Pipeline for large-scale genome changes analysis of genome datasets.
The active use repository has migrated over to: https://github.com/darrenabbey/ymap The repository here was errantly created with some large binary files included. Attempts to extract the files from the history here have failed. A copy of the history was successfully scrubbed and then hosted at github. -------- Eukaryotic pathogens have complicated and dynamic genomes. To facilitate analysis of copy number variations (CNV), single nucleotide polymorphisms (SNPs), and loss of heterozygosity (LOH) events in Candida albicans, the most common human fungal pathogen, we developed a pipeline for analyzing diverse genome-scale datasets from microarray, deep sequencing, and restriction site associated DNA sequence experiments for clinical and laboratory strains. The YMAP pipeline automatically illustrates genome-wide information in a single intuitive figure and is readily modified for the analysis of other categories of data and other pathogen species with small genomes.
orchestrator / cluster deployment tool
The Orchestrator server is responsible for distribution and launch of simple apply/rollback shell scripts in a particular order across multiple servers . If for any reason deployment is failing at a particular stage the process will stop and you can rollback any changes done until then. In case you want to deploy your code or just call your preferred DSC client to apply the configuration locally the Orchestrator can be a handy tool. The operation can be started manually or scheduled, depending on your needs. In terms of audit and trace capabilities, the system is collecting all console output of your shell scripts from all servers and saves the logs centrally for review.
Gameserver Installer/Startscript for HL1 and HL2 Games
Gameserver Installation Scripts for Linux Supported Games HL1 Engine -Counter-Strike 1.6 -Counter-Strike: Condition Zero -Day of Defeat Supprted Games HL2 Engine -Counter-Strike: Source -Counter-Strike: Global Offensive -Team Fortress 2 -Day of Defeat: Source -Left 4 Dead 2 -Garrys Mod Minecraft -Minecraft Server Version 1.6.1 Supported Languages -German -English
Musix es un Sistema Operativo Multimedia 100% Libre
Musix es un Sistema Operativo Multimedia 100% Libre destinado a músicos, técnicos sonidistas, DJs, cineastas, diseñadores gráficos, y usuarios en general; una enorme colección de programas libres que pueden reemplazar a otros sistemas privativos. Musix es el resultado del trabajo colaborativo de toda una comunidad de usuarios y desarrolladores. [eng] Musix it's a 100% Free/Libre Multimedia Operating System aimed at musicians, sound technicians, DJs, filmakers, graphic designers and user in general; a huge collection of free (as in freedom) programs that can replace other opeating systems. Musix is a result of colaborative work of a entire comunity of users and developers.
OpenSearch GeoSpatial Catalogue
Install packages that apt-get can't.
Sh scripts for (un)installing packages that can't be installed by default with apt-get.
A tiny wheezy Distribution for Raspberry PI
There are many distribution of wheezy on the net which are much larger in size. This is my small attempt to make a mini-wheezy distribution which is just 8 Mb, for Raspberry PI. Although it is mini, but you can use debian-wheezy repository, for additional application. Download file, and extract the image. Copy the image to a SD card, and Insert the SD card in Raspberry PI and there you go. The password is pi:raspberry and root:root.
A video and audio converting tool customized on Tinycore Linux.
MobileMate is an open source video and audio converting tool customized on Tinycore Linux. It use Bash to glue open source tools such as Mplayer, FFmpeg(Libav), Zenity, Grep, Sed, etc.. It features as a self-booting tiny linux, can easy expand to your language, small size, easy to custom as your needs, etc..
Flak Is An Automation Frame-Work For MDK3 It Help's Users To Use MDK3 With Ease And in Interactive Way.
Controlling a Hague Pan/Tilt head with a raspberry pi
A simple way to control a Hague pan/tilt head wirelessly, using a raspberry pi for the webinterface & the GPIO pins connected to the 'remote input'.
Unix-based preparation and analysis toolbox for molecular simulations
Unix-based preparation and analysis toolbox for Nanomaterials and Room Temperature Ionic Liquids in Bulk and Slab using bash scripts, Gromacs tools and Matlab functions. NaRIBaS provides a framework that decouples user input parameter and terminal based command lines. NaRIBaS does not replace a simulation software and specific analysis tools like Gromacs, but it allows iterative repetition of tasks while changing specific input parameter. The toolbox is to be understood as a scripting framework rather than a black-box software. Task specific input and preparation or analysis function, are easy expandable to meet the scientific characteristic of constant changing properties. Concepts for efficiently storing and analysing large files in conjunction with graphical visualization and numerical data processing are presented in a Manual. A documented script collection that allows reproducing all simulations and analysis results presented in the Doctoral thesis of the author.
Li-f-e: Linux for Education based on Ubuntu
Li-f-e: Linux for Education distribution, ARM stuff, miscellaneous files and scripts. * https://lizards.opensuse.org/2016/07/04/future-of-li-f-e-linux-for-education-distribution/ * https://lizards.opensuse.org/2014/12/16/ltsp-client-goes-banana-pi/ * https://lizards.opensuse.org/2013/05/09/opensuse-12-3-on-android/
detecting & genotyping intergenic CNVs using off-target exome data
cnvOffSeq is a set of Java-based command-line tools for detecting and genotyping intergenic copy number variation (CNV) using off-target data from whole-exome sequencing experiments.
Command line tools to push updates of resource on a Moodle 2 server.
