How to launch emboss from terminal

Question

[marongiu.luigi]

Hello,

I have installed emboss on ubuntu 19.

$ sudo apt-get install emboss
Reading package lists... Done
Building dependency tree       
Reading state information... Done
emboss is already the newest version (6.6.0+dfsg-7).
0 to upgrade, 0 to newly install, 0 to remove and 15 not to upgrade.

how do I launch it?

$ emboss

Command 'emboss' not found, did you mean:

  command 'jemboss' from deb jemboss (6.6.0+dfsg-7)

Try: sudo apt install <deb name>
$ jemboss

Command 'jemboss' not found, but can be installed with:

sudo apt install jemboss

Answer 1

[h.mon]

For the Debian / Ubuntu packaged EMBOSS, the EMBOSS cons has been renamed to em_cons, to avoid conflict with another cons, a perl replacement for make.

The Debian team frequently rename package names and / or executables to avoid conflicts.

[GenoMax]

It may be in latest dev release. It is still cons in EMBOSS v.6.6.0.

[marongiu.luigi]

em_cons worked, thank you!

Answer 2

[GenoMax]

EMBOSS suite is a collections of programs. You don't launch emboss per se. If you need a GUI to use the suite, then you will need to install jemboss as suggested above.

[marongiu.luigi]

fair enough, so if I wanted to launch the tool cons to get a consensus from alignment, what would be the call?

$ cons

Command 'cons' not found, but can be installed with:

sudo apt install cons

[GenoMax]

If EMBOSS is properly installed and bin directory included in your $PATH then calling cons should generate the following (output truncated to save space). Otherwise use full path to cons.

$ cons -h
Create a consensus sequence from a multiple alignment
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers:
  [-sequence]          seqset     File containing a sequence alignment.
  [-outseq]            seqout     [<sequence>.<format>] Sequence filename and
                                  optional format (output USA)