oweidner

#!/bin/bash

## Description: 
## 
## pystrap.sh is a shell script to bootstrap a Python environment
## in user space that includes pip and virtualenv. It can be used 
## to bootstrap a Python environment remotely, e.g., on a cluster
## where setuptools, virtualenv, etc. are usually not installed.
##        
## Example: pystrap via Globus:

oweidner

(*  RSL script that bootstraps Air (http://oweidner.github.com/air/)        *)
(*  on a remote machine and uses it to execute /bin/id.                     *)
(*                                                                          *)
(*  Copyright 2011 Ole Christian Weidner ([email protected])               *)
(*  Latest version: https://gist.github.com/1322898                         *)
(*                                                                          *)
(*  Run it like this (replace GRAM URL with your own)                       *)
(*  globusrun -b -r tuscany.med.harvard.edu:2119/jobmanager-fork -f job.rsl *) 

&(executable=/bin/sh)

oweidner

#!/bin/bash

##  PBS script that bootstraps Air (http://oweidner.github.com/air/)    
##  on a remote machine and uses it to execute /bin/id.                 
##                                                                      
##  Copyright 2011 Ole Christian Weidner ([email protected])           
##  Latest version: https://gist.github.com/gists/1323198                     
##                                                                      
##  Run it with qsub: qsub air_via_pbs.sh
##  or even directly via curl/qsub:

oweidner

#!/usr/bin/env python

import sys, time
import bliss.saga as saga

def main(jobno, session, jobservice):
   
    bfast_base_dir = saga.Url("sftp://india.futuregrid.org/N/u/oweidner/software/bfast/")
 
    try:

oweidner

universe=vanilla
executable=/home/oweidner/software/bfast/bin/bfast
transfer_executable=True
when_to_transfer_output = ON_EXIT
transfer_input_files=/home/oweidner/software/bfast/data/small/reference/hg_2122.fa,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.10.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.1.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.2.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.3.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.4.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.5.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.6.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.7.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.8.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.9.1.bif,/home/oweidner/software/bfast/data/small/reference/hg_2122.fa.cs.brg,/home/oweidner

oweidner

import saga

try:
  jd = saga.job.description()
  jd.set_attribute       ("Executable", "/home/oweidner/software/bfast/bin/bfast")
  jd.set_vector_attribute("Arguments", ["match", "-r", "reads.10.fastq", "-A", "1", "-f", "hg_2122.fa"])
  jd.set_attribute       ("Output", "my_out.$(Cluster).$(Process)")
  jd.set_attribute       ("Error", "my_err.$(Cluster).$(Process)")

  input_files = ["/home/oweidner/software/bfast/data/small/reference/hg_2122.fa > hg_2122.fa",

oweidner

""" Example application demonstrating how to submit a simple 
    /bin/date job with BigJob. 
        
"""

import os
import time
import pdb
import sys

oweidner

""" Example application demonstrating how to submit a simple 
    /bin/echo job with BigJob. 
        
"""

import os
import time
import pdb
import sys

oweidner

#!/bin/bash -l

# Copyright 2022 Ole Weidner ([email protected])
# Licensed under the MIT License

# -----------------------------------------------------------------------------
# Global variables.
#
UPDATE_INTERVAL=300
BUILD_COMMAND="true"

oweidner

using Pkg
Pkg.add("Plots")

using Plots
gr()

# Generalized SuperformulaU 2D returns the radius for a given angle phi.
SuperformulaU2D(phi, a, b, y, z , n1, n2, n3) = 
    ( abs( cos(y*phi/4) / a )^n2 + abs( sin(z*phi/4) / b )^n3 ) ^ (-1/n1)