.. _backbone-label: Emboss ============================== Introduction ~~~~~~~~ Emboss is "The European Molecular Biology Open Software Suite". | For more information, please check: | BioContainers: https://biocontainers.pro/tools/emboss | Home page: http://emboss.open-bio.org .. note:: Please follow the recommended citation guidelines from the developers when you use the tool in research. Versions ~~~~~~~ .. list-table:: :width: 100 % :widths: 25 75 :header-rows: 1 * - Cluster - Version(s) * - ANVIL - 6.6.0 * - BELL - 6.6.0 * - GAUTSCHI - 6.6.0 * - NEGISHI - 6.6.0 * - SCHOLAR - 6.6.0 Commands ~~~~~~~ - aaindexextract - abiview - acdc - acdgalaxy - acdlog - acdpretty - acdtable - acdtrace - acdvalid - aligncopy - aligncopypair - antigenic - assemblyget - backtranambig - backtranseq - banana - biosed - btwisted - cachedas - cachedbfetch - cacheebeyesearch - cacheensembl - cai - chaos - charge - checktrans - chips - cirdna - codcmp - codcopy - coderet - compseq - cons - consambig - cpgplot - cpgreport - cusp - cutgextract - cutseq - dan - dbiblast - dbifasta - dbiflat - dbigcg - dbtell - dbxcompress - dbxedam - dbxfasta - dbxflat - dbxgcg - dbxobo - dbxreport - dbxresource - dbxstat - dbxtax - dbxuncompress - degapseq - density - descseq - diffseq - distmat - dotmatcher - dotpath - dottup - dreg - drfinddata - drfindformat - drfindid - drfindresource - drget - drtext - edamdef - edamhasinput - edamhasoutput - edamisformat - edamisid - edamname - edialign - einverted - embossdata - embossupdate - embossversion - emma - emowse - entret - epestfind - eprimer3 - eprimer32 - equicktandem - est2genome - etandem - extractalign - extractfeat - extractseq - featcopy - featmerge - featreport - feattext - findkm - freak - fuzznuc - fuzzpro - fuzztran - garnier - geecee - getorf - godef - goname - helixturnhelix - hmoment - iep - infoalign - infoassembly - infobase - inforesidue - infoseq - isochore - jaspextract - jaspscan - jembossctl - lindna - listor - makenucseq - makeprotseq - marscan - maskambignuc - maskambigprot - maskfeat - maskseq - matcher - megamerger - merger - msbar - mwcontam - mwfilter - needle - needleall - newcpgreport - newcpgseek - newseq - nohtml - noreturn - nospace - notab - notseq - nthseq - nthseqset - octanol - oddcomp - ontocount - ontoget - ontogetcommon - ontogetdown - ontogetobsolete - ontogetroot - ontogetsibs - ontogetup - ontoisobsolete - ontotext - palindrome - pasteseq - patmatdb - patmatmotifs - pepcoil - pepdigest - pepinfo - pepnet - pepstats - pepwheel - pepwindow - pepwindowall - plotcon - plotorf - polydot - preg - prettyplot - prettyseq - primersearch - printsextract - profit - prophecy - prophet - prosextract - pscan - psiphi - rebaseextract - recoder - redata - refseqget - remap - restover - restrict - revseq - runJemboss.sh - seealso - seqcount - seqmatchall - seqret - seqretsetall - seqretsplit - seqxref - seqxrefget - servertell - showalign - showdb - showfeat - showorf - showpep - showseq - showserver - shuffleseq - sigcleave - silent - sirna - sixpack - sizeseq - skipredundant - skipseq - splitsource - splitter - stretcher - stssearch - supermatcher - syco - taxget - taxgetdown - taxgetrank - taxgetspecies - taxgetup - tcode - textget - textsearch - tfextract - tfm - tfscan - tmap - tranalign - transeq - trimest - trimseq - trimspace - twofeat - union - urlget - variationget - vectorstrip - water - whichdb - wobble - wordcount - wordfinder - wordmatch - wossdata - wossinput - wossname - wossoperation - wossoutput - wossparam - wosstopic - xmlget - xmltext - yank Module ~~~~~~~~ You can load the modules by:: module load biocontainers module load emboss Example job ~~~~~ .. warning:: Using ``#!/bin/sh -l`` as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use ``#!/bin/bash`` instead. To run emboss on our clusters: .. tab-set:: .. tab-item:: Anvil .. code-block:: bash #!/bin/bash #SBATCH -A myallocation # Allocation name #SBATCH -p wholenode # Partition name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=emboss #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers emboss # Your emboss workflow... .. tab-item:: Bell, Gautschi, or Negishi .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p cpu # Partition name #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=emboss #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers emboss # Your emboss workflow... .. tab-item:: Gautschi-AI .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p ai # Partition name #SBATCH --gres=gpu:1 # Number of GPUs #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=emboss #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers emboss # Your emboss workflow... .. tab-item:: Gilbreth .. code-block:: bash #!/bin/bash #SBATCH -A mygroup # Group name #SBATCH -p a100 # Partition name #SBATCH --gres=gpu:1 # Number of GPUs #SBATCH --mem=2G # Memory #SBATCH -q normal # QOS name (optional) #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=emboss #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers emboss # Your emboss workflow... .. tab-item:: Scholar .. code-block:: bash #!/bin/bash #SBATCH -A queue # Queue name #SBATCH -t 1:00:00 #SBATCH -N 1 #SBATCH -n 1 #SBATCH --job-name=emboss #SBATCH --mail-type=FAIL,BEGIN,END #SBATCH --error=%x-%J-%u.err #SBATCH --output=%x-%J-%u.out module --force purge module biocontainers emboss # Your emboss workflow...