How To Install EMBOSS on Fedora 34
EMBOSS is The European Molecular Biology Open Software Suite
Introduction
In this tutorial we learn how to install EMBOSS on Fedora 34.
What is EMBOSS
EMBOSS is a new, free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. Reference for EMBOSS “EMBOSS Trends in Genetics June 2000, vol 16, No 6. pp.276-277
We can use yum or dnf to install EMBOSS on Fedora 34. In this tutorial we discuss both methods but you only need to choose one of method to install EMBOSS.
Install EMBOSS on Fedora 34 Using dnf
Update yum database with dnf using the following command.
sudo dnf makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 kB 00:00
Metadata cache created.
After updating yum database, We can install EMBOSS using dnf by running the following command:
sudo dnf -y install EMBOSS
Install EMBOSS on Fedora 34 Using yum
Update yum database with yum using the following command.
sudo yum makecache --refresh
The output should look something like this:
Fedora 34 - x86_64 20 kB/s | 6.6 kB 00:00
Fedora 34 openh264 (From Cisco) - x86_64 1.4 kB/s | 989 B 00:00
Fedora Modular 34 - x86_64 68 kB/s | 6.5 kB 00:00
Fedora 34 - x86_64 - Updates 3.5 kB/s | 6.2 kB 00:01
Fedora Modular 34 - x86_64 - Updates 17 kB/s | 5.9 kB 00:00
Metadata cache created.
After updating yum database, We can install EMBOSS using yum by running the following command:
sudo yum -y install EMBOSS
How To Uninstall EMBOSS on Fedora 34
To uninstall only the EMBOSS package we can use the following command:
sudo dnf remove EMBOSS
EMBOSS Package Contents on Fedora 34
/etc/profile.d/emboss.csh
/etc/profile.d/emboss.sh
/usr/bin/aaindexextract
/usr/bin/abiview
/usr/bin/acdc
/usr/bin/acdgalaxy
/usr/bin/acdlog
/usr/bin/acdpretty
/usr/bin/acdtable
/usr/bin/acdtrace
/usr/bin/acdvalid
/usr/bin/aligncopy
/usr/bin/aligncopypair
/usr/bin/antigenic
/usr/bin/assemblyget
/usr/bin/backtranambig
/usr/bin/backtranseq
/usr/bin/banana
/usr/bin/biosed
/usr/bin/btwisted
/usr/bin/cachedas
/usr/bin/cachedbfetch
/usr/bin/cacheebeyesearch
/usr/bin/cacheensembl
/usr/bin/cai
/usr/bin/charge
/usr/bin/checktrans
/usr/bin/chips
/usr/bin/cirdna
/usr/bin/codcmp
/usr/bin/codcopy
/usr/bin/coderet
/usr/bin/compseq
/usr/bin/cons
/usr/bin/consambig
/usr/bin/cpgplot
/usr/bin/cpgreport
/usr/bin/cusp
/usr/bin/cutgextract
/usr/bin/cutseq
/usr/bin/dan
/usr/bin/dbiblast
/usr/bin/dbifasta
/usr/bin/dbiflat
/usr/bin/dbigcg
/usr/bin/dbtell
/usr/bin/dbxcompress
/usr/bin/dbxedam
/usr/bin/dbxfasta
/usr/bin/dbxflat
/usr/bin/dbxgcg
/usr/bin/dbxobo
/usr/bin/dbxreport
/usr/bin/dbxresource
/usr/bin/dbxstat
/usr/bin/dbxtax
