BOL: All

Pack a perl program with their dependencies on Ubuntu !

Jit — Mon, 16 Mar 2020 03:56:48 -0500

#Follow steps to create your own executable ./web

jit@jit-HP-Pro-3335-MT:~/Downloads/autoConTAMPR/bin$ sudo apt install libpar-packer-perl
Reading package lists... Done
Building dependency tree       
Reading state information... Done
The following additional packages will be installed:
  libgetopt-argvfile-perl libmodule-scandeps-perl libmodule-signature-perl libpar-dist-perl
  libpar-perl
The following NEW packages will be installed:
  libgetopt-argvfile-perl libmodule-scandeps-perl libmodule-signature-perl libpar-dist-perl
  libpar-packer-perl libpar-perl
0 upgraded, 6 newly installed, 0 to remove and 0 not upgraded.
Need to get 2,098 kB of archives.
After this operation, 5,989 kB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libgetopt-argvfile-perl all 1.11-3 [26.4 kB]
Get:2 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libmodule-scandeps-perl all 1.24-1 [28.6 kB]
Get:3 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libmodule-signature-perl all 0.81-1 [22.9 kB]
Get:4 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libpar-dist-perl all 0.49-2 [22.4 kB]
Get:5 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libpar-perl all 1.015-1 [74.1 kB]
Get:6 http://in.archive.ubuntu.com/ubuntu bionic/universe amd64 libpar-packer-perl amd64 1.041-2 [1,924 kB]
Fetched 2,098 kB in 3s (729 kB/s)             
Selecting previously unselected package libgetopt-argvfile-perl.
(Reading database ... 193749 files and directories currently installed.)
Preparing to unpack .../0-libgetopt-argvfile-perl_1.11-3_all.deb ...
Unpacking libgetopt-argvfile-perl (1.11-3) ...
Selecting previously unselected package libmodule-scandeps-perl.
Preparing to unpack .../1-libmodule-scandeps-perl_1.24-1_all.deb ...
Unpacking libmodule-scandeps-perl (1.24-1) ...
Selecting previously unselected package libmodule-signature-perl.
Preparing to unpack .../2-libmodule-signature-perl_0.81-1_all.deb ...
Unpacking libmodule-signature-perl (0.81-1) ...
Selecting previously unselected package libpar-dist-perl.
Preparing to unpack .../3-libpar-dist-perl_0.49-2_all.deb ...
Unpacking libpar-dist-perl (0.49-2) ...
Selecting previously unselected package libpar-perl.
Preparing to unpack .../4-libpar-perl_1.015-1_all.deb ...
Unpacking libpar-perl (1.015-1) ...
Selecting previously unselected package libpar-packer-perl.
Preparing to unpack .../5-libpar-packer-perl_1.041-2_amd64.deb ...
Unpacking libpar-packer-perl (1.041-2) ...
Setting up libmodule-scandeps-perl (1.24-1) ...
Setting up libgetopt-argvfile-perl (1.11-3) ...
Setting up libpar-dist-perl (0.49-2) ...
Setting up libmodule-signature-perl (0.81-1) ...
Setting up libpar-perl (1.015-1) ...
Setting up libpar-packer-perl (1.041-2) ...
Processing triggers for man-db (2.8.3-2ubuntu0.1) ...

#you can find the test script web.pl at https://bioinformaticsonline.com/snippets/view/41440/perl-script-to-reads-and-extract-webpage-contents

jit@jit-HP-Pro-3335-MT:~/Downloads/autoConTAMPR/bin$ pp web.pl -o web web.pl 

jit@jit-HP-Pro-3335-MT:~/Downloads/autoConTAMPR/bin$ ./web https://bioinformaticsonline.com  

#It return this

Wide character in say at script/dumptest.pl line 13.



	
	
	
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#More at https://metacpan.org/pod/pp

Perl script to reads and extract webpage contents !

