Logiciels

Les logiciels installés sur le cluster de calcul de l'IGBMC sont tous disponibles à travers l'outil module.

Pour charger un logiciel dans votre session, utilisez la commande module load:

Par exemple, vous pouvez charger Matlab en utilisant la commande suivante :

$ module load matlab

Si vous voulez utilisez une version spécifique d'un logiciel :

$ module load matlab/R2016b

Vous pouvez charger plusieurs logiciels en même temps.

Pour décharger un logiciel, utilisez la commande suivante :

$ module unload <software_name>

Pour voir la liste des logiciels en cours de chargé :

$ module list

Si vous voulez voir la liste des logiciels disponible :

$ module avail -l

Documentation complète de l'outil Module...

Logiciel Version Description Comment y accéder
bedtools 2.26.0 A powerful toolset for genome arithmetic source activate ngs
bowtie 1.2.1.1 Bowtie is an ultrafast, memory-efficient short read aligner source activate ngs
bowtie2 2.2.5 source activate ngs
ccp4 7.0 CCP4 provides software for every stage of the crystallographic structure solution process source ccp4_env.sh
conda 4.3.21 Conda is an open source,[1] cross-platform,[2] language-agnostic[3] package manager and environment management system Disponible par défaut
ctffind4 4.1.8 ctffind4 is a program for finding CTFs of electron micrographs Inclus dans scipion
4.1.13
cutadapt 1.14 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads source activate ngs
deeptools 2.5.3 Tools for exploring deep sequencing data source activate ngs
dials 1.8.0 Diffraction Integration for Advanced Light Sources source dials_env.sh
fastqc 0.11.5 A quality control tool for high throughput sequence data source activate ngs
fastx_toolkit 0.0.14 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing source activate ngs
frealign 9.07 Frealign is a program for high-resolution refinement of 3D reconstructions from cryo-EM images of single particles Inclus dans scipion
gatk 3.6.24 Variant Discovery in High-Throughput Sequencing Data source activate ngs
Gctf 1.6 Real-time CTF determination and correction Inclus dans scipion
H5toXds 1.1.0 The XDS package uses H5ToXds for processing of EIGER HDF5 data Disponible par défaut
homer 4.9.1 Software for motif discovery and next-gen sequencing analysis source activate ngs
macs2 2.1.1.20160309 Model-based Analysis of ChIP-Seq source activate ngs
mageck 0.5.6 performs sgRNA, gene and pathway analysis on CRISPR-Cas9 screening source activate mageck
matlab R2016b MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment
Toolboxes included :
- Curve Fitting Toolbox
- Image Processing Toolbox
- Optimization Toolbox
- Statistics Toolbox
Disponible par défaut
mosflm 7.2.1 Evolving Methods for Macromolecular Crystallography source ccp4_env.sh
motioncor2 17.01.30 Algorithm to correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images Inclus dans scipion
neggia 1.0.1 XDS plugin that reads hdf5 files Disponible dans /shared/software/xds/plugins
picard 2.14 A set of command line tools for manipulating high-throughput sequencing data and formats source activate ngs
phenix 1.12-2829 Python-based Hierarchical ENvironment for Integrated Xtallography source phenix_env.sh
python2 2.7 Python programming language Disponible par défaut
python3 3.5 and 3.6 Disponible par défaut
relion 2.1.b1 RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM) Disponible par défaut and included in scipion
resmap 1.1.5s2 ResMap is a software package for computing the local resolution of 3D density maps studied in structural biology, primarily electron cryo-microscopy (cryo-EM) Inclus dans scipion
samtools 1.6 SAM Tools provide various utilities for manipulating alignments in the SAM format source activate ngs
scipion 1.1 Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM) Disponible par défaut
simple 2.1 Single-particle IMage Processing Linux Engine is a program package for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles Inclus dans scipion
2.5 source simple_env.sh
solexaqa 3.1.7.1 SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data source activate ngs
snakemake 3.13.3 Snakeake is a Python based language and execution environment for GNU Make-like workflows source activate snakemake
sratoolkit 2.8.1 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives source activate ngs
summovie 1.0.2 Summovie uses the alignment results from a prior run of unblur to calculate movie frame sums Inclus dans scipion
tadtool 0.75 An interactive tool for the identification of meaningful parameters in TAD-calling algorithms for Hi-C data.
tophat 2.1.1 TopHat is a program that aligns RNA-Seq reads to a genome in order to identify exon-exon splice junctions source activate ngs
unblur 1.0.2 Unblur is used to align the frames of movies recorded on an electron microscope to reduce image blurring due to beam-induced motion Inclus dans scipion
xds 2017.6.1 X-ray Detector Software for processing single-crystal monochromatic diffraction data recorded by the rotation method Disponible par défaut
2018.1.26
2019.3.15