############# Administrator's Note #################
###
### $Author='Guo-Hua XU';
### $Content='The Construction of IBI-ZJU SERVER';
### $Destination='Make it easy to administer this Server
### for next Administrator';
### $LastUpdate='2004/04/06';
###
########################################################
#
# $Index='OS HTTPD XDMCP mrtg+snmp Didier
# SRS EMBOSS BLAST ClustalW Genscan Readseq';
#
########################################################
sub OS{
$Title='Linux_Installation';
$Date='2004/01/17';
$Version='RedHat Linux(GNU/Unix) 8.0';
$Content='SCSI harddisk(65GB) mounted on "/"
DiskMatrix(269GB) mounted on "/home" ';
}
sub HTTPD{
$Title='The Installation and Configuration of Web Server';
$Date='2004/01/17';
$Version='Apache/2.0.40';
$Content='the website of ibi can be visited, but the homepage index.html
can not be normally showed in browser because of the default
code setting of Apache Server is "iso-8859-1", so, i reconfigured the file:
/etc/httpd/conf/httpd.conf, i changed the line belowed:
AddDefaultCharset ISO-8859-1
-->
AddDefaultCharset GB2312 ';
sub What_I_Did{
$Title='what i did in /etc/httpd/conf/httpd.conf ';
$Content0=HTTPD($Content);
$Content1='Add two line belowed
ServerAdmin ghxu@zju.edu.cn
ServerName ibi.zju.edu.cn ';
$Content2='#Configure the tmp directory
Alias /tmp/ "/tmp/www/"
#define .cgi file to be cgi-script
AddHandler cgi-script .cgi ';
}
}
sub SRS{
$Title='The Installation and Configuration of SRS';
$Date='2004/02/25';
$Link='Run SRS here';
sub SRS_Installation{
$Content0='Download SRS 7.1.3 here (srs7.1.3.standard.tar.gz, srs7.1.3.standard.linux7.tar.gz)';
$Content1='redhat 8(or 9) is not actually supported. In order to install srs on it, I need to use the
srs7.1.3.standard.linux7.tar.gz distribution file. But after untarring it, rename
srs/bin/linux7 to srs/bin/linux73 ';
$Content2='Alias configuration in the /etc/httpd/conf/httpd.conf';
$Content3='Here is more information about installing SRS 7.1.3';
}
sub SRS_Adding_libraries{
$Title='There is a Example of Adding library belowed, this example is "How to adding Genbank "';
$Content0='Download database (ftp://ftp.ncbi.nih.gov/genbank/)';
$Content1='Put those database in a large disk (I put it on DiskMatrix what is mounted on "/home") and
$ gunzip gb*.seq.gz ';
$Content2='Add Environment variable:
$ source srs/etc/prep_srs.sh ';
$Content3='Edit $SRSSITE/srsdb.i
$LibLoc:[$GENBANK_DB enabled:y # 'n-->y' to enalbe this database
includeFiles:{"SRSDB:genbank.i" "SRSDB:genbank.it"} # need not change
indexDir:"/home/SRS/index/" # SRS will write index file in indexDir (size=?0GB)
]
$LibLoc:[$GENBANKREL_DB enabled:y #in this $LibLoc, I have not defined the indexDir, it's default.
includeFiles:{"SRSDB:genbank.i" "SRSDB:genbankrelease.it"}
dir:"/home/database/genbank/" #dir is a directory where I stored the database files
offDir:"/home/SRS/offDir/genbank_tmp/" #temp directory
]
$LibLoc:[$GENBANKNEW_DB enabled:y
includeFiles:{"SRSDB:genbank.i" "SRSDB:genbanknew.it"}
indexDir:"/home/SRS/index/"
dir:"/home/database/genbank/genbank_new/"
offDir:"/home/SRS/offDir/genbank_new_tmp/"
] ';
$Content4='Edit $SRSDB/genbank.i
Change the searchName line to make sure that SRS will find those data file.