/usr/bin/dbxuncompress
/usr/bin/degapseq
/usr/bin/density
/usr/bin/descseq
/usr/bin/diffseq
/usr/bin/distmat
/usr/bin/dotmatcher
/usr/bin/dotpath
/usr/bin/dottup
/usr/bin/dreg
/usr/bin/drfinddata
/usr/bin/drfindformat
/usr/bin/drfindid
/usr/bin/drfindresource
/usr/bin/drget
/usr/bin/drtext
/usr/bin/edamdef
/usr/bin/edamhasinput
/usr/bin/edamhasoutput
/usr/bin/edamisformat
/usr/bin/edamisid
/usr/bin/edamname
/usr/bin/edialign
/usr/bin/einverted
/usr/bin/em_chaos
/usr/bin/em_remap
/usr/bin/em_wordcount
/usr/bin/embossdata
/usr/bin/embossupdate
/usr/bin/embossversion
/usr/bin/emma
/usr/bin/emowse
/usr/bin/entret
/usr/bin/epestfind
/usr/bin/eprimer3
/usr/bin/eprimer32
/usr/bin/epscan
/usr/bin/equicktandem
/usr/bin/est2genome
/usr/bin/etandem
/usr/bin/extractalign
/usr/bin/extractfeat
/usr/bin/extractseq
/usr/bin/featcopy
/usr/bin/featmerge
/usr/bin/featreport
/usr/bin/feattext
/usr/bin/findkm
/usr/bin/freak
/usr/bin/fuzznuc
/usr/bin/fuzzpro
/usr/bin/fuzztran
/usr/bin/garnier
/usr/bin/geecee
/usr/bin/getorf
/usr/bin/godef
/usr/bin/goname
/usr/bin/helixturnhelix
/usr/bin/hmoment
/usr/bin/iep
/usr/bin/infoalign
/usr/bin/infoassembly
/usr/bin/infobase
/usr/bin/inforesidue
/usr/bin/infoseq
/usr/bin/isochore
/usr/bin/jaspextract
/usr/bin/jaspscan
/usr/bin/lindna
/usr/bin/listor
/usr/bin/makenucseq
/usr/bin/makeprotseq
/usr/bin/marscan
/usr/bin/maskambignuc
/usr/bin/maskambigprot
/usr/bin/maskfeat
/usr/bin/maskseq
/usr/bin/matcher
/usr/bin/megamerger
/usr/bin/merger
/usr/bin/msbar
/usr/bin/mwcontam
/usr/bin/mwfilter
/usr/bin/needle
/usr/bin/needleall
/usr/bin/newcpgreport
/usr/bin/newcpgseek
/usr/bin/newseq
/usr/bin/nohtml
/usr/bin/noreturn
/usr/bin/nospace
/usr/bin/notab
/usr/bin/notseq
/usr/bin/nthseq
/usr/bin/nthseqset
/usr/bin/octanol
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/usr/bin/pepwindowall
/usr/bin/plotcon
/usr/bin/plotorf
/usr/bin/polydot
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/usr/bin/profit
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/usr/bin/restover
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/usr/bin/runJemboss.sh
/usr/bin/seealso
/usr/bin/seqcount
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/usr/bin/seqret
/usr/bin/seqretsetall
/usr/bin/seqretsplit
/usr/bin/seqxref
/usr/bin/seqxrefget
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/usr/share/EMBOSS/test/data/prot.m-ncbi
/usr/share/EMBOSS/test/data/prot.m-swiss
/usr/share/EMBOSS/test/data/prot.nbrf
/usr/share/EMBOSS/test/data/prot.ncbi
/usr/share/EMBOSS/test/data/prot.swiss
/usr/share/EMBOSS/test/data/prot.text
/usr/share/EMBOSS/test/data/site.dat
