Mike Dacre MikeDacre
MikeDacre
/ python.snippets
Last active
June 29, 2024 18:15
UltiSnips: Add import to top of file with other imports
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| global !p | |
| def first_blank_line(): | |
| """ Search current vim buffer for first blank line. If not found return current line """ | |
| b = snip.buffer | |
| index = 0 | |
| break_index = 100 | |
| com_delim = re.compile(r'^(\s+)?(""")') | |
| in_comment = False | |
| for line in b: | |
| index += 1 |
MikeDacre
/ format_alleleseq_output.py
Created
December 15, 2015 01:08
Format the output of the alleleseq pipeline into gene and snp level tab-delimited outputs sorted by tissue
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| #!/usr/bin/env python3 | |
| # -*- coding: utf-8 -*- | |
| # vim:fenc=utf-8 tabstop=4 expandtab shiftwidth=4 softtabstop=4 | |
| """ | |
| #============================================================================# | |
| # # | |
| # AUTHOR: Michael D Dacre, [email protected] # | |
| # ORGANIZATION: Stanford University # | |
| # LICENSE: MIT License, property of Stanford, use as you wish # | |
| # CREATED: 2015-12-13 10:07 # |
MikeDacre
/ nicstat-PKGBUILD.patch
Created
August 11, 2015 18:02
Patch for nicstat PKGBUILD from version 1.92 to 1.95
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| --- nicstat/PKGBUILD 2015-06-14 06:52:34.000000000 -0700 | |
| +++ PKGBUILD 2015-08-11 10:56:27.331639326 -0700 | |
| @@ -3,7 +3,7 @@ | |
| # vim:set ts=2 sw=2 et ft=sh tw=100: expandtab | |
| pkgname=nicstat | |
| -pkgver=1.92 | |
| +pkgver=1.95 | |
| pkgrel=3 | |
| pkgdesc='Network traffic statics utility' |
MikeDacre
/ tmux-server-filtered.diff
Last active
August 29, 2015 14:25
Diff of functioning and nonfunctioning tpm tmux server logs. Left file (>) is functional, right file (<) is not
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| 75c75 | |
| < cmdq set-option -g default-shell /usr/bin/zsh (client -1) | |
| --- | |
| > cmdq set-option -g default-shell /afs/ir/users/d/a/dacre/usr/bin/zsh (client -1) | |
| 113c113 | |
| < cmdq set-environment -g TMUX_PLUGIN_MANAGER_PATH /home/dacre/.tmux/plugins/ (client 11) | |
| --- | |
| > cmdq set-environment -g TMUX_PLUGIN_MANAGER_PATH /afs/ir/users/d/a/dacre/.tmux/plugins/ (client 11) | |
| 115c115 | |
| < cmdq bind-key I run-shell /home/dacre/.tmux/plugins/tpm/scripts/install_plugins.sh >/dev/null 2>&1 (client 11) |
MikeDacre
/ tmux-server.diff
Created
July 23, 2015 18:33
Diff of https://gist.github.com/MikeDacre/f437480f43f741c1413b and https://gist.github.com/MikeDacre/66de259f2a18c42785a0
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| 1,74c1,74 | |
| < server started, pid 12371 | |
| < cmdq 0x1b73ce0: bind-key C-b send-prefix (client -1) | |
| < cmdq 0x1b73ce0: bind-key C-o rotate-window (client -1) | |
| < cmdq 0x1b73ce0: bind-key C-z suspend-client (client -1) | |
| < cmdq 0x1b73ce0: bind-key Space next-layout (client -1) | |
| < cmdq 0x1b73ce0: bind-key ! break-pane (client -1) | |
| < cmdq 0x1b73ce0: bind-key " split-window (client -1) | |
| < cmdq 0x1b73ce0: bind-key # list-buffers (client -1) | |
| < cmdq 0x1b73ce0: bind-key $ command-prompt -I#S "rename-session '%%'" (client -1) |
MikeDacre
/ tmux-server-12371.log
Created
July 23, 2015 18:23
tmux -vvvv server log output for Arch Linux machine; fails to execute tpm
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| server started, pid 12371 | |
| cmdq 0x1b73ce0: bind-key C-b send-prefix (client -1) | |
| cmdq 0x1b73ce0: bind-key C-o rotate-window (client -1) | |
| cmdq 0x1b73ce0: bind-key C-z suspend-client (client -1) | |
| cmdq 0x1b73ce0: bind-key Space next-layout (client -1) | |
| cmdq 0x1b73ce0: bind-key ! break-pane (client -1) | |
| cmdq 0x1b73ce0: bind-key " split-window (client -1) | |
| cmdq 0x1b73ce0: bind-key # list-buffers (client -1) | |
| cmdq 0x1b73ce0: bind-key $ command-prompt -I#S "rename-session '%%'" (client -1) | |
| cmdq 0x1b73ce0: bind-key % split-window -h (client -1) |
MikeDacre
/ tmux-server-32072.log
Created
July 23, 2015 18:22
tmux -vvvv server log output for Ubuntu machine; successfully executes tpm
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| server started, pid 32072 | |
| cmdq 0x1e8a6f0: bind-key C-b send-prefix (client -1) | |
| cmdq 0x1e8a6f0: bind-key C-o rotate-window (client -1) | |
| cmdq 0x1e8a6f0: bind-key C-z suspend-client (client -1) | |
| cmdq 0x1e8a6f0: bind-key Space next-layout (client -1) | |
| cmdq 0x1e8a6f0: bind-key ! break-pane (client -1) | |
| cmdq 0x1e8a6f0: bind-key " split-window (client -1) | |
| cmdq 0x1e8a6f0: bind-key # list-buffers (client -1) | |
| cmdq 0x1e8a6f0: bind-key $ command-prompt -I#S "rename-session '%%'" (client -1) | |
| cmdq 0x1e8a6f0: bind-key % split-window -h (client -1) |
MikeDacre
/ run-lines.vim
Created
April 13, 2015 19:56
Vim-IPython IDE. Execute python and shell lines, cells (like matlab), selected text, and blocks in an interactive session using vim-screen.
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| "" This part runs commands in an interactive session, it requires | |
| "" [vim-screen](https://github.com/ervandew/screen) to function | |
| " Start Screen Session, Default to IPython in python files | |
| fun StartScreenTmux() | |
| if !g:ScreenShellActive | |
| if &filetype == 'python' | |
| :IPython | |
| elseif &filetype == 'python3' | |
| :IPython |
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| #!/bin/bash | |
| if [ $# != 2 ]; then | |
| echo "USAGE: watch_job <submit_script> <email_address>" | |
| exit 1 | |
| fi | |
| job=$1 | |
| email=$2 | |
| while true; do |
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| #!/usr/bin/env python3 | |
| import subprocess, sys, os, re | |
| from collections import OrderedDict | |
| jvarkit="/usr/share/jvarkit" | |
| install_location="/usr/local/bin" | |
| def print_tools(tools): | |
| """ Pretty print a list of running interactive jobs from create_queue """ |