searchName:'gb*.seq' ';
$Content5='Run those command belowed:
$ srssection
$ srscheck
$ srsdo ';
$Content6='PDB data file need not to gunzip ';
}
}
sub EMBOSS{
$Title='Installing EMBOSS and adding it into SRS';
$Date='2004/02/25';
$Content0='Installed but not added yet';
}
sub wwwBLAST{
$Title='Build the webserver of BLAST';
$Date='2004/01/29';
$Content0='1st: Download the software from NCBI
wwwblast-20031121-ia32-linux.tar.gz
2ed: Decompress the software and put those decompressed files under /var/www/cgi-bin/blast/
3rd: $ cp /var/www/cgi-bin/blast/*.html /var/www/html/blast/
4th: Edit /var/www/html/blast/index.html
5th: Edit /var/www/html/blast/*_cs.html to make sure that form action is point to CGI files under /var/www/cgi-bin/blast/';
$Content1='#Adding database for BLAST (NOT FINISHED)';
$Link='Run BLAST here';
}
sub ClustalW{
$Title='www interface for ClustalW';
$Date='2004/02/09';
$Content0='Download the software of ClustalW';
$Content1='Write the CGI (www interface) for ClustalW';
$SourceFile='Here is the CGI what I wrote';
$Link='Run ClustalW here';
}
sub Readseq{
$Title='www interface for Readseq';
$Date='2004/02/09';
$Content0='Download the software of Readseq';
$Content1='Write the CGI (www interface) for Readseq';
$SourceFile='Here is the CGI what I wrote';
$Link='Run Readseq here';
}
sub Genscan{
$Title='www interface for Genscan';
$Date='2004/02/09';
$Content0='Download the software of Genscan';
$Content1='Write the CGI (www interface) for Genscan';
$SourceFile='Here is the CGI what I wrote';
$Link='Run Genscan here';
}
sub XDMCP{
$Title='Build the XDMCP server for x-win32 client';
$Date='2004/01/17';
$Link='i finished it followed the article ';
$Content='
1.in the file /etc/rc.d/init.d/xfs
daemon xfs -droppriv -daemon
-->
daemon xfs -droppriv -daemon -port 7100
2.in the file /etc/X11/xdm/Xaccess,
#* # any host can get a login window
-->
* # any host can get a login window
3.in the file /etc/X11/gdm/gdm.conf
[xdmcp]
...
Enable=false
-->
Enable=true
4.in the file /etc/inittab
id:3:initdefault:
-->
id:5:initdefault:
5.in the file /etc/X11/xdm/XServers
:0 local /usr/X11R6/bin/X
-->
:0 A local /usr/X11R6/bin/X :0
:1 B local /usr/X11R6/bin/X :1
:2 C local /usr/X11R6/bin/X :2
6.chmod 755 /etc/X11/xdm/Xsetup_0
7.in the file /etc/inittab
x:5:respawn:/etc/X11/prefdm -nodaemon
-->
x:5:respawn:/usr/bin/gdm
';
}
sub mrtg+snmp{
$Title='Build mrtg+snmp To monitor the SERVER-STATUS by auto-generated HTML pages containing graphical images
which provide a LIVE visual representation. ';
$Date='2004/02/20';
$Link='Monitor IBI-ZJU here';
$Content='
1.Packages required: GCC?Perl?gd?libpng and zlib. It's necessary to check those packages.
$ rpm -qa|grep gd #( to check the gd package. )
2.Install mrtg (It's installed in the default installation of RedHat Linux 8.0)
3.Install snmp (Also installed.)
4.Run and check snmpd:
$ /etc/rc.d/init.d/snmpd start
Starting snmpd: [ OK ]
$ ps -aef | grep snmpd
$ vi /etc/snmp/snmpd.conf
#view systemview included mib2
-->
view mib2 included .iso.org.dod.internet.mgmt.mib-2 fc
access notConfigGroup "" any noauth exact systemview none none
-->
access notConfigGroup "" any noauth exact mib2 none none
$ /etc/rc.d/init.d/snmpd restart
5.Configration of mrtg.cfg:
$ mkdir /var/www/html/mrtg/all/
$ cfgmaker --global "WorkDir: /var/www/html/mrtg/all/"
\--global "Options[_]: growright,bits"
\--ifref=ip
\--output /etc/mrtg/mrtg.cfg
\public@ibi.zju.edu.cn
6.Run mrtg:
$ /usr/bin/mrtg /etc/mrtg/mrtg.cfg
7.Write the line below into /etc/crontab (make sure mrtg will autorun per 5 minutes
0-59/5 * * * * /usr/bin/mrtg /etc/mrtg/mrtg.cfg
8.After those 7 steps above, the network traffic can be monitored by watch the pages in http://ibi.zju.edu.cn/mrtg/all/
9.But, I want know more about the server status, so I put 3 shell scripts under /etc/mrtg/.
Their are cpustat.sh, mfree.sh, and iostat.sh .
10.It's neccessary to edit /etc/snmp/snmpd.conf and /etc/mrtg/mrtg.cfg to run those 3 file above,
in /etc/snmp/snmpd.conf:
exec .1.3.6.1.4.1.2021.53 mfree /bin/sh /root/mfree.sh
exec .1.3.6.1.4.1.2021.54 cpustat /bin/sh /root/cpustat.sh
exec .1.3.6.1.4.1.2021.55 iostat /bin/sh /root/iostat.sh
in /etc/mrtg/mrtg.cfg: SKIP ( check it yourself )
';
}