hmartiniano

#!/usr/bin/python

# Run KING to generate sample QC and IBD summary stats
# ./king_1.9 -b <data>.bed --bysample --prefix <prefix_for_output>
# ./king_1.9 -b <data>.bed --kinship --related --degree 2 --prefix <prefix_for_output>
#
# Run this script to create a list of exclusions (member of pair with least data will be excluded)
# python king.py --prefix <prefix_for_output> --out <output_file_name>

# Add error if no samples in kinship file.

hmartiniano

import subprocess
from goatools.semantic import get_info_content
from goatools.base import get_godag
from goatools.semantic import TermCounts
from goatools.anno.factory import get_objanno


godag = get_godag("go-basic.obo")
return_code = subprocess.call("wget https://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/goa_human.gpa.gz && gunzip goa_human.gpa.gz", shell=True)
anno = get_objanno('goa_human.gpa', 'gpad', godag=godag)

hmartiniano

from pybiomart import Dataset

dataset = Dataset(name='hsapiens_gene_ensembl', host='http://www.ensembl.org')


df = dataset.query(attributes=['ensembl_gene_id', 'external_gene_name', 'ensembl_transcript_id', 'transcript_is_canonical'])

hmartiniano

#!/usr/bin/env python

# Author: Guillaume Bouvier -- guillaume.bouvier@pasteur.fr
# https://research.pasteur.fr/en/member/guillaume-bouvier/
# 2016-08-26 13:20:35 (UTC+0200)

# DSSP_SECONCARY.PY

# Trajectories of Secondary Structure by DSSP
#    The keys  [" ","B","E","G","H","I","T","S"]

hmartiniano

#!/bin/bash

cd /opt

export VERSION=1.14.12 OS=linux ARCH=amd64 && \
    wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz && \
    sudo tar -C /usr/local -xzvf go$VERSION.$OS-$ARCH.tar.gz && \
    rm go$VERSION.$OS-$ARCH.tar.gz
    
echo 'export GOPATH=${HOME}/go' >> ~/.bashrc && \

hmartiniano

---
- hosts: all
  user: root
  vars:
    users:
    - username: data
      groups: ""
      shell: /bin/true
    - username: "test"
      groups: sudo, data, docker

hmartiniano

---
- hosts: all
  user: root
  tasks:
  - name: Install prerequisites
    apt:
      name: ['apt-transport-https', 'ca-certificates', 'curl', 'gnupg2' ,'software-properties-common']
      update_cache: yes

  - name: Add Docker GPG key

hmartiniano

---
- hosts: compute
  vars:
    singularity_version: 3.5.2
  become: yes
  tasks:
  - name: install prerequisites
    apt:
      update_cache: yes
      autoclean: yes

hmartiniano

' Adapted from https://stackoverflow.com/questions/34280088/ms-word-macro-for-converting-track-changes-markup-into-text 
Sub TrackChangesToMarkup()

Dim chgAdd As Word.Revision

If ActiveDocument.Revisions.Count = 0 Then
    MsgBox "There are no revisions in this document", vbOKOnly
Else
    ActiveDocument.TrackRevisions = False
    For Each chgAdd In ActiveDocument.Revisions

hmartiniano

#!/bin/bash
# script to transfer the contents of a remote directory to a local machine
# the script use a brute force approach where the transfer is repeated if
# the return code of the rsync command is anything other than 0 (e.g. if an error occurs)

USERNAME=root
REMOTE_HOST=192.168.1.1
REMOTE_DIR=/home/example
LOCAL_DIR=.