The Rational

Pipelines are logically organised workflows made up of tools and custom scripts. Serving code in an appropriate and reusable way is important to mantain the reproducibility of a scientific product and to provide the community with a way to face a problem task by task.

"Computational analysis tools and pipelines should make the effort to be easily installable."

Altuna Akalin Bioinformatics Scientist.

The concept of installability is challenged by the ticking away of times because tools evolve and change constantly, that's it.

"Linux is an operating system and its core is just a kernel. [...] We contribute at the rate of about [...] ten patches a day, twenty four hours a day, seven days a week, go into this code. It's constantly updated, constantly revised, constantly changing because the world changes. We have to react to a change in world. If an operating system stops change and of course if the world doesn't stop changing it will die. Linux constantly is improved, constantly is updated in order to handle the changing world. "

Greg Khroah-Hartman fellow at The Linux Foundation.

Description

LInk COntroller (LICO) is a schedulable utility for monitoring the link integrity and allows you to promptly identify broken links that crack the installation process of a pipeline. LICO does test the integrity of the links that point to a specific version of a tools integrated into your pipeline. LICO operates silently in the background in a scheduled manner and returns a report to your Telegram account with info concerning the integrity of the links. LICO relies on:

1. cron: a job scheduler;
2. telegram-send: a command-line tool to send messages over Telegram to your account.

While cron schedules the frequency at which you want to monitor the integrity of your links, telegram-send notifies you with a multi-message report.

NOTE: If you are not interested in sheduling/Telegram you can run monitorSR.sh, instead. The output will be printed on the terminal.

monitor.sh and monitorSR.sh syntax:

monitor.sh -h
Usage:
monitor.sh -l <file.txt> -p <rundir> -n <pipeline>

<file.txt>: a txt file with the GitHub/HTTP links (one link per line);

<rundir>: path to /favorite/dir where file.txt is stored;

<pipeline>: the name of your pipeline (to send you a meaningful report).

NOTE: If you run monitorSR.sh you do not need to proceed further in this README.

What you need

1. COPY monitor.sh inside your /favorite/dir
   note1: add +x permission to monitor.sh
2. CRON and TELEGRAM-SEND

CRON and TELEGRAM-SEND installation

Install both cron and telegram-send following the installation instructions,

Create a BOT on Telegram

From the command line run

telegram-send --configure

the steps to follow will be printed on the shell.

Be nice, say " Hi! " to your BOT, it is going to help you.

Configure CRON

cron needs to know how frequently you want to run monitor.sh.

Change the configuration file running crontab -e and add, for example:

0 0 1 */1 * monitor.sh <txt> <rundir> <pipeline>

note2: the script above assumes that /favorite/dir is in $PATH.

0 0 1 */1 * specifies how frequently you want to monitor the link integrity.

The searchbar at CronTab.guru allows you to set your favorite schedule up.

Using this setup, monitor.sh will silently run in the background on the 1^st of each month at midnight 🌕.

note3: do not forget to specify SHELL and PATH inside crontab and make sure the file ends with a newline.

SHELL=/bin/sh
PATH=/all/the/paths/in/your/$PATH

0 0 1 */1 * monitor.sh <listoflinks.txt> <rundir> <pipeline>

Example

After the installation of the dependencies,

I locate soft.txt and monitor.sh in /home/ntellini/LICO.

soft.txt contains :

https://github.com/rrwick/Filtlong.git
https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/3.6-6/GenomeAnalysisTK.jar
http://topaz.genetics.utah.edu/maker_downloads/static/maker-3.00.0-beta.tgz
http://eddylab.org/software/tRNAscan-SE/tRNAscan-SE.tar.gz

i.e. a GitHub repo, two broken links, and a working link.

My crontab looks like this:

SHELL=/bin/sh
PATH=/opt/def/anaconda3/bin:/opt/tvs/bin:/home/tools/bin:/home/ntellini/.local/bin:/usr/local/bin:/usr/bin:/bin:/usr/lib/mit/sbin:/snap/bin:/home/ntellini/LICO
*/5 * * * * monitor.sh soft.txt /home/ntellini/LICO sppcomp

The run will start in 5 min afetr saving the crontab confing file.

note4: At the end of the run, remind to remove the folder with <pipeline> name inside your /favorite/dir (in my case/home/ntellini/LICO/sppcomp) before the next run starts.

The OUTPUT

At the end of the run, the bot sends the report to your Telegram account.

The 4^th message is the MOST important.

It tells us that, during the download of the packages:

the packages Filtlong and tRNAscan-SE.tar.gz have been successfully downloaded (OK) while, both GATK and maker downloads ended up with an error (Exit).

RELEASE HISTORY

• v1.0.0 Released on 2023

DEPENDENCIES

• cron;
• telegram-send.