section 1p · User commands 💻

1484 pages · page 1 of 8

A

acdcheck(1p)✨
ack(1p)grep-like text finder✨
add_bug_to_estraier(1p)add a bug log to an estraier database✨
add_tradis_tags(1p)check if tr tag is present✨
admin(1p)create and administer SCCS files (DEVELOPMENT)✨
aeftpd(1p)FTP Server✨
alias(1p)define or display aliases✨
alien(1p)Convert or install an alien binary package✨
all-knowing-dns(1p)Tiny DNS server for IPv6 Reverse DNS✨
alleleCounter.pl(1p)Generate tab seperated file with allelic counts and depth for each specified locus.✨
alleleCounterToJson.pl(1p)Generate JSON format file from the tab seperated format✨
altree(1p)Association and Localisation tests using phylogenetic Trees✨
altree-add-S(1p)Title...✨
altree-convert(1p)Title...✨
analizo(1p)multi-language source code analysis toolkit✨
analizo-files-graph(1p)dependency graph generator among files✨
analizo-graph(1p)dependency graph generator✨
analizo-help(1p)displays the help✨
analizo-metrics(1p)analizo's metric reporting tool✨
analizo-metrics-batch(1p)processes several source code directories in batch✨
analizo-metrics-history(1p)processes a Git repository collection metrics✨
analizo-tree-evolution(1p)watch the evolution of the source code✨
annex-to-annex(1p)use hardlinks to migrate files between git annex repos✨
annex-to-annex-dropunused(1p)drop old hardlinks migrated by annex-to-annex✨
annex-to-annex-reinject(1p)use 'git annex reinject' to redo annex-to-annex✨
appendpdf(1p)Append one PDF to another✨
apply_diff_relay_logs(1p)Generating differential relay logs between the latest slave and target slave, and applying all binlog/relay log files. This command is automatically executed from MHA Manager on failover, and manual…✨
applypatch(1p)apply 'makepatch' generated script to update a source tree✨
apt-show-source(1p)Lists source-packages.✨
apt-show-versions(1p)Lists available package versions with distribution✨
apt-src(1p)manage debian source package trees✨
ar(1p)create and maintain library archives✨
argon2-calibrate(1p)a script to find the appropriate argon2 parameters✨
asa(1p)interpret carriage-control characters✨
asp-perl(1p)Apache::ASP CGI and command line script processor✨
at(1p)execute commands at a later time✨
atoms(1p)Make lists of atomic coordinates from crystallographic data✨
ATR_analysis(1p)analyse a smart card ATR✨
audio_rename(1p)rename an audio file via information got via MP3::Tag.✨
authorized-keys-test(1p)Validate a authorized_keys file✨
autodia(1p)a perl script using the Autodia modules to create UML Class Diagrams or documents. from code or other data sources.✨
AutoSearch(1p)a web-search tracking application✨
average_genome_size(1p)Calculate the average genome size (in bp) of species in a Grinder library✨
awk(1p)pattern scanning and processing language✨

