Hi ,
I am having one situation in which I need to run some simple unix commands after doing "chroot" command in a shell script. Which in turn creates a new shell.
So scenario is that
- I need to have one shell script which is ran as a part of crontab
- in this shell script I need to do a... (2 Replies)
Hi
I tried with bash --login option. but the output is
siva:~$ bash --login
siva:~$
is there any way to make the shell ask for user id and password ( and login as different user instead of using sudo / su )
Thx in advance
Siva (3 Replies)
i have a small problem getting a batxh shell script to run in shell
this is the code
the problem seems to be centered around the ffmpeg command, something maybe to do with the ' ' wrapping around the vhook part command
this is a strange problem , if i take the ffmpeg command and... (1 Reply)
Hi,
I am using HP-UNIX.
I have a requirement as below
I have to change env twice like:
cadenv <env>
cadenv <env>
ccm start -d /dbpath
ccm tar -xvf *.tar
ccm rcv ....
mv *.tar BACKUP
but after I do the first cadenv <env> , I am unable to execute any of the later commands .
... (6 Replies)
Hi,
I am new to unix and using linux 7.2. I would like to create a script that would make it easyer for me to run my java programms. At the moment I have to type java myJavaprogram
I am trying to write a script that will allow me to type something like this "myscript myJavaprogram" or maybe... (4 Replies)
Hello gurus,
I have three korn shell script 3.1, 3.2, 3.3. I would like to call three shell script in one shell script.
i m looking for something like this
call 3.1;
If 3.1 = "complete" then
call 3.2;
if 3.2 = ''COMPlete" then
call 3.3;
else
exit
The... (1 Reply)
basically i'm tired of hitting the left arrow a few dozen times when correcting a mistake or modifying a history command
i'd like to use vim style key shortcuts while on the command line so that a 55 moves the cursor 55 places to the left...
and i want all the other vi goodies, search of... (3 Replies)
Dear Friends,
Please help me on this
my script name is send.csh
In this i have written the statement like this
set args = ( city state country price )
I want to pass this array to another c shell called receiver.csh. and i want to use it in this c shell
or
how to pass to... (2 Replies)
Discussion started by: SA_Palani
2 Replies
LEARN ABOUT DEBIAN
bp_classify_hits_kingdom
BP_CLASSIFY_HITS_KINGDOM(1p) User Contributed Perl Documentation BP_CLASSIFY_HITS_KINGDOM(1p)NAME
classify_hits_kingdom - classify BLAST hits by taxonomic kingdom
USAGE
classify_hits_kingdom [-i tab_file] [-i second_BLAST_file] [-e evalue_cutoff]
[-t dir_where_TAXONOMY_files_are] [-g gi2taxid]
[-z PATH_TO_zcat] [-v]
DESCRIPTION
Will print out the taxonomic distribution (at the kingdom level) for a set of hits against the NR database. This script assumes you've
done a search against the protein database, you'll have to make minor changes in the gi_taxid part to point to the gi_taxid_nuc.dump file.
This expects BLAST files in tabbed -m9 or -m8 format. Output with -m 8 or use blast2table.pl to convert (or fastam9_to_table.PLS if using
FASTA).
Input values:
-t/--taxonomy directory where the taxonomy .dmp files are (from NCBI)
-g/--gi Location of gi_taxid_prot.dmp (or gi_taxid_nucl.dmp if
the search was against a NT db)
-i/--in The name of the tab delimited -m8/-m9 output files to
process.
-e/--evalue Provide an E-value cutoff for hits to be considered
-z/--zcat Path to the 'zcat' executable, can also be 'gunzip -c'
if no zcat on your system.
Flags
-v/--verbose To turn on verbose messages
-h/--help Display this helpful information
This is intended to be useful starting script, but users may want to customize the output and parameters. Note that I am summarizing the
kingdoms here and Eukaryota not falling into Metazoa, Viridiplantae, or Fungi gets grouped into the general superkingdom Eukaryota. for
simplicity. There are comments in the code directing you to where changes can be made if you wanted to display hits by phylum for example.
Note that you must wipe out the cache file 'gi2class' that is craeed in your directory after making these changes.
AUTHOR
Jason Stajich jason_at_bioperl_dot_org
perl v5.14.2 2012-03-02 BP_CLASSIFY_HITS_KINGDOM(1p)