Publishing updates of resources on a Moodle server requires to click click and click again. If you propose several resources and want to update them times to times, this becomes boring. The proposed tools may ease this. Then, you can for instance automate your update with a script. Moreover you can easily adapt those tools to your needs. (These are shell scripts.)
parastructure is a perl script collection to run the population genetics software STRUCTURE from Pritchard et al. 2000 (http://pritch.bsd.uchicago.edu/structure.html) in parallel on a cluster (beowulf type). Each run of K (the number of populations) is executed separately on each CPU of the cluster trough queue system based on PBS. A summary statistics table and distruct figures (Noah Rosenberg: http://www.stanford.edu/group/rosenberglab/distruct.html) are built at the end of the run. A patch for the structure (ran.c) is also provided in order to correct the generation of the seed number.
EFortika is essentially a fully functional mail server built upon a combination of freely available open source software with a focus towards ease of deployment, management and security with insecure protocols disabled by default. The project aim is to produce a functional email server that can easily installed by the average sysadmin with minimal configuration and with an expectation of stability and security. The primary target audience is individuals keen to move away from public email services (see Gmail, Hotmail .etc) and towards their own low-cost privately managed email solution. The design of Efortika is scalable enough to suit many small to medium business needs however, larger scale deployments requiring modular or highly available solutions are not currently supported but are in included in the project plan. Please see the project wiki for further documentation, installation requirements and installation instructions: https://sourceforge.net/p/efortika/wiki/EFortika
Ban IPs based on #failed login attempts (Systemd version)
Scan systemd journal file for failed sshd login attempts in a given period. Add iptables rules to ban offenders.
LinxBooks – Have faith and carry on. Overview LinxBook is a simple and easy-to-use business accounting application. Linxbooks includes basic features that help the businesses create invoices, quotations, manage payments, payrolls, contracts and expenses Download at GitHub: https://github.com/LinxHQ/linxbooks Demo is at: http://linxbooks.com/demo (user: admin, password: admin123)
Digital operating for Ham Radio on ARM Single board computers.
Ham ARM Linux - Digital operations mainly focused on AX.25 using packet modems. This project is about making the ARM single board computers come to life for Ham Radio in a controlled and structured way, so operators can learn the ins and outs of packet radio. There will be an image for each supported board, and a set of shell scripts to help the user to configure their system simply and properly. HAL hopes to cut out the days of circular searching on the internet for how to get a simple packet system running! Initial offering will result in a fully functional one or two radio AX.25 packet system, and optionally a Net/ROM port, Uronode, AxMailFax, and the venerable FBB BBS system, all supported by the Direwolf sound modem software. Later APRS support and application choices will also be added.
A simple armv7h sdk
This is my sdk for usage with slackware on A20 devices like bananapi, cubietruck and olimex-som. For more info see https://github.com/tjohann/a20_sdk .
TCP Experiment Automation Controlled Using Python
TEACUP automates many aspects of running TCP performance experiments in a specially-constructed physical testbed. TEACUP enables repeatable testing of different TCP algorithms over a range of emulated network path conditions, bottleneck rate limits and bottleneck queuing disciplines. TEACUP utilises a text-based configuration file to define experiments as combinations of parameters specifying desired network path and end host conditions. When multiple values are provided (e.g. for TCP congestion control algorithm), an experiment is made up of multiple tests. For each experiment and test, TEACUP collects a range of data, such as tcpdump files of traffic seen or TCP stack information (e.g. using Web10G). TEACUP also collects a variety of metadata from the end hosts and bottleneck router, such as the actual OS/kernel version(s) used. TEACUP also provides some simple tools for analysing the results of experiments, such as plotting a flow's experienced RTT over time.
Chrome crx thumbnailer for Gnome
crx-thumbnailer is a thumbnailer for Gnome that will give Chrome .crx files an icon based on their embedded icon.
Just bring Linux for a better world
U M I, pronounce "ou" "ème" "aie" to an approach of "you & I" expression, is meant to be a derivative of Ubuntu, a Linux distribution. U M I is a system that wants generalist, simple and tailored to your needs. M I perhaps as "Maths Infos", "Mission Impossible", "Micro Imagination", "Museum Incarnation", ..., "Mandela Ideologie", ...,"Magne Isapèt" :), ... ; but in reality M I for "Me Inside", inside Linux, inside Debian, inside Ubuntu. This project designates all logistics associated developments. The goal is to promote the development of secure and robust software combining beauty and elegance for Linux platforms .
Multi Channel Classification and Clustering
Here we present an image-based Multi Channel Classification and Clustering System (MCCCS). It is an generalized, script-based classification system for processing various kinds of image data. Due to the modular design, individual processing-components can be easily adapted, extended or exchanged by own extensions. See project website for installation instructions.
Install Arch Linux In A Damn Hurry!
The Damn Hurry Arch Linux installer provides a quick and easy Arch Linux install with the desktop of your choice. Simply boot into my custom archiso and type 'arch-installer' and you will be in the whiptail program interface. This installer is intended not only for beginners who want a fresh Arch Linux install without going through the long process of learning the install. But also for experienced Arch Linux users who wish to simplify and automate the task of installing Arch Linux. Currently supports the following partitioning methods: Automatic Partitioning Automatic LUKS on LVM encryption Manual Partitioning Provides a quick and easy Arch Linux install, while still providing you with full control of how you wish to configure your system. This installer is in step with 'The Arch Way' of being simple, light weight, and fast. And comes in 65M smaller than the official archiso! View my project on github: https://github.com/deadhead420/archlinux/tree/master/arch-installer