[GeneX-dev] Re: GeneX installation troubleshoot

[Harry M. <man...@ho...>]

Ron Ophir wrote:

> > I couldn't find dtd2html at the URL specified in the script?
> =

> It should be in the same directory as the GeneX-Server:
> =

> http://genebox.ncgr.org/download/genex-server/perlSGML.2001Jan23.tar.gz=

> =

> **This worked !! thanks!!

OK, one thing down.


> **Addressing to these links I couldn't download the entire package succ=
esfully. The connection always broke down even if I used the multiple fil=
e option.
> **I manage to download the zip file (not the rpm) of jre1.3 however the=
 installation documentation instruct me to put me the unziped package und=
er /usr/local/java and so I **did. I gave this path once and once /usr/lo=
cal/java/bin/i386/green_threads/,  in the ISA but still it couldn't find =
it.



http://www-106.ibm.com/developerworks/java/jdk/linux130/jre-info.html
go to the download section, register if you havevn't yet, and try it from=
 there.

There's often net congestion, so you might try it today if you can.  From=
 here, it's not super-speedy, but I'm getting decent speed.

and the following one should have been printed to your screen if it faile=
d to find jar in the 1st place).

http://java.sun.com/j2se/1.3/docs/api/java/util/jar/package-summary.html

If you just can't get it to install properly (the zip file may be the win=
dows version), then the other way of getting around this problem for now =
is to ignore it or edit the install-all.pl file and
comment out the line (~223) that looks like:

jar =3D> 'http://java.sun.com/j2se/1.3/docs/api/java/util/jar/package-sum=
mary.html',

It also looks like your PATH doesn't include the java/bin directory where=
 you installed it.   =


PATH =3D /usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/sbin: =
\                      /sbin:/usr/sbin:/bin:/usr/bin:/usr/X11R6/bin:/root=
/bin

you probably have to add:

:/usr/local/java/bin

to the end of yor PATH string, either by adding it to your shell environm=
ent PATH or explicitly creating one for the installation (line ~240) by c=
ommenting out the line:

   PATH     =3D>  $ENV{PATH},	# if this is too liberal, comment this line=
 =

                                # and use the next one

and UNcommenting the line beneath it, setting the PATH explicitly

#  PATH    =3D>  '/bin:/usr/bin:/usr/local/bin:/usr/bin/X11:/home/genex/b=
in:/usr/lib:/usr/local/lib',

 =

> **In addition from some reason the ISA couldn't find xgvis. It finds xg=
obi but not xgvis. =


That's odd; it should be installed in the same place as xgobi, but don't =
worry about xgvis yet.  It's not used directly yet.  Did you install xgob=
i and install both xgobi and xgvis in the same place?


> **In order to help you to help me I include the following information (=
the Option.Reminder file; find on xgvis; path list of java directory) :

THANKS!  This is helpful!

It looks like it found NEITHER xgobi nor xgvis..


> ** Option.Reminder
> Following are the Directory and URLs you set or allowed to be set:
> CGIDIR =3D /var/www/cgi-bin
> CGITMPDIR =3D /tmp/genex
> CGITMPURL =3D http://linux-104.weizmann.ac.il/genex/tmp
> CGI_ROOT_URL =3D http://linux-104.weizmann.ac.il/cgi-bin
> CONTACT_EMAIL =3D ron...@we...
> CURA_TOOL =3D genex/curation-tool
> CYBERT_DIR =3D genex/cybert
> CyberT_Demo_DIR =3D genex/CyberT-Demo
> DB_NAME =3D genex
> DOWNLOAD_DIR =3D genex/download
> DTD2HTML =3D /usr/local/bin/dtd2html
> DTD_DIR =3D genex/DTD
> DTD_HTML_DIR =3D /usr/local/genex/lib/dtd/genexml-html
> DTD_HTML_URL =3D http://linux-104.weizmann.ac.il/genex/DTD/genexml-html=

> ENV_HOME =3D /tmp/genex
> GENEXML_DIR =3D /usr/local/genex/lib/dtd
> GENEXML_URL =3D http://linux-104.weizmann.ac.il/genex/DTD
> GENEX_CACHE_DIR =3D /usr/local/genex/cache
> GENEX_CB_CACHE_DIR =3D /usr/local/genex/cache/db2xml/