telatin

Bootstrap: docker
From: centos:centos7.6.1810


%environment
    source /opt/software/conda/bin/activate /opt/software/conda_env

 
%post
    yum -y install epel-release wget which nano curl zlib-devel

telatin

#!/usr/bin/env python3

from scholarly import scholarly
import sys
def stderr(*args, **kwargs):
    print(*args, file=sys.stderr, **kwargs)


author_id = 'Bua3yncAAAAJ'
author = scholarly.search_author_id(author_id).fill()

telatin

#!/usr/bin/env python3
"""
Rename Mp3 from iTunes library (F00/FAYX.mp3) to

outputdir/AlbumName/Artist-TrackTitle.mp3

"""
import eyed3
import os, sys, re

telatin

#!/usr/bin/env perl

use 5.012;
use Term::ANSIColor;

# Andrea Telatin <[email protected]>
# Sept 2014

my $version = '0.04';

telatin

#!/bin/bash
#wget https://files.plutof.ut.ee/public/orig/98/AE/98AE96C6593FC9C52D1C46B96C2D9064291F4DBA625EF189FEC1CCAFCF4A1691.gz

#Decompress. The downloaded file is actually a tar.gz file and so needs to be decompressed with:
tar xzf 98AE96C6593FC9C52D1C46B96C2D9064291F4DBA625EF189FEC1CCAFCF4A1691.gz

#Move into the developer directory.
cd sh_qiime_release_04.02.2020/developer/

#Fix formatting errors that prevent importation of the reference sequences into QIIME2. 

telatin

IMG=/path/to/img
singularity exec $IMG $(basename "$0") "$@"

telatin

#!/bin/sh
EXT='fastq.gz'
USER=ftp-username
PASS=ftp-password
HOST=ftp.host
REMOTEDIR=uploads/

# see "-z" to try to resume transfers
#ncftpput -u "$USER" -p "$PASS"  "$HOST" "$REMOTEDIR" *.$EXT

telatin

#!/usr/bin/env perl

use 5.012;
use warnings;
use lib '/qib/platforms/Informatics/GMH/bin/perl5/lib/perl5/';
use Getopt::Long;
use FASTX::Reader;

my $opt_contigs;
my $opt_gff;

telatin

library(edgeR)

# Input file and columns (ctrl, treated)
x <- read.delim("counts.tsv",row.names="Geneid")
group <- factor(c(1,1,1,2,2,2))


y <- DGEList(counts=x,group=group)
y <- calcNormFactors(y)
design <- model.matrix(~group)

telatin

import heapqueue

type
  coverage = ref object
    forward: int
    reverse: int


# Class that stores info about the end position of alignments, used in the alignment queue
type