouse.xml
@@ -0,0 +1,44 @@
+
+
+ 1390
+ 254
+ 0
+
+ default
+ 1
+ 2
+ 5
+ 41
+ 41
+ 39
+ 40
+ 5
+ 5
+ 5
+ 1
+ 33
+ 34
+ 36
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 1
+ 73
+ 1
+ 72
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 0
+ 1
+
+
\ No newline at end of file
diff --git a/mrconfig b/mrconfig
new file mode 100644
index 0000000..842a679
--- /dev/null
+++ b/mrconfig
@@ -0,0 +1,454 @@
+### 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
diff --git a/ports/PortIndex b/ports/PortIndex
new file mode 100644
index 0000000..d546ab7
--- /dev/null
+++ b/ports/PortIndex
@@ -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
diff --git a/ports/PortIndex.quick b/ports/PortIndex.quick
new file mode 100644
index 0000000..29cd8c9
--- /dev/null
+++ b/ports/PortIndex.quick
@@ -0,0 +1 @@
+tasksh 0
diff --git a/ports/office/tasksh/Portfile b/ports/office/tasksh/Portfile
new file mode 100644
index 0000000..27b95f0
--- /dev/null
+++ b/ports/office/tasksh/Portfile
@@ -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
diff --git a/ports/office/tasksh/files/patch-readline.diff b/ports/office/tasksh/files/patch-readline.diff
new file mode 100644
index 0000000..a4b8ef5
--- /dev/null
+++ b/ports/office/tasksh/files/patch-readline.diff
@@ -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)
diff --git a/taskrc b/taskrc
new file mode 100644
index 0000000..843f756
--- /dev/null
+++ b/taskrc
@@ -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
diff --git a/tmux.conf b/tmux.conf
index f0f571c..bdb3fab 100644
--- a/tmux.conf
+++ b/tmux.conf
@@ -1,18 +1,15 @@
-# Ensure tmux doesn't launch a login shell
-set -g default-command /usr/local/bin/zsh
-
# Automatic window title
setw -g automatic-rename
# 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
set -g prefix C-a
unbind C-b
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
# 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-right-length 140
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 -sg escape-time 0
@@ -49,8 +46,5 @@ set-option -g destroy-unattached 'off'
# Enable mouse control (clickable windows, panes, resizable panes)
set -g mouse on
-bind-key -t vi-copy MouseDragEnd1Pane copy-pipe "pbcopy"
-bind-key -t vi-copy v begin-selection
-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"
+bind-key -Tcopy-mode-vi 'v' send -X begin-selection
+bind-key -Tcopy-mode-vi 'y' send -X copy-pipe-and-cancel pbcopy
diff --git a/vimrc b/vimrc
index b61baaa..936fbb4 100644
--- a/vimrc
+++ b/vimrc
@@ -23,6 +23,20 @@ call plug#begin()
Plug 'francoiscabrol/ranger.vim'
" Delimited file querying
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()
set t_Co=256
@@ -91,8 +105,8 @@ set writebackup
" change the mapleader from \ to ,
let mapleader=" "
-" ranger config
-map :RangerWorkingDirectory
+" fzf config
+map :FZF
" PEP8 formatting
au BufNewFile,BufRead *.py
@@ -125,10 +139,16 @@ nmap l :bnext
" cycle to previous buffer
nmap h :bprevious
-set rtp+=/usr/local/opt/fzf
-
" flake8 config
let g:flake8_show_in_gutter = 1
let g:flake8_error_marker = 'EE'
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
diff --git a/zsh/zpreztorc b/zsh/zpreztorc
index 886d285..bec0fd1 100644
--- a/zsh/zpreztorc
+++ b/zsh/zpreztorc
@@ -87,7 +87,7 @@ zstyle ':prezto:module:git:alias' skip 'yes'
# Set the prompt theme to load.
# Setting it to 'random' loads a random theme.
# Auto set to 'off' on dumb terminals.
-zstyle ':prezto:module:prompt' theme 'cloud'
+zstyle ':prezto:module:prompt' theme 'peepcode'
#
# Screen
diff --git a/zsh/zshenv b/zsh/zshenv
index 0997dee..b57a502 100644
--- a/zsh/zshenv
+++ b/zsh/zshenv
@@ -26,38 +26,6 @@ if [[ -z "$LANG" ]]; then
export LANG='en_US.UTF-8'
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
#
@@ -85,3 +53,41 @@ TMPPREFIX="${TMPDIR%/}/zsh"
if [[ ! -d "$TMPPREFIX" ]]; then
mkdir -p "$TMPPREFIX"
fi
+
+#
+# Paths
+#
+
+# shortcuts to projects
+export CDPATH="$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=(
+ $path
+ /usr/local/{bin,sbin}
+)
+
+export -U PATH
diff --git a/zsh/zshrc b/zsh/zshrc
index e7e36b8..ff2f15e 100644
--- a/zsh/zshrc
+++ b/zsh/zshrc
@@ -9,10 +9,9 @@ fi
# shortcuts
alias mailserver="sudo python -m smtpd -n -c DebuggingServer localhost:25"
alias mongod="mongod --config /usr/local/etc/mongod.conf"
-alias postgres="postgres -D /usr/local/var/postgres"
alias venv="source venv/bin/activate"
alias devenv="deactivate"
-alias q="source activate q2dev-2017.10"
+alias q="source activate q2dev"
alias i="ipython3"
BASE16_SHELL=$HOME/.config/base16-shell/
@@ -62,4 +61,3 @@ function back_things_up() {
ln -s $dest_root/$date $dest_root/latest
# TODO: once confident pruning is working well, add that in here
}
-alias gmg=$GOPATH/bin/go-many-git