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althapalignr_py

Python script to combine BAM files and intersect them with a GTF file, used in jknightlab/AltHapAlignR

carla-git

Repo for useful scripts originally written by Carla. Only ibsub is maintained

command-launcher

Command launcher written in PyQT that adds a menu to the system tray

containers

Fork of BioContainers/containers. Only used to submit pull requests

docker-ensembl-linuxbrew-basic-dependencies

Docker image with the basic dependencies for the Ensembl linuxbrew installation

docker-ensembl-linuxbrew-compara

Docker image with all dependencies to run the Ensembl Compara pipelines

ehive-blockly

Playground for Blockly and eHive

ensembl-compara

The Ensembl Compara Perl API and SQL schema

ensembl-download-java

Java code to download genomes and orthologues from Ensembl

ensembl-hive

EnsEMBL Hive - a system for creating and running pipelines on a distributed compute resource

ensembl-hive-docker-swarm

'Docker Swarm' implementation of Ensembl Hive Meadow interface

ensembl-hive-htcondor

HTCondor Meadow for Ensembl Hive. Additional code to test GitHub workflows and packages

ensembl-hive-pbspro

'PBS Pro' implementation of Ensembl Hive Meadow interface

ensembl-hive-sge

SGE Meadow for Ensembl Hive

ensembl-hive-slurm

Slurm Meadow for Ensembl Hive

ensembl-mysql-monitor

Cron scripts to monitor the Ensembl Compara MySQL servers

ensembl-tools

Various tools that simplify working in Ensembl

ensembl-webcode-sandbox

Configuration files for an Ensembl sandbox website

ensj-healthcheck

Ensembl's Automated QC Framework

guihive

Graphical interface for the eHive workflow manager

hcluster

My git clone of Heng Li's hcluster from http://sourceforge.net/p/treesoft/code/HEAD/tree/branches/lh3/

mitohifi

Fork of marcelauliano/MitoHiFi. Only used to submit pull requets

muffato

muffato.github.io

The Jekyll source code and content of my personal website

pairtools

Fork of open2c/pairtools. Only used to submit pull requests

phd-thesis-scripts

Backup of the scripts I used during my PhD thesis to build the Agora ancestral-genome reconstruction toolkit

pyensemblrest

Python wrapper of the Ensembl REST API

pywaltrap

Python interface for the community detection program Walktrap

singularity-hpc

Fork of singularityhub/singularity-hpc. Only used to submit pull requests

snipmate.vim

Fork of msanders/snipmate.vim to keep my vim configuration