Matthieu Muffato's repositories
command-launcher
Command launcher written in PyQT that adds a menu to the system tray
pyEnsemblRest
Python wrapper of the Ensembl REST API
SSH-control-panel
Control panel for SSH tunnels and SSHFS mounts
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
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
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
MitoHiFi
Fork of marcelauliano/MitoHiFi. Only used to submit pull requets
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
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
treebest
My git clone of Heng Li's treebest from http://sourceforge.net/p/treesoft/code/HEAD/tree/branches/lh3/ . Further modifications (fork from Ensembl/treebest) are on the ensembl_master branch