Question: How to launch emboss from terminal
0
gravatar for marongiu.luigi
10 months ago by
Germany, Mannheim, UMM
marongiu.luigi520 wrote:

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
terminal emboss tools • 264 views
ADD COMMENTlink written 10 months ago by marongiu.luigi520
3
gravatar for h.mon
10 months ago by
h.mon31k
Brazil
h.mon31k wrote:

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.

ADD COMMENTlink modified 10 months ago • written 10 months ago by h.mon31k

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

ADD REPLYlink written 10 months ago by genomax89k

em_cons worked, thank you!

ADD REPLYlink written 10 months ago by marongiu.luigi520
2
gravatar for genomax
10 months ago by
genomax89k
United States
genomax89k wrote:

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.

ADD COMMENTlink modified 10 months ago • written 10 months ago by genomax89k

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
ADD REPLYlink written 10 months ago by marongiu.luigi520

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)
ADD REPLYlink modified 10 months ago • written 10 months ago by genomax89k
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