Jit — Sat, 14 Mar 2020 03:44:52 -0500

use 5.010;
use strict;
use warnings;

use WWW::Mechanize;

my ($url) = @ARGV;
die "Usage: $0 URL\n" if not $url;

my $w = WWW::Mechanize->new;

$w->get($url);
say $w->content;

#Run 
#jit@jit-HP-Pro-3335-MT:~/Downloads/testDock$ perl web.pl https://bioinformaticsonline.com

Installing docker for Bioinformatics on Ubuntu !

Jit — Sat, 14 Mar 2020 02:30:14 -0500

jit@jit-HP-Pro-3335-MT:~/Downloads$ sudo apt-get remove docker docker-engine docker.io containerd runc
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Package 'docker-engine' is not installed, so not removed
Package 'docker' is not installed, so not removed
Package 'containerd' is not installed, so not removed
Package 'docker.io' is not installed, so not removed
Package 'runc' is not installed, so not removed
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.

jit@jit-HP-Pro-3335-MT:~/Downloads$ curl -fsSL https://get.docker.com -o get-docker.sh

jit@jit-HP-Pro-3335-MT:~/Downloads$ chmod 777 get-docker.sh

jit@jit-HP-Pro-3335-MT:~/Downloads$ ./get-docker.sh 
# Executing docker install script, commit: 442e66405c304fa92af8aadaa1d9b31bf4b0ad94
+ sudo -E sh -c apt-get update -qq >/dev/null
+ sudo -E sh -c DEBIAN_FRONTEND=noninteractive apt-get install -y -qq apt-transport-https ca-certificates curl >/dev/null
+ sudo -E sh -c curl -fsSL "https://download.docker.com/linux/ubuntu/gpg" | apt-key add -qq - >/dev/null
Warning: apt-key output should not be parsed (stdout is not a terminal)
+ sudo -E sh -c echo "deb [arch=amd64] https://download.docker.com/linux/ubuntu bionic stable" > /etc/apt/sources.list.d/docker.list
+ sudo -E sh -c apt-get update -qq >/dev/null
+ [ -n  ]
+ sudo -E sh -c apt-get install -y -qq --no-install-recommends docker-ce >/dev/null
+ sudo -E sh -c docker version
Client: Docker Engine - Community
 Version:           19.03.8
 API version:       1.40
 Go version:        go1.12.17
 Git commit:        afacb8b7f0
 Built:             Wed Mar 11 01:25:46 2020
 OS/Arch:           linux/amd64
 Experimental:      false

Server: Docker Engine - Community
 Engine:
  Version:          19.03.8
  API version:      1.40 (minimum version 1.12)
  Go version:       go1.12.17
  Git commit:       afacb8b7f0
  Built:            Wed Mar 11 01:24:19 2020
  OS/Arch:          linux/amd64
  Experimental:     false
 containerd:
  Version:          1.2.13
  GitCommit:        7ad184331fa3e55e52b890ea95e65ba581ae3429
 runc:
  Version:          1.0.0-rc10
  GitCommit:        dc9208a3303feef5b3839f4323d9beb36df0a9dd
 docker-init:
  Version:          0.18.0
  GitCommit:        fec3683
If you would like to use Docker as a non-root user, you should now consider
adding your user to the "docker" group with something like:

  sudo usermod -aG docker jit

Remember that you will have to log out and back in for this to take effect!

WARNING: Adding a user to the "docker" group will grant the ability to run
         containers which can be used to obtain root privileges on the
         docker host.
         Refer to https://docs.docker.com/engine/security/security/#docker-daemon-attack-surface
         for more information.

jit@jit-HP-Pro-3335-MT:~/Downloads$ docker

Usage:	docker [OPTIONS] COMMAND

A self-sufficient runtime for containers

Options:
      --config string      Location of client config files (default "/home/jit/.docker")
  -c, --context string     Name of the context to use to connect to the daemon (overrides DOCKER_HOST env var and default context set with "docker context use")
  -D, --debug              Enable debug mode
  -H, --host list          Daemon socket(s) to connect to
  -l, --log-level string   Set the logging level ("debug"|"info"|"warn"|"error"|"fatal") (default "info")
      --tls                Use TLS; implied by --tlsverify
      --tlscacert string   Trust certs signed only by this CA (default "/home/jit/.docker/ca.pem")
      --tlscert string     Path to TLS certificate file (default "/home/jit/.docker/cert.pem")
      --tlskey string      Path to TLS key file (default "/home/jit/.docker/key.pem")
      --tlsverify          Use TLS and verify the remote
  -v, --version            Print version information and quit