/usr/share/EMBOSS/test/data/tranalign.pep
/usr/share/EMBOSS/test/data/tranalign.seq
/usr/share/EMBOSS/test/data/untrimmed.seq
/usr/share/EMBOSS/test/data/vtest.seq
/usr/share/EMBOSS/test/data/withrefm
/usr/share/EMBOSS/test/data/z83307.seq
/usr/share/EMBOSS/test/embl
/usr/share/EMBOSS/test/embl/acnum.hit
/usr/share/EMBOSS/test/embl/acnum.trg
/usr/share/EMBOSS/test/embl/condiv.dat
/usr/share/EMBOSS/test/embl/des.hit
/usr/share/EMBOSS/test/embl/des.trg
/usr/share/EMBOSS/test/embl/division.lkp
/usr/share/EMBOSS/test/embl/entrynam.idx
/usr/share/EMBOSS/test/embl/est.dat
/usr/share/EMBOSS/test/embl/fun.dat
/usr/share/EMBOSS/test/embl/hum1.dat
/usr/share/EMBOSS/test/embl/inv.dat
/usr/share/EMBOSS/test/embl/keyword.hit
/usr/share/EMBOSS/test/embl/keyword.trg
/usr/share/EMBOSS/test/embl/pln.dat
/usr/share/EMBOSS/test/embl/pro.dat
/usr/share/EMBOSS/test/embl/rod.dat
/usr/share/EMBOSS/test/embl/seqvn.hit
/usr/share/EMBOSS/test/embl/seqvn.trg
/usr/share/EMBOSS/test/embl/sts.dat
/usr/share/EMBOSS/test/embl/syn.dat
/usr/share/EMBOSS/test/embl/taxon.hit
/usr/share/EMBOSS/test/embl/taxon.trg
/usr/share/EMBOSS/test/embl/vrl.dat
/usr/share/EMBOSS/test/embl/vrt.dat
/usr/share/EMBOSS/test/embl/wgs.dat
/usr/share/EMBOSS/test/genbank
/usr/share/EMBOSS/test/genbank/acnum.hit
/usr/share/EMBOSS/test/genbank/acnum.trg
/usr/share/EMBOSS/test/genbank/des.hit
/usr/share/EMBOSS/test/genbank/des.trg
/usr/share/EMBOSS/test/genbank/division.lkp
/usr/share/EMBOSS/test/genbank/entrynam.idx
/usr/share/EMBOSS/test/genbank/gbbct1.seq
/usr/share/EMBOSS/test/genbank/gbest1.seq
/usr/share/EMBOSS/test/genbank/gbinv1.seq
/usr/share/EMBOSS/test/genbank/gbpln1.seq
/usr/share/EMBOSS/test/genbank/gbpln2.seq
/usr/share/EMBOSS/test/genbank/gbpri1.seq
/usr/share/EMBOSS/test/genbank/gbrod1.seq
/usr/share/EMBOSS/test/genbank/gbsts1.seq
/usr/share/EMBOSS/test/genbank/gbvrl1.seq
/usr/share/EMBOSS/test/genbank/gbvrt.seq
/usr/share/EMBOSS/test/genbank/keyword.hit
/usr/share/EMBOSS/test/genbank/keyword.trg
/usr/share/EMBOSS/test/genbank/seqvn.hit
/usr/share/EMBOSS/test/genbank/seqvn.trg
/usr/share/EMBOSS/test/genbank/taxon.hit
/usr/share/EMBOSS/test/genbank/taxon.trg
/usr/share/EMBOSS/test/pir
/usr/share/EMBOSS/test/pir/acnum.hit
/usr/share/EMBOSS/test/pir/acnum.trg
/usr/share/EMBOSS/test/pir/des.hit
/usr/share/EMBOSS/test/pir/des.trg
/usr/share/EMBOSS/test/pir/division.lkp
/usr/share/EMBOSS/test/pir/entrynam.idx
/usr/share/EMBOSS/test/pir/keyword.hit
/usr/share/EMBOSS/test/pir/keyword.trg
/usr/share/EMBOSS/test/pir/pir1.header
/usr/share/EMBOSS/test/pir/pir1.names
/usr/share/EMBOSS/test/pir/pir1.numbers