B

bacteria_tradis(1p)Perform full tradis analysis✨
basename(1p)return non-directory portion of a pathname✨
basepods(1p)print out pod paths for the standard perl manpages✨
batch(1p)schedule commands to be executed in a batch queue✨
bc(1p)arbitrary-precision arithmetic language✨
bdf2gdfont(1p)Convert X11 "BDF" fonts into a loadable font format for GD.✨
bdf2gdfont.pl(1p)Convert X11 "BDF" fonts into a loadable font format for GD.✨
beancounter(1p)Stock portfolio performance monitor tool✨
bed2gff3(1p)Convert UCSC Genome Browser-format gene files into GFF files suitable for loading into gbrowse✨
bg(1p)run jobs in the background✨
biber(1p)A bibtex replacement for users of biblatex✨
binhex.pl(1p)use Convert::BinHex to encode files as BinHex✨
blhc(1p)build log hardening check, checks build logs for missing hardening flags✨
blinkenlights(1p)DNSSEC-Tools rollerd GUI✨
bot-basicbot-pluggable(1p)A standard Bot::BasicBot::Pluggable script✨
bot-training(1p)Command-line interface Bot::Training✨
boxer(1p)boxer command line utils✨
bp_aacomp(1p)amino acid composition of protein sequences✨
bp_biblio(1p)bioperl client for accessing and querying a bibliographic repository✨
bp_biofetch_genbank_proxy(1p)Caching BioFetch-compatible web proxy for GenBank✨
bp_bioflat_index(1p)index sequence files using Bio::DB::Flat✨
bp_biogetseq(1p)sequence retrieval using OBDA registry✨
bp_bulk_load_gff(1p)Bulk-load a Bio::DB::GFF database from GFF files.✨
bp_dbsplit(1p)script to split an input set of database(s) into smaller pieces✨
bp_download_query_genbank(1p)script to query Genbank and retrieve records✨
bp_einfo(1p)Query einfo to find all available databases or information about a specific database (field information or links to other NCBI databases).✨
bp_extract_feature_seq(1p)extract the corresponding sequence for a specified feature type✨
bp_fast_load_gff(1p)Fast-load a Bio::DB::GFF database from GFF files.✨
bp_fastam9_to_table(1p)turn FASTA -m 9 output into NCBI -m 9 tabular output✨
bp_fetch(1p)fetches sequences from bioperl indexed databases✨
bp_filter_search(1p)filters searchio results, outputting a tab delimited summary✨
bp_find-blast-matches(1p)extract DNA sequences based on BLAST hits✨
bp_flanks(1p)finding flanking sequences for a variant in a sequence position✨
bp_gccalc(1p)GC content of nucleotide sequences✨
bp_genbank2gff(1p)Load a Bio::DB::GFF database from GENBANK files.✨
bp_genbank2gff3(1p)Genbank->gbrowse-friendly GFF3✨
bp_genbank_ref_extractor(1p)Retrieves all related sequences for a list of searches on Entrez gene✨
bp_generate_histogram(1p)Generate a histogram of Bio::DB::GFF features✨
bp_hmmer_to_table.pl(1p)turn HMMER output into tabular format✨
bp_index(1p)indexes files for use by bp_fetch.pl✨
bp_load_gff(1p)Load a Bio::DB::GFF database from GFF files.✨
bp_local_taxonomydb_query(1p)query a local TaxonomyDB for species or taxonid✨
bp_make_mrna_protein(1p)Convert an input mRNA/cDNA sequence into protein✨
bp_mask_by_search(1p)mask sequence(s) based on its alignment results✨
bp_meta_gff(1p)Get/set Bio::DB::GFF meta-data✨
bp_mrtrans(1p)implement a transformer of alignments from protein to mrna coordinates✨
bp_multi_hmmsearch.pl(1p)perform a hmmsearch into multiple FASTA files using an INDEX file✨
bp_mutate(1p)randomly mutagenize a single protein or DNA sequence✨
bp_nexus2nh(1p)convert nexus format trees (from PAUP* and MrBayes) to new hampshire✨
bp_nrdb(1p)a script to emulate Warren Gish's nrdb, make a unique sequence database from a set of input databases✨
bp_oligo_count(1p)oligo count and frequency✨
bp_pairwise_kaks(1p)calculate pairwise Ka,Ks for a set of sequences✨
bp_panalysis.pl(1p)An example/tutorial script how to access analysis tools✨
bp_papplmaker.pl(1p)Analysis tools module generator✨
bp_parse_hmmsearch.pl(1p)parse single/multiple HMMSEARCH results file(s) with different output options✨
bp_process_gadfly(1p)Massage Gadfly/FlyBase GFF files into a version suitable for the Generic Genome Browser✨
bp_process_sgd(1p)Massage SGD annotation flat files into a version suitable for the Generic Genome Browser✨
bp_process_wormbase.pl(1p)Massage WormBase GFF files into a version suitable for the Generic Genome Browser✨
bp_query_entrez_taxa(1p)query Entrez taxonomy database and print out information✨
bp_remote_blast.pl(1p)script for submitting jobs to a remote blast server (ncbi blast queue at this time)✨
bp_revtrans-motif(1p)Reverse translate a Profam-like protein motif✨
bp_run_neighbor.pl(1p)run Phylip's 'neighbor' program through Bioperl✨
bp_run_protdist.pl(1p)run Phylip's 'protdist' program through Bioperl✨
bp_search2alnblocks(1p)Turn SearchIO parseable reports(s) into a set of aligned blocks✨
bp_search2gff(1p)turn a SearchIO report into GFF✨
bp_search2table(1p)turn SearchIO parseable reports into tab delimited format like NCBI's -m 9✨
bp_search2tribe(1p)Turn SearchIO parseable reports(s) into TRIBE matrix✨
bp_seq_length(1p)lists the number of bases and number of sequences in specified sequence database files✨
bp_seqconvert(1p)generic BioPerl sequence format converter✨
bp_seqcut(1p)cut FASTA sequences with a given range✨
bp_seqfeature_load(1p)Load GFF into a SeqFeature database✨
bp_seqpart(1p)Takes one or more sequence files and splits them into a number of load balanced files.✨
bp_seqret(1p)bioperl implementation of sequence fetch from local db (like EMBOSS seqret)✨
bp_seqretsplit(1p)split a sequence (or stream) into a single file per sequence✨
bp_split_seq(1p)splits a sequence into equal sized chunks with an optional overlapping range✨
bp_sreformat(1p)convert sequence formats✨
bp_taxid4species(1p)simple script which returns the NCBI Taxonomic id for a requested species✨
bp_taxonomy2tree(1p)Building a taxonomic tree based on the full lineages of a set of species names✨
bp_translate_seq(1p)translates a sequence✨
bp_tree2pag(1p)convert Bio::TreeIO parseable format trees to pagel format✨
bp_unflatten_seq(1p)unflatten a genbank or genbank-style feature file into a nested SeqFeature hierarchy✨
break(1p)exit from for, while, or until loop✨
bubbles(1p)DNSSEC-Tools Rollrec Simple GUI Display✨
bucardo(1p)utility script for controlling the Bucardo program✨
buildrealms(1p)assist in building a DNSSEC-Tools realms environment✨

