Is there a way to run Staden programs from command line?

Tim Cutts timc at chiark.greenend.org.uk
Mon Dec 11 04:53:23 EST 2000


In article <01C0622F.A2A967D0 at ym151015.ym.edu.tw>,  <yang at ym.edu.tw> wrote:
>	Although an X-windows interface is friendly,
>it is inconvenient to run batches of jobs. Is there a
>way to run some of the programs in NIP4 and SIP4
>from command line?

I don't know about those two, but they are probably constructed in a
similar manner to GAP4; i.e. a tcl/tk user interface around a C/FORTRAN
core.

One can certainly script gap4; you can access all of the assembly
functionality and so on using tcl.  For example:

#!/bin/env stash

load_package gap

# open a database
set io [open_db -name "foo" -version 0 -access rw -create 0]

# Get the number of reads in the database
set num_reads [db_info num_readings $io]

puts "Database has $num_readings reads in it"

# Close the database
close_db -io $io

You can probably do this sort of thing for NIP too, certainly, typing
"load_package nip" at a stash prompt does not return an error, so
the functionality is there.  Whether it's documented anywhere, of
course, is another matter, although you could probably look at the
tcl/tk scripts which make up the NIP4 user interface to find out what
many of the commands are.

Tim.






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