Instructions:
https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/amazon-linux-2-virtual-machine.html
OS images can be found at:
https://cdn.amazonlinux.com/os-images/2.0.20220912.1/
Generate seed iso
#!/usr/bin/env python | |
import sys | |
import json | |
if len(sys.argv) != 2: | |
exit() | |
print("{\"docs\": [") | |
with open(sys.argv[1]) as infile: |
Instructions:
https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/amazon-linux-2-virtual-machine.html
OS images can be found at:
https://cdn.amazonlinux.com/os-images/2.0.20220912.1/
Generate seed iso
#!/usr/bin/env bash | |
CONFILE=${1:-nextflow.config} | |
OUTDIR=${2:-./singularity} | |
if [ ! -e $CONFILE ]; then | |
echo "$CONFILE does not exist" | |
exit | |
fi |
echo "scale=2; $(fd --full-path -t f --regex '\.fa+$|\.fasta$' /nfs/db/ensembl -x du {}|datamash sum 1) / (1024^3)" | bc |
#!/usr/bin/env bash | |
# Placed in a different machine than production with a cron | |
# Server | |
URL="https://example.com" | |
HTTP=$(curl --silent --insecure -m 30 -I GET "${URL}"|perl -lane 'if ($_=~/HTTP/) {$_=~/HTTP\S+\s+(\d+)\s+/; print $1;} ') | |
# Normal situation codes | |
CODES=(200) | |
MSG="Something is wrong with ${URL}. CODE: ${HTTP}" |
[INCLUDES] | |
before = common.conf | |
[Definition] | |
_auth_worker = (?:dovecot: )?auth(?:-worker)? | |
_daemon = (?:dovecot(?:-auth)?|auth) | |
prefregex = ^%(__prefix_line)s(?:%(_auth_worker)s(?:\([^\)]+\))?: )?(?:%(__pam_auth)s(?:\(dovecot:auth\))?: |(?:pop3|imap)-login: )?(?:Error: )?<F-CONTENT>.+</F-CONTENT>$ |
on: | |
push: | |
branches: | |
# Default branches below | |
- main | |
- master | |
name: renderbook |
# -*- coding: utf-8 -*- | |
""" | |
Pergola webservice client | |
~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
More details at: https://pergola.crg.eu | |
Usage: python pergola-webservice.py myconfig.json myoutput.zip | |
""" | |
import requests | |
import json | |
import sys |
#!/usr/bin/env perl | |
# List of IDs - one per line | |
my $list = shift; | |
# File with potential IDs, it can be GFF but also othersH | |
my $gff = shift; | |
my @ids; | |
open( LIST, $list ) || die "Cannot open $list"; |
#!/bin/bash | |
# Based on https://github.com/sylabs/singularity/issues/1537 | |
# Usage: bash docker2singularity.sh mydockerimg mysingularity.simg | |
set -ueo pipefail | |
IMG=$1 | |
FILEOUT=$2 | |
PORT=${3:-5000} |