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epigenomiking

Francois Serra fransua

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epigenomiking
51 followers · 56 following
  • Computational Biology - BSC
  • Barcelona, Spain
  • 16:16 (UTC +02:00)
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@sestaton
sestaton / build_ecolopy.sh
Last active August 29, 2015 13:57
build deps for GMPY2 and install Ecolopy
#!/bin/bash
## Location for local build of gmpy2 and deps
cd apps
mkdir gmpy2 && cd gmpy2
## Download and compile gmp
wget https://ftp.gnu.org/gnu/gmp/gmp-5.1.3.tar.bz2 && tar xjf gmp-5.1.3.tar.bz2
cd gmp-5.1.3
./configure --prefix=/home/jmblab/statonse/apps/gmpy2
@nathanhaigh
nathanhaigh / sra_process.sh
Created July 11, 2013 05:24
Example script for downloading (using aspera) and extracting paired-end data from the SRA and performing parallel compression using pigz.
#!/bin/bash
# Bash script to download a bunch of *.sra files from the NCBI SRA, using
# the aspera client, and extract FASTQ data using the SRA Toolkit.
max_bandwidth_mbps=50
# These SRA files are for the durum genome
files=(
'SRR567512.sra'
'SRR567559.sra'
@fransua
fransua / search_palindromes.py
Created November 8, 2012 18:47
searchs for potential loops in single strand sequences
"""
08 Nov 2012
"""
from string import maketrans
REV = maketrans('ATGC', 'TACG')
@andrewyatz
andrewyatz / synteny_to_psl.pl
Created May 3, 2011 08:38
A script for extracting synteny regions from Ensembl & Ensembl Genomes databases into PSL (UCSC/Blat alignment report format).
#!/bin/env perl
use strict;
use warnings;
use Getopt::Long;
use Pod::Usage;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::Scalar qw(wrap_array);
use IO::String;