Conda must not be installed in your /home folder since there is only little space. If you prefer to have conda plus over 720 open source packages, install Anaconda. We recommend using your own installation of conda.The fastest way to obtain conda is to install Miniconda, a mini version of Anaconda that includes only conda and its dependencies. Thus, it is not advised to use at the same time modules and conda environment installed in your personal space.Ĭonda environments allow to easly create, use and share software environments.
Please note that if you are using your own conda installation (installed in /LAB-DATA or /SCRATCH-BIRD), the IFB conda installation path will be prepended into your PATH environment variable when loading a module. Since most tools on the IFB core cluster are installed with conda, this behavior is mandatory. Loading a tool from the a IFB module implies adding a conda environment installation path into your environment. "/LAB-DATA/BiRD/apps/ifb-nncr/modulesfiles" # modules of tools installed on the IFB core cluster."/sandbox/apps/bioinfo/modulefiles" # modules of bioinformatics tools."/sandbox/apps/systeme/modulefiles" # modules of programming langages and other tools which are not specific to bioinformatics.Three main paths for module locations are set on the BiRD Cluster: Then, module command will search for modules in this local directory, additionally to the system directory. This command add the new directory in MODULEPATH environment variable. Instead of java -Xmx2g -jar /sandbox/apps/bioinfo/binaries/gatk/GenomeAnalysisTK-3.3.0/GenomeAnalysisTK.jar Īdd a local directory in module PATH module use -a /home/monlogin/modules Set_alias("gatk", "java -Xmx2g -jar /sandbox/apps/bioinfo/binaries/gatk/3.8/GenomeAnalysisTK.jar") Prepend_path("PATH", pathJoin(base,"bin")) Local base = pathJoin("/sandbox/apps/bioinfo/binaries",pkgName,pkgVersion)
Il est possible de définir des alias dans l'environement module.Įxemple de l'utilisation de GATK (programme java sous forme de jar): whatis("Name: gatk") Users can define alias with module, for example to launch a Java command : Prepend_path("PATH", pathJoin(base,"bin")) Use aliases with module Local base = pathJoin("/SCRATCH-BIRD/users/mylogin/mypath/binaries",pkgName,pkgVersion) Nano samtools/1.4.lua 1.4.lua file content (add samtools paths) : whatis("Name: samtools") Module whatis modulename #show description of a toolĮach user can load automatically a module at login : module initadd modulename Create a moduleĮx for samtools : cd /SCRATCH-BIRD/users/mylogin Module remove modulename #to remove a tool from your environment Module load modulename/version #to load a specific version of a tool Module environment is useful to load specific software environment. We recommend using either module or conda environnement to manage your softwares.
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