search

simroux / VirSorter

Source code of the VirSorter tool, also available as an App on CyVerse/iVirus (https://de.iplantcollaborative.org/de/)
GNU General Public License v2.0
104 stars 30 forks source link

check for all required tools at startup. #54

Open EricDeveaud opened 4 years ago

EricDeveaud commented 4 years ago

Hello,

I would like to suggest that all required tools will be checked at startup time as it is curently done for hmmsearch, blastp, and diamond in wrapper_phage_contigs_sorter_iPlant.pl

why all the necessary tools, aka: hmmbuild, mcl, mga, hmmsearch, blastp, makeblastdb, hmmpress, diamond, mcxload, muscle

1) ensure that are necessary tools are found and will avoid to run any process if there is a missing tool 2) avoid duplicate checking for some tools eg blastp, diamond checked 3 times: wrapper_phage_contigs_sorter_iPlant.pl, Step_0_make_new_clusters.pl, Step_first_add_custom_phage_sequence.pl hmmsearch checkd twice: wrapper_phage_contigs_sorter_iPlant, Step_first_add_custom_phage_sequence.pl ...