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This is the command gt that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



gt - The GenomeTools genome analysis system.


gt [option ...] [tool | script] [argument ...]


-i [yes|no]
enter interactive mode after executing tool or script

-q [yes|no]
suppress warnings

-test [yes|no]
perform unit tests and exit

-seed [value]
set seed for random number generator manually. 0 generates a seed from current time
and process id

display help and exit

display version information and exit


· bed_to_gff3

· cds

· chain2dim

· chseqids

· clean

· compreads

· condenseq

· congruence

· convertseq

· csa

· dot

· dupfeat

· encseq

· encseq2spm

· eval

· extractfeat

· extractseq

· fastq_sample

· featureindex

· fingerprint

· genomediff

· gff3

· gff3_to_gtf

· gff3validator

· gtf_to_gff3

· hop

· id_to_md5

· inlineseq_add

· inlineseq_split

· interfeat

· loccheck

· ltrclustering

· ltrdigest

· ltrharvest

· matchtool

· matstat

· md5_to_id

· merge

· mergefeat

· mgth

· mkfeatureindex

· mkfmindex

· mmapandread

· orffinder

· packedindex

· prebwt

· readjoiner

· repfind

· scriptfilter

· seed_extend

· select

· seq

· seqfilter

· seqids

· seqmutate

· seqorder

· seqstat

· seqtransform

· seqtranslate

· sequniq

· shredder

· shulengthdist

· simreads

· sketch

· sketch_page

· snpper

· speck

· splicesiteinfo

· splitfasta

· stat

· suffixerator

· tagerator

· tallymer

· tirvish

· uniq

· uniquesub

· wtree

Set the environment variable GT_MEM_BOOKKEEPING=on to enable memory bookkeeping (e.g.,
like this: env GT_MEM_BOOKKEEPING=on gt).

Set the environment variable GT_ENV_OPTIONS=-spacepeak to show a spacepeak after program
run. Set the environment variable GT_ENV_OPTIONS=-showtime to show processing times for
some program parts if implemented.

Set the environment variable GT_SEED to an integer value to supply a seed for the random
number generator. Can be overridden by the -seed option.

Combinations are possible. Running the gt binary with GT_ENV_OPTIONS=-help shows all
possible "environment options".


Report bugs to <gt-users@genometools.org>.

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