BEAST2 and conda environment

[Helene Schulz]

Hello,

I am trying to download BEAST packages to out cluster. Apparently it needs to be done in conda.

we have tried:

$ sbatch -p NMLResearch -c 1 --mem=1G -o beast_pacInstall1.out --wrap="conda install -y -c bioconda bacter=2.2.0 BADTRIP=1.0.0 BASTA=3.0.1 bdmm=0.3.3 BDSKY=1.4.2 BEAST_CLASSIC=1.4.0 BEASTLabs=1.8.1 BEASTShell=1.4.0 BEASTvntr=0.1.2 bModelTest=1.1.2 BREAK_AWAY=1.0.0 CA=1.3.0 CodonSubstModels=1.1.0 DENIM=0.3.1 EpiInf=7.1.1 FLC=1.1.0 GEO_SPHERE=1.2.0 Mascot=1.1.2 MASTER=6.1.0 MGSM=0.3.0 MM=1.1.1 MODEL_SELECTION=1.4.2 MSBD=1.0.0 MultiTypeTree=7.0.0 NS=1.0.3 PhyDyn=1.3.1 phylodynamics=1.3.0 PoMo=1.0.1 RBS=1.4.0 SA=2.0.0 SCOTTI=2.0.1 SNAPP=1.4.2 SpeciesNetwork=0.12.2 SSM=1.1.0 STACEY=1.2.4 StarBEAST2=0.15.1 substBMA=1.2.2 TMA=1.0.0 TreeStat2=0.0.2"

and also:

$ sbatch -p NMLResearch -c 1 --mem=1G -o beast_pacInstall5.out --wrap="packagemanager -add bacter=2.2.0 BADTRIP=1.0.0 BASTA=3.0.1 bdmm=0.3.3 BDSKY=1.4.2 BEAST_CLASSIC=1.4.0 BEASTLabs=1.8.1 BEASTShell=1.4.0 BEASTvntr=0.1.2 bModelTest=1.1.2 BREAK_AWAY=1.0.0 CA=1.3.0 CodonSubstModels=1.1.0 DENIM=0.3.1 EpiInf=7.1.1 FLC=1.1.0 GEO_SPHERE=1.2.0 Mascot=1.1.2 MASTER=6.1.0 MGSM=0.3.0 MM=1.1.1 MODEL_SELECTION=1.4.2 MSBD=1.0.0 MultiTypeTree=7.0.0 NS=1.0.3 PhyDyn=1.3.1 phylodynamics=1.3.0 PoMo=1.0.1 RBS=1.4.0 SA=2.0.0 SCOTTI=2.0.1 SNAPP=1.4.2 SpeciesNetwork=0.12.2 SSM=1.1.0 STACEY=1.2.4 StarBEAST2=0.15.1 substBMA=1.2.2 TMA=1.0.0 TreeStat2=0.0.2"

But both attempts failed. Can someone comment please?

Much appreciated.

Helene

[Walter Xie]

Hi Helene,

You cannot install the software using the job submission command. You should ask the IT support of the cluster how to install the software by yourself. Here is a page to explain this: https://sites.google.com/a/case.edu/hpc-upgraded-cluster/home/important-notes-for-new-users/software-installation-guide, but please note the procedure and commands will be different according to the architecture of the cluster that you are using.  

Cheers,

Walter