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Classifer: CLARK-S

Open jfy133 opened this issue 3 years ago • 2 comments

Description of feature

Reported as being a good performer:

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-022-08803-2#Sec6

Available on bioconda:

https://bioconda.github.io/recipes/clark/README.html?highlight=clark+s

however may need some tweaking of the recipe, as currently the auxiliary scripts (some which we may need to use) are missing from path, although they are in the environment

http://clark.cs.ucr.edu/Overview/

jfy133 avatar Sep 05 '22 13:09 jfy133

auxiliary scripts are missing from path, although they are in the environment

Theses scripts are in opt directory (e.g., ~/miniconda3/opt/clark/, if the software was installed in the base environment). In particular, they are required for database creation (set_targets.sh). classify_metagenome.sh is a wrapper for CLARK binaries (which are in the $PATH), so it could be re-implemented inside the module script.

vmikk avatar Oct 10 '22 15:10 vmikk

Example code to build the database:

~/miniconda3/opt/clark/set_targets.sh DB   fungi --genus
~/miniconda3/opt/clark/set_targets.sh DB2 bacteria --species

vmikk avatar Oct 11 '22 07:10 vmikk