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Vladimir (Vlad) Kiselev wikiselev

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wikiselev / create-azure-batch-pool-nf.py
Created December 15, 2022 16:25
A script to configure (file share and blob container mounting) and create an Azure Batch pool suitable for Nextflow Tower.
from azure.identity import DefaultAzureCredential
from azure.mgmt.batch import BatchManagementClient
import os
from dotenv import load_dotenv
import sys
load_dotenv()
AZURE_SUBSCRIPTION_ID = os.getenv('AZURE_SUBSCRIPTION_ID')
AZURE_BATCH_RESOURCE_GROUP_NAME = os.getenv('AZURE_BATCH_RESOURCE_GROUP_NAME')
@wikiselev
wikiselev / easy-Report.sh
Created November 2, 2013 22:58
Quick run of easy-Report script All output files will be located in 'report' folder
git clone https://github.com/wikiselev/easy-Report.git
cd easy-Report
Rscript easy-Report.R script.Rmd report
@wikiselev
wikiselev / copasi_api_model_sbml_load.py
Created January 8, 2013 15:13
# Acquire the model from an SBML file
dataModel = CCopasiRootContainer.addDatamodel()
dataModel.importSBML("model_name.xml")
model = dataModel.getModel()
@wikiselev
wikiselev / IGV_snapshot_combine.tex
Created October 19, 2012 15:57
Tex script to combine snapshot created by IGV genomic browser
\documentclass[landscape,letterpaper]{article}
\renewcommand{\rmdefault}{phv} % Arial
\setlength{\oddsidemargin}{-0.9in}
\setlength{\textwidth}{10.7in}
\setlength{\textheight}{7in}
\setlength{\topmargin}{-1.0in}
\setlength{\headsep}{0.25in}
\setlength{\parskip}{1.2ex}
\setlength{\parindent}{0mm}
@wikiselev
wikiselev / IGV_script.txt
Created October 19, 2012 15:37
Script for IGV automated snapshotting
new
load /Users/Vladimir/IGV/protein_list/protein1.BED,/Users/Vladimir/IGV/protein_list/protein2.BED # all other protein data files
snapshotDirectory /Users/Vladimir/IGV/snapshots/
goto gene1_location
snapshot gene1.png
goto gene2_location
@wikiselev
wikiselev / gene_list
Created October 19, 2012 15:31
gene_list example
# Examples of the values:
gene1 # PTGS2
gene1_full_name # Prostaglandin-endoperoxide synthase 2 (COX-2)
gene1_url # http://www.ncbi.nlm.nih.gov/gene/5743
gene1_location # chr1:186,640,920-186,641,060
gene2
gene2_full_name
gene2_url
gene2_location