Update R package when running DAS_Tool module OR update DAS_module

[JSBoey]

@DininduSenanayake Can you update the "pillar" R package?

Error: package or namespace load failed for ‘ggplot2’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 namespace ‘pillar’ 1.4.2 is being loaded, but >= 1.4.3 is required
Execution halted

[DininduSenanayake]

@JSBoey Can I update DAS_Tools version to it's latest 1.1.5 ?. If yes, I can do it with R/4.2.1-gimkl-2022a which has the latest versions of all those libraries

[JSBoey]

I think so. From the docs it does not look too different.

[DininduSenanayake]

@JSBoey I have installed the latest versions of DAS_Tool. .( DAS_Tool/1.1.5-gimkl-2022a-R-4.2.1

Ran a test with sample_data which comes with the repo

$ module purge

$ module load DAS_Tool/1.1.5-gimkl-2022a-R-4.2.1

$ DAS_Tool  -i sample_data/sample.human.gut_concoct_contigs2bin.tsv,\
sample_data/sample.human.gut_maxbin2_contigs2bin.tsv,\
sample_data/sample.human.gut_metabat_contigs2bin.tsv,\
sample_data/sample.human.gut_tetraESOM_contigs2bin.tsv \
-l concoct,maxbin,metabat,tetraESOM \
-c sample_data/sample.human.gut_contigs.fa \
-o sample_output_production/DASToolRun1
Warning:  Output directory does not exist. Attempting to create: sample_output_production

DAS Tool 1.1.5 
Analyzing assembly 
Predicting genes 
Annotating single copy genes using diamond 
Dereplicating, aggregating, and scoring bins 

$ ls sample_output_production/
DASToolRun1_DASTool_contig2bin.tsv  DASToolRun1_proteins.faa.archaea.scg
DASToolRun1_DASTool.log             DASToolRun1_proteins.faa.bacteria.scg
DASToolRun1_DASTool_summary.tsv     DASToolRun1_proteins.faa.findSCG.b6
DASToolRun1_proteins.faa            DASToolRun1_proteins.faa.scg.candidates.faa
DASToolRun1_proteins.faa.all.b6     DASToolRun1.seqlength

FYI. This version doesn't produce PDF outputs anymore as they have deprecated the function as per https://github.com/cmks/DAS_Tool/issues/86

[JSBoey]

Thanks @DininduSenanayake. I also counter-checked the outputs from version 1.1.5 with those generated by Dave, the resulting bins were the same. I think this is all good now.