Updated R version

Author: fredericlemoine

02_covid/run.sh

@@ -4,7 +4,7 @@ singularity pull docker://evolbioinfo/r-extended:v4.3.3
 
 goalign="singularity exec goalign_dev0537492.sif goalign"
 gotree="singularity exec gotree_devb324e73.sif gotree"
-rscript="singularity exec r-extended_v4.2.3_2 Rscript"
+rscript="singularity exec r-extended_v4.3.3 Rscript"
 
 ## Random selection of 800 sequences among dataset of the paper doi:10.5802/crbiol.29
 mkdir results_random_800

03_ebola/run.sh

@@ -4,7 +4,7 @@ singularity pull docker://evolbioinfo/r-extended:v4.3.3
 
 goalign="singularity exec goalign_dev0537492.sif goalign"
 gotree="singularity exec gotree_devb324e73.sif gotree"
-rscript="singularity exec r-extended_v4.2.3_2 Rscript"
+rscript="singularity exec r-extended_v4.3.3 Rscript"
 
 git clone git@github.com:evolbioinfo/bdei.git
 nextflow run main.nf --msa bdei/ebola/data/aln.ids.fa --collapse 0.1 --collapseref false --results results

04_RVFV/run.sh

@@ -4,7 +4,7 @@ singularity pull docker://evolbioinfo/r-extended:v4.3.3
 
 goalign="singularity exec goalign_dev0537492.sif goalign"
 gotree="singularity exec gotree_devb324e73.sif gotree"
-rscript="singularity exec r-extended_v4.2.3_2 Rscript"
+rscript="singularity exec r-extended_v4.3.3 Rscript"
 
 nextflow run convert.nf --ncbi data/sequences.fasta --gb data/sequence.gb
 

05_real_datasets/run.sh

@@ -4,7 +4,7 @@ singularity pull docker://evolbioinfo/r-extended:v4.3.3
 
 goalign="singularity exec goalign_dev0537492.sif goalign"
 gotree="singularity exec gotree_devb324e73.sif gotree"
-rscript="singularity exec r-extended_v4.2.3_2 Rscript"
+rscript="singularity exec r-extended_v4.3.3 Rscript"
 
 wget https://cme.h-its.org/exelixis/material/raxml_adaptive_data.tar.gz
 tar -xzvf raxml_adaptive_data.tar.gz

06_simulations/run.sh

@@ -6,7 +6,7 @@ singularity pull docker://evolbioinfo/r-extended:v4.3.3
 
 goalign="singularity exec goalign_dev0537492.sif goalign"
 gotree="singularity exec gotree_devb324e73.sif gotree"
-rscript="singularity exec r-extended_v4.2.3_2 Rscript"
+rscript="singularity exec r-extended_v4.3.3 Rscript"
 
 $TREE = "../03_ebola/results/aln.ids_subsamp.phylip_phyml_tree.txt"
 $ALIGN = "../03_ebola/results/aln.ids_subsamp.phylip"