experchange > linux.misc

Rita (12-29-05, 09:09 PM)
Hi All
I have a red hat linux.I am new in Linux.
How I can find some software in linux.
like I am running 1 Bioinformatics related programm.when i write
command
bl2seq -i temp1 -j temp2 -p blastn.
It is working.
but i want to know that where is this bl2seq program is in computer.
any help will be appritiated.thanks
General Schvantzkoph (12-29-05, 09:15 PM)
On Thu, 29 Dec 2005 11:09:39 -0800, Rita wrote:

> Hi All
> I have a red hat linux.I am new in Linux.
> How I can find some software in linux.
> like I am running 1 Bioinformatics related programm.when i write
> command
> bl2seq -i temp1 -j temp2 -p blastn.
> It is working.
> but i want to know that where is this bl2seq program is in computer.
> any help will be appritiated.thanks


slocate filename

If you haven't run slocate before you'll have to create a database for it.
You do this as follows,

su
updatedb
Robert M. Riches Jr. (12-29-05, 09:15 PM)
On 2005-12-29, Rita <ritu_minda> wrote:
> Hi All
> I have a red hat linux.I am new in Linux.
> How I can find some software in linux.
> like I am running 1 Bioinformatics related programm.when i write
> command
> bl2seq -i temp1 -j temp2 -p blastn.
> It is working.
> but i want to know that where is this bl2seq program is in computer.


Welcome to penguin-land. :-)

Two commands are useful for this type of thing:

which bl2seq

slocate bl2seq | grep bin/

The first will (usually) tell you the path to the executable
that is run when you type 'bl2seq'. The second will show
you the paths to all files containing 'bl2seq' in their name
and located in a directory whose name ends in 'bin'.
Rita (12-29-05, 09:23 PM)
Thanks Schvantzkoph and Robert.
Martin Fenelon (12-30-05, 12:02 AM)
Just one point. By default 'which' usually gives you the first location
of the requested binary. 'which -a <binary>' will list all.
M (12-30-05, 01:04 AM)
"General Schvantzkoph" <schvantzkoph> wrote in message
news:3315
> On Thu, 29 Dec 2005 11:09:39 -0800, Rita wrote:
> slocate filename
> If you haven't run slocate before you'll have to create a database for it.
> You do this as follows,
> su
> updatedb


Just after startup I have noticed the HDD thrashing, went to look in
processes and noticed "updatedb".
So that is what it is :-)

Regards,

M
Chris F.A. Johnson (12-30-05, 04:25 AM)
On 2005-12-29, Rita wrote:
> Hi All
> I have a red hat linux.I am new in Linux.
> How I can find some software in linux.
> like I am running 1 Bioinformatics related programm.when i write
> command
> bl2seq -i temp1 -j temp2 -p blastn.
> It is working.
> but i want to know that where is this bl2seq program is in computer.
> any help will be appritiated.thanks


All Bourne-type shells (bash, ksh, etc., but not [t]csh) have the
"type" command, which will tell you what executable the shell will
use:

type bl2seq

But why do you need to know?
Robert M. Riches Jr. (12-30-05, 07:39 AM)
On 2005-12-29, Martin Fenelon <fenm> wrote:
> Just one point. By default 'which' usually gives you the first location
> of the requested binary. 'which -a <binary>' will list all.


I guess that depends on what you're using. With MandrX
LE2005 and csh, I get the following:

PROMPT> which -a cat
-a: Command not found.
/bin/cat

What's funny is I once wrote a short program for my own use
that, IIRC, used the -a option to report all paths.
Chris F.A. Johnson (12-30-05, 07:58 AM)
On 2005-12-30, Robert M. Riches Jr. wrote:
> On 2005-12-29, Martin Fenelon <fenm> wrote:
> I guess that depends on what you're using. With MandrX
> LE2005 and csh, I get the following:
> PROMPT> which -a cat
> -a: Command not found.
> /bin/cat


There are various incarnations of 'which'. It started as a csh
script that would not work in a Bourne-type shell. It is now a
built-in command in tcsh.

There have been a number of implementations for wider use, but it
is not a standard command, and the options differ from one to
another.

In a Bourne-type shell, use 'type'.
Moe Trin (12-30-05, 10:14 PM)
On Thu, 29 Dec 2005, in the Usenet newsgroup comp.os.linux.misc, in article
<AXZsf.16697$iz3.12130>, M wrote:

>"General Schvantzkoph" <schvantzkoph> wrote


>> If you haven't run slocate before you'll have to create a database for it.
>> You do this as follows,
>> su
>> updatedb


>Just after startup I have noticed the HDD thrashing, went to look in
>processes and noticed "updatedb".
>So that is what it is :-)


Running anacron, or fcron in the non-continuous mode. On a system running
24/7 (and using Dillon's "dcron" or the more common Vixie-Cron), this job
is normally run at Oh-Dark-Thirty along with 'makewhatis' because both tasks
are disk and CPU intensive.

[compton ~]$ ls -l /var/lib/locatedb /usr/share/man/whatis
-rw-r--r-- 1 root root 563690 Dec 30 04:02 /usr/share/man/whatis
-rw-r--r-- 1 root root 1332007 Dec 30 04:07 /var/lib/locatedb
[compton ~]$

Note that locatedb (the database used by the 'locate' or 'slocate' is a
snapshot of the file names on the system at the time 'updatedb' was run,
and isn't aware of files created/deleted since then.

Old guy
Bill Marcum (01-04-06, 01:24 AM)
On Fri, 30 Dec 2005 05:39:21 GMT, Robert M. Riches Jr.
<spamtrap42> wrote:
[..]
Rita (01-04-06, 04:03 PM)
All right ,Thanks to all.
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