From 8d16ed159ba59a02453c0111155fc8f51bcfba66 Mon Sep 17 00:00:00 2001 From: Matthew Dillon Date: Tue, 12 Feb 2019 10:15:47 -0700 Subject: [PATCH] Misc Updates (#1) --- README.md | 66 ++- aspell.en.pws | 16 +- homebrew-install | 96 ---- install.conf.yaml | 2 + mouse.xml | 44 ++ mrconfig | 454 ++++++++++++++++++ ports/PortIndex | 2 + ports/PortIndex.quick | 1 + ports/office/tasksh/Portfile | 35 ++ ports/office/tasksh/files/patch-readline.diff | 42 ++ taskrc | 47 ++ tmux.conf | 16 +- vimrc | 30 +- zsh/zpreztorc | 2 +- zsh/zshenv | 70 +-- zsh/zshrc | 4 +- 16 files changed, 770 insertions(+), 157 deletions(-) delete mode 100644 homebrew-install create mode 100644 mouse.xml create mode 100644 mrconfig create mode 100644 ports/PortIndex create mode 100644 ports/PortIndex.quick create mode 100644 ports/office/tasksh/Portfile create mode 100644 ports/office/tasksh/files/patch-readline.diff create mode 100644 taskrc 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