pansapiens

#!/bin/bash

set -e
# Downloads the lastet release of Uniprot, putting it in a release-specific directory.
# Creates associated BLAST databases.

# We need makeblastdb on our PATH, somehow
# module load blast

# Better to use a stable DOWNLOAD_TMP name to support resuming downloads

pansapiens

#!/bin/sh
set -e

if grep PRIVATE $1 >/dev/null; then
   echo "Use the public key ($1.pub), not the private one !"
   exit -1
fi

cat $1 | ssh $2 'umask 0077; mkdir -p .ssh; cat >> .ssh/authorized_keys && echo "Key $1 added to .ssh/authorized_keys on $2"'

pansapiens

##
#  Update - no longer works. You need to also:
#  edit: /lib/systemd/system/docker.service
#  then run: sudo systemctl daemon-reload
#  see, https://medium.com/@ibrahimgunduz34/how-to-change-docker-data-folder-configuration-33d372669056
#
#  TODO: Fix this to use sed or similar to edit /lib/systemd/system/docker.service
##

# From: https://forums.docker.com/t/how-do-i-change-the-docker-image-installation-directory/1169

pansapiens

import requests
from cashier import cache

"""
TO  ALL MY INTELLIGENT FRIENDS: WHAT DO THESE 7 WORDS HAVE IN COMMON?

I  am sending this only to my smart friends. I could not figure it out. See if  you can figure out what these seven words all have in  common

1.  Banana
2.  Dresser

pansapiens

# Lightly modified from: https://gist.github.com/kjpgit/ceab4fc029c778dd1675bea8592e3bc1
# Useful to ensure two copies of a script aren't running concurrently (assuming they use
# the same lock file, trying to lock it twice will raise IOError).
import fcntl

def _lock_file_exclusively(path):
    """
    Open @path and lock it exlusively.
    Return: file object, which you must maintain a reference to 
    (if it is closed, the lock is released).

pansapiens

#!/bin/bash
# For MyTardis 3.7 - YMMV for other versions

set USER=ubuntu
set MYTARDIS_ADMIN_NAME=admin
set [email protected]
set MYTARDIS_DATA_DIR=/data/mytardis
set SETUP_DYNAMIC_DNS=no
set CREATE_DATA_VOLUME=no

pansapiens

#!/usr/bin/env python
# Creates a PDF from a set of images in a directory (one image per page, alphanumeric ordering).
#
# Usage:
# python images2pdf.py output_file.pdf
#
# Requires:
# pip install fpdf

from fpdf import FPDF

pansapiens

pansapiens

friend = {'}':'{', ']':'[', ')':'('}
close = friend.keys()
open = friend.values()

def check(input):
    stack = []
    for c in input:
        if c in open:
            stack.append(c)
        elif c in close:

pansapiens

############################################################
# Dockerfile to build bcl2fastq container images
# Based on CentOS images made by fatherlinux
# fatherlinux is a RedHat developer
# http://developerblog.redhat.com/2014/05/15/practical-introduction-to-docker-containers/
# Fork from version by: Cyril Firmo <[email protected]>
############################################################
# Build:
# docker build -t bcl2fastq:2.19.0.316 -t bcl2fastq:2.19 -t bcl2fastq:latest .
#