cmdln: Run a command via terminal/command prompt

In phylotaR: Automated Phylogenetic Sequence Cluster Identification from 'GenBank'

Description

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.

Usage

cmdln(cmd, args, lgfl = NULL)

Arguments

cmd	Command to be run
args	Vector of command arguments, each parameter and value must be a separate element
lgfl	File to which stdout/err will be written

Details

Note, stdout/err are returned as 'raw'. Use rawToChar() to convert to characters.

Value

status, integer or character

See Also

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

phylotaR documentation built on May 1, 2019, 9:26 p.m.