Software

SLURM Cluster
  • On our Web site (Resources): Software
  • On front-end servers with alias command "search_module" (case insensitive):

search_module soft_name (or part of soft_name)

  • On front-end servers with " ls" command:

ls /usr/local/bioinfo/src|grep -i soft_name

  • On front-end servers with "module" command:

module avail : display all available software installed on the cluster

module avail category/soft_name : display available versions for a specific application (with category in bioinfo,compiler,mpi or system) (case sensitive)

module avail -t 2>&1 | grep -i soft_name : display available versions for a specific application

Examples :

$ search_module blast
bioinfo/blast-2.2.26
bioinfo/ncbi-blast-2.2.29+
bioinfo/ncbi-blast-2.6.0+
bioinfo/RMBlast-2.6.0
bioinfo/samblaster-v.0.1.24
bioinfo/WuBlast2.0

 

$ module avail bioinfo/cutadapt

$-------------/tools/share/Modules ----------------------------------------
bioinfo/cutadapt-1.14-python-2.7.2 bioinfo/cutadapt-1.14-python-3.4.3

 

$ module avail -t 2>&1 | grep -i openmpi
mpi/openmpi-1.6.5
mpi/openmpi-1.8.1
mpi/openmpi-1.8.8
mpi/openmpi-1.8.8-intel2018.0.128
mpi/openmpi-2.1.2
mpi/openmpi-2.1.2-intel2018.0.128

 

Find Python package:

On front-end servers with alias command "search_Python_package" (case insentitive):

search_Python_package package_name

Find R package:

On front-end servers with alias command "search_R_package" (case sensitive):

search_R_package package_name

On Genobioinfo cluster:

  • Bioinfo: /usr/local/bioinfo/src/
  • Compilers:  /tools/compilers
  • Libraries:  /tools/lib
  • Languages (Python, R , Java, Singularity..): /tools/statistics,/tools/containers,tools/devel
  • Other system tools : /tools/others_tools
  • Useful scripts: /tools/bin (sarray, squota_cpu, saccount_info…).  In user’s default PATH.

Software installation or update are performed by complete the following form: Software installation

  • Run a specific application

We  now use Environment Modules to dynamically set up environments for different applications (see "How to use module command ?" section of this FAQ for more information).

To run a software you need to load  the corresponding module.

Examples:

To use blast:

$ module load bioinfo/blast-2.2.26

To verify:

$ which blastall
/usr/local/bioinfo/src/NCBI_Blast/blast-2.2.26/bin/blastall

To use Python 2.7.2

$ module load system/Python-2.7.2
$ which python
/tools/python/2.7.2/bin/python

  • Software documentation

Typically , documentation is provided by the soft in the installation folder (/usr/local/bioinfo/src/soft_name) and on the web site of the software (we give the link to the website of each software on the Software page).

  • Use on SLURM cluster

You can also find specific information in a "How_to_use_SLURM_soft_name" file in the software installation directory (/usr/local/bioinfo/src/soft_name) or on our web site Software page  (Avaibility/Use column, click on SLURM cluster link) .

  • Example directory

In the software installation directory, there is often a basic example submission job in an "example_on_cluster" directory (you need to copy it in your work space to run it to test, otherwise you'll have permission issues). 

Example with bowtie:

$ ls -1 /usr/local/bioinfo/src/bowtie/
bowtie-1.2.1.1
bowtie-1.2.1.1-linux-x86_64.zip
bowtie2-2.2.9
bowtie2-2.3.3.1
bowtie2-2.3.3.1-linux-x86_64.zip
example_on_cluster
How_to_use_SLURM_bowtie

$ ls -1 /usr/local/bioinfo/src/bowtie/example_on_cluster/
errot.txt
example
lambda_virus.1.bt2
lambda_virus.2.bt2
lambda_virus.3.bt2
lambda_virus.4.bt2
lambda_virus.rev.1.bt2
lambda_virus.rev.2.bt2
output.txt
test_v2-2.2.9.sh

  • Others useful commands:

On front-end servers, to find the path of  the "How_to_use_SLURM_soft_name" file, use module help command:

$ module help bioinfo/bowtie2-2.2.9

----------- Module Specific Help for 'bioinfo/bowtie2-2.2.9' ---------------------------

See How_to_use file: /usr/local/bioinfo/src/bowtie/How_to_use_SLURM_bowtie

In your web browser, to retrieve all "How_to_use_SLURM_soft_name" files:

http://vm-genobiotoul.toulouse.inra.fr/How_to_Softs/

The basic command to use is module:

module : (no arguments) print usage instructions
module avail : list available software module
module load modulename : add a module to your environment
module unload modulename : unload remove a module
module purge : remove all modules
module show modulename : show what changes a module will make to your environment
module help modulename : path to the "How_to_use_SLURM_soft_name" file

For more documentation, you can see the Environment Module website.

Tutorial describing how to run R scripts and compile Rmarkdown files on genologin/SLURM cluster:

On front-end servers with alias command "search_R_package" (case sensitive):

search_R_package package_name

On front-end servers with alias command "search_Python_package" (case insentitive):

search_Python_package package_name

Launch java onto the nodes for the java command:
java -Xmx4g

Choose a specific java version:
module load system/Java8 (genologin)

module load devel/java/17.0.6 (genobioinfo)

To see available compiler:

module avail compiler

Exemple to load a compiler:

module load compiler/gcc-7.2.0

  • Create modulefile with header:

#%Module1.0###############################################################
##

  • Add environment:

module load existant module
prepend-path PATH /usr/local/bioinfo/src/MultAlin/multalin.5.4.1/
setenv MULTALIN /usr/local/bioinfo/src/MultAlin/multalin.5.4.1/

  • Load your module file:

module load -f /path/to/your/modulefile

Example:

  • Create your module:

vi ~/save/my_own_module

#%Module1.0###############################################################
##

module load bioinfo/bowtie2-2.2.9
module load bioinfo/bwa-0.7.15
module load bioinfo/samtools-1.4

prepend-path PATH /usr/local/bioinfo/src/MultAlin/multalin.5.4.1/
setenv MULTALIN /usr/local/bioinfo/src/MultAlin/multalin.5.4.1/

  • Load your module:

module load -f ~/save/my_own_module

  • Environment verification:

$ which bowtie2
/usr/local/bioinfo/src/bowtie/bowtie2-2.2.9/bowtie2

$ which bwa
/usr/local/bioinfo/src/bwa/bwa-0.7.15/bwa

$ which samtools
/usr/local/bioinfo/src/samtools/samtools-1.4/samtools

  • To unload one module:

module unload bioinfo/bowtie2-2.2.9

  • To unload all module and specific variable:

module purge

 

For more documentation, you can see the Environment Module website.

Some software default directory (ex: .nextflow, .conda, .beast, .ncbi, .R ...) are usually located at your home directory whose allocated space is very limited.
A simple solution consist in create (or move if it already exist) . directory in your work space and making a symbolic link to this
directory in your home

Example with nextflow:

mkdir ~/work/.nextflow (or mv ~/.nextflow ~/work/)
ln -s ~/work/.nextflow  ~/.nextflow

Example with conda:

mkdir ~/work/.conda (or mv ~/.conda ~/work/)
ln -s ~/work/.conda   ~/.conda