C

c99(1p)compile standard C programs✨
cal(1p)print a calendar✨
carton(1p)Perl module dependency manager (aka Bundler for Perl)✨
cat(1p)concatenate and print files✨
catalyst.pl(1p)Bootstrap a Catalyst application✨
catmandu(1p)LibreCat command line tools✨
ccconfig(1p)Get Convert::Binary::C configuration for a compiler✨
ccdiff(1p)Colored Character diff✨
ccon(1p)Cluster administration tool✨
cd(1p)change the working directory✨
Ceni(1p)Curses /etc/network/interfaces✨
cflow(1p)generate a C-language flowgraph (DEVELOPMENT)✨
cgiapp-starter(1p)creates a skeleton CGI::Application project✨
chalow(1p)weblog tool that converts ChangeLog to HTML✨
change_paired_read_orientation(1p)Change the orientation of paired-end reads in a FASTA file✨
changepagestring(1p)Search and replace in all PDF pages✨
changepdfstring(1p)Search and replace in PDF metadata✨
changerefkeys(1p)Search and replace PDF object numbers in the Trailer✨
chartex(1p)A utility to extract charts from an Excel file for insertion into a Spreadsheet::WriteExcel file.✨
check-zone-expiration(1p)displays how long until a zone's records expire✨
check_perldiag(1p)check a localized version of perldiag for consistency✨
check_postgres(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others✨
check_postgres_archive_ready(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_autovac_freeze(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_backends(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_bloat(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_checkpoint(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_cluster_id(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_commitratio(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_connection(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_custom_query(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_database_size(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_dbstats(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_disabled_triggers(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_disk_space(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_fsm_pages(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_fsm_relations(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_hitratio(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_hot_standby_delay(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_index_size(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_indexes_size(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_last_analyze(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_last_autoanalyze(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_last_autovacuum(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_last_vacuum(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_listener(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_locks(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_logfile(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_new_version_bc(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_new_version_box(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_new_version_cp(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_new_version_pg(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_new_version_tnm(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_partman_premake(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgagent_jobs(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgb_pool_cl_active(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgb_pool_cl_waiting(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgb_pool_maxwait(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgb_pool_sv_active(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgb_pool_sv_idle(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgb_pool_sv_login(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgb_pool_sv_tested(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgb_pool_sv_used(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgbouncer_backends(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgbouncer_checksum(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_pgbouncer_maxwait(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_prepared_txns(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_query_runtime(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_query_time(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_relation_size(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨
check_postgres_replicate_row(1p)a Postgres monitoring script for Nagios, MRTG, Cacti, and others This documents describes check_postgres version 2.26.0✨