naive question

[nicedad]

Hello everyone,

again a simple question....
how to run GS assembler from command line, I know one should use (runAssemply) command.
My question is, should i set up a path to run it from the command line. because I tried to use it, unfortunately did not work even though I could run gsAssembler from the shortcut on the desktop.

thanks for your patient.

[flxlex]

What happens if you write on the command line

whereis runAssembly

or

which runAssembly

?

[nicedad]

Here what I got

akram@evo-zapus:~>
akram@evo-zapus:~> whereis runAssembly
runAssembly: /opt/454/bin/runAssembly
akram@evo-zapus:~>
akram@evo-zapus:~> which runAssembly
which: no runAssembly in (/usr/lib64/mpi/gcc/openmpi/bin:/home/akram/bin:/usr/local/bin:/usr/bin:/bin:/usr/bin/X11:/usr/X11R6/bin:/usr/games:/usr/lib64/jvm/jre/bin:/Root/opt/454/apps/assembly/bin/gsAssembly:/Root/opt/454/apps/assembly/bin/runAssembly:/Root/opt/454/apps/assembly/bin/doAmplicon:/Root/opt/454/apps/amplicons/bin/gsAmplicon:/Root/opt/454/apps/assembly/bin/gsAssembler:/Root/opt/454/apps/mapper/bin/gsMapper)
akram@evo-zapus:~>

[flxlex]

You could try

export $PATH=/opt/454/bin/:$PATH
runAssembly yourfile.sff

It looks like the location of the program is not in your PATH...

[nicedad]

done, thanks again flxlex!!