Provide the command and arguments as a vector. Also can take a lgfl to which all stdout and stderr is written. If lgfl is not provided, a list is returned of 'status', 'stdout' and 'stderr'. Else only the status is returned - 1 success, 0 failed.
cmdln(cmd, args, lgfl = NULL)Command to be run
Vector of command arguments, each parameter and value must be a separate element
File to which stdout/err will be written
status, integer or character
Note, stdout/err are returned as 'raw'. Use rawToChar() to convert to characters.
Other run-private: batcher,
blast_clstr, blast_filter,
blast_setup, blast_sqs,
blastcache_load,
blastcache_save, blastdb_gen,
blastn_run, cache_rm,
cache_setup, clade_select,
clstr2_calc, clstr_all,
clstr_direct, clstr_sqs,
clstr_subtree, clstrarc_gen,
clstrarc_join, clstrrec_gen,
clstrs_calc, clstrs_join,
clstrs_merge,
clstrs_renumber, clstrs_save,
descendants_get,
download_obj_check, error,
hierarchic_download, info,
ncbicache_load,
ncbicache_save, obj_check,
obj_load, obj_save,
parameters_load,
parameters_setup, parent_get,
progress_init, progress_read,
progress_reset,
progress_save, rank_get,
safely_connect,
search_and_cache,
searchterm_gen, seeds_blast,
seq_download, seqarc_gen,
seqrec_augment,
seqrec_convert, seqrec_gen,
seqrec_get, sids_check,
sids_get, sids_load,
sids_save, sqs_count,
sqs_load, sqs_save,
stage_args_check, stages_run,
tax_download, taxdict_gen,
taxtree_gen, txids_get,
txnds_count, warn