Management Commands:
  builder     Manage builds
  config      Manage Docker configs
  container   Manage containers
  context     Manage contexts
  engine      Manage the docker engine
  image       Manage images
  network     Manage networks
  node        Manage Swarm nodes
  plugin      Manage plugins
  secret      Manage Docker secrets
  service     Manage services
  stack       Manage Docker stacks
  swarm       Manage Swarm
  system      Manage Docker
  trust       Manage trust on Docker images
  volume      Manage volumes

Commands:
  attach      Attach local standard input, output, and error streams to a running container
  build       Build an image from a Dockerfile
  commit      Create a new image from a container's changes
  cp          Copy files/folders between a container and the local filesystem
  create      Create a new container
  deploy      Deploy a new stack or update an existing stack
  diff        Inspect changes to files or directories on a container's filesystem
  events      Get real time events from the server
  exec        Run a command in a running container
  export      Export a container's filesystem as a tar archive
  history     Show the history of an image
  images      List images
  import      Import the contents from a tarball to create a filesystem image
  info        Display system-wide information
  inspect     Return low-level information on Docker objects
  kill        Kill one or more running containers
  load        Load an image from a tar archive or STDIN
  login       Log in to a Docker registry
  logout      Log out from a Docker registry
  logs        Fetch the logs of a container
  pause       Pause all processes within one or more containers
  port        List port mappings or a specific mapping for the container
  ps          List containers
  pull        Pull an image or a repository from a registry
  push        Push an image or a repository to a registry
  rename      Rename a container
  restart     Restart one or more containers
  rm          Remove one or more containers
  rmi         Remove one or more images
  run         Run a command in a new container
  save        Save one or more images to a tar archive (streamed to STDOUT by default)
  search      Search the Docker Hub for images
  start       Start one or more stopped containers
  stats       Display a live stream of container(s) resource usage statistics
  stop        Stop one or more running containers
  tag         Create a tag TARGET_IMAGE that refers to SOURCE_IMAGE
  top         Display the running processes of a container
  unpause     Unpause all processes within one or more containers
  update      Update configuration of one or more containers
  version     Show the Docker version information
  wait        Block until one or more containers stop, then print their exit codes

Run 'docker COMMAND --help' for more information on a command.

Uninstall a perl module !

BioStar — Fri, 13 Mar 2020 05:41:10 -0500

# uninstall_perl_module.pl from PerlTricks.com

use 5.14.2;
use ExtUtils::Installed;
use ExtUtils::Packlist;

# Exit unless a module name was passed
die ("Error: no Module::Name passed as an argument. E.G.\n\t perl $0 Module::Name\n") unless $#ARGV == 0;

my $module = shift @ARGV;

my $installed_modules = ExtUtils::Installed->new;

# iterate through and try to delete every file associated with the module
foreach my $file ($installed_modules->files($module)) {
    print "removing $file\n";
    unlink $file or warn "could not remove $file: $!\n";
}

# delete the module packfile
my $packfile = $installed_modules->packlist($module)->packlist_file;
print "removing $packfile\n";
unlink $packfile or warn "could not remove $packfile: $!\n";

# delete the module directories if they are empty
foreach my $dir (sort($installed_modules->directory_tree($module))) {
    print("removing $dir\n");
    rmdir $dir or warn "could not remove $dir: $!\n";
}

#Run
#perl uninstall_perl_module.pl Bio::SCF

Download with Snakemake !

