Software

SLURM Cluster (available on 16/03/2018)

 

  • On our Web site (Resources): Software
  • On genologin server with ls command:

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

  • On genologin server 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 (case insensitive)

Examples :

$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

  • Bioinfo software: /usr/local/bioinfo/src/
  • Others tools and libraries: /tools/
  • Compilers: /tools/compilers

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. 

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 genologin 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.

  • 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.

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

Choose a specific java version:
module load system/Java8 (for java 8)

To see available compiler:

module avail compiler

Exemple to load a compiler:

module load compiler/gcc-7.2.0

SGE Cluster

 

  • On our Web site (Resources): Software
  • On genotoul server:

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

  • Bioinfo software: /usr/local/bioinfo/src/
  • Others tools and libraries: /tools/libraries
  • Compilers: /tools/compilers

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

Typically , documentation is provided by the soft in the installation folder and on the web site of the software (we give the link to the website of each software on the Software page).
When a software needs some special requirements to be used, you can find How_to_use and/or Readme file in the software installation directory.

Example with HiFive:

ls /usr/local/bioinfo/src/HiFive/
hifive HiFive_env How_to_use Install

Launch java onto the nodes:
java -Xmx4g

Choose a specific java version:
module load bioinfo/Java8 (for java 8)

To see available compiler:

module avail

Exemple to load a compiler:

module load compilers/gcc-4.9.1