/usr/share/EMBOSS/test/pir/pir1.offset
/usr/share/EMBOSS/test/pir/pir1.ref
/usr/share/EMBOSS/test/pir/pir1.seq
/usr/share/EMBOSS/test/pir/pir2.header
/usr/share/EMBOSS/test/pir/pir2.names
/usr/share/EMBOSS/test/pir/pir2.numbers
/usr/share/EMBOSS/test/pir/pir2.offset
/usr/share/EMBOSS/test/pir/pir2.ref
/usr/share/EMBOSS/test/pir/pir2.seq
/usr/share/EMBOSS/test/pir/pir3.header
/usr/share/EMBOSS/test/pir/pir3.names
/usr/share/EMBOSS/test/pir/pir3.numbers
/usr/share/EMBOSS/test/pir/pir3.offset
/usr/share/EMBOSS/test/pir/pir3.ref
/usr/share/EMBOSS/test/pir/pir3.seq
/usr/share/EMBOSS/test/pir/pir4.header
/usr/share/EMBOSS/test/pir/pir4.names
/usr/share/EMBOSS/test/pir/pir4.numbers
/usr/share/EMBOSS/test/pir/pir4.offset
/usr/share/EMBOSS/test/pir/pir4.ref
/usr/share/EMBOSS/test/pir/pir4.seq
/usr/share/EMBOSS/test/pir/taxon.hit
/usr/share/EMBOSS/test/pir/taxon.trg
/usr/share/EMBOSS/test/swiss
/usr/share/EMBOSS/test/swiss/acnum.hit
/usr/share/EMBOSS/test/swiss/acnum.trg
/usr/share/EMBOSS/test/swiss/des.hit
/usr/share/EMBOSS/test/swiss/des.trg
/usr/share/EMBOSS/test/swiss/division.lkp
/usr/share/EMBOSS/test/swiss/entrynam.idx
/usr/share/EMBOSS/test/swiss/keyword.hit
/usr/share/EMBOSS/test/swiss/keyword.trg
/usr/share/EMBOSS/test/swiss/seq.dat
/usr/share/EMBOSS/test/swiss/seqvn.hit
/usr/share/EMBOSS/test/swiss/seqvn.trg
/usr/share/EMBOSS/test/swiss/taxon.hit
/usr/share/EMBOSS/test/swiss/taxon.trg
/usr/share/EMBOSS/test/swnew
/usr/share/EMBOSS/test/swnew/acnum.hit
/usr/share/EMBOSS/test/swnew/acnum.trg
/usr/share/EMBOSS/test/swnew/des.hit
/usr/share/EMBOSS/test/swnew/des.trg
/usr/share/EMBOSS/test/swnew/division.lkp
/usr/share/EMBOSS/test/swnew/entrynam.idx
/usr/share/EMBOSS/test/swnew/keyword.hit
/usr/share/EMBOSS/test/swnew/keyword.trg
/usr/share/EMBOSS/test/swnew/seqvn.hit
/usr/share/EMBOSS/test/swnew/seqvn.trg
/usr/share/EMBOSS/test/swnew/taxon.hit
/usr/share/EMBOSS/test/swnew/taxon.trg
/usr/share/EMBOSS/test/swnew/trembl.dat
/usr/share/EMBOSS/test/testdb
/usr/share/EMBOSS/test/testdb/acnum.hit
/usr/share/EMBOSS/test/testdb/acnum.trg
/usr/share/EMBOSS/test/testdb/des.hit
/usr/share/EMBOSS/test/testdb/des.trg
/usr/share/EMBOSS/test/testdb/division.lkp
/usr/share/EMBOSS/test/testdb/entrynam.idx
/usr/share/EMBOSS/test/testdb/testdb.fasta
/usr/share/doc/EMBOSS
/usr/share/doc/EMBOSS/AUTHORS
/usr/share/doc/EMBOSS/ChangeLog
/usr/share/doc/EMBOSS/FAQ
/usr/share/doc/EMBOSS/INSTALL
/usr/share/doc/EMBOSS/NEWS
/usr/share/doc/EMBOSS/README
/usr/share/doc/EMBOSS/THANKS
References
Summary
In this tutorial we learn how to install EMBOSS on Fedora 34 using yum and dnf.