Surabhi Chaudhary — Wed, 11 Mar 2020 07:16:44 -0500

# list sample names & download URLs.
sample_links = {"ERR458493": "https://osf.io/5daup/download",
                "ERR458494":"https://osf.io/8rvh5/download",
                 "ERR458495":"https://osf.io/2wvn3/download",
                 "ERR458500":"https://osf.io/xju4a/download",
                 "ERR458501": "https://osf.io/nmqe6/download",
                 "ERR458502": "https://osf.io/qfsze/download"}

# the sample names are dictionary keys in sample_links. extract them to a list we can use below
SAMPLES=sample_links.keys()

# download yeast rna-seq data from Schurch et al, 2016 study
rule download_all:
    input:
        expand("rnaseq/raw_data/{sample}.fq.gz", sample=SAMPLES)

# rule to download each individual file specified in sample_links
rule download_reads:
    output: "rnaseq/raw_data/{sample}.fq.gz" 
    params:
        # dynamically generate the download link directly from the dictionary
        download_link = lambda wildcards: sample_links[wildcards.sample]
    shell: """
        curl -L {params.download_link} -o {output}
        """

Exit Bash Script When Any Command Fails

Jit — Sat, 07 Mar 2020 01:10:17 -0600

This can actually be done with a single line using the set builtin command with the -e option.

#1------------------------------------------------------------------------
# exit when any command fails
#Putting this at the top of a bash script will cause the script to exit if any commands return a non-zero exit code. 
set -e

#all other commands

#2------------------------------------------------------------------------

#Other fancy way, by keeping the track of each command

# exit when any command fails
set -e

# keep track of the last executed command
trap 'last_command=$current_command; current_command=$BASH_COMMAND' DEBUG
# echo an error message before exiting
trap 'echo "\"${last_command}\" command filed with exit code $?."' EXIT


#3---------------------------------------------------------------------
#With a subs

exit_on_error() {
    exit_code=$1
    last_command=${@:2}
    if [ $exit_code -ne 0 ]; then
        >&2 echo "\"${last_command}\" command failed with exit code ${exit_code}."
        exit $exit_code
    fi
}

# enable !! command completion
set -o history -o histexpand

Install conda on remote server !

Rahul Nayak — Sat, 07 Mar 2020 00:52:01 -0600

Please take a look at the Anaconda repo archive page https://repo.continuum.io/archive/

and select an appropriate version that you like to install.

$ wget -c https://repo.continuum.io/archive/Anaconda3-vers.num-Linux-x86_64.sh
$ bash Anaconda3-version.num-Linux-x86_64.sh

$ wget -c https://repo.continuum.io/archive/Anaconda3-5.0.1-Linux-x86_64.sh
$ bash Anaconda3-5.0.1-Linux-x86_64.sh

OR try this

# Go to home directory
cd ~

# You can change what anaconda version you want at 
# https://repo.continuum.io/archive/
wget https://repo.continuum.io/archive/Anaconda3-4.2.0-Linux-x86_64.sh
bash Anaconda3-4.2.0-Linux-x86_64.sh -b -p ~/anaconda
rm Anaconda3-4.2.0-Linux-x86_64.sh
echo 'export PATH="~/anaconda/bin:$PATH"' >> ~/.bashrc 

# Refresh basically
source .bashrc

conda update conda

Correct bash command to zip your vcf file

biogeek — Wed, 04 Mar 2020 04:32:17 -0600

bgzip -c file.vcf > file.vcf.gz
tabix -p vcf file.vcf.gz

#More at http://www.htslib.org/doc/tabix.html

Circos with circosJS

Rahul Nayak — Mon, 02 Mar 2020 23:29:38 -0600

R script to plot VCF file

Jit — Mon, 02 Mar 2020 01:00:51 -0600

library(vcfR)

vcf_file <- system.file("file.vcf$", package = pkg)

vcf <- read.vcfR( vcf_file, verbose = FALSE )

chrom <- create.chromR(name='Supercontig', vcf=vcf)

plot(chrom)

#MORE at https://cran.r-project.org/web/packages/vcfR/vignettes/intro_to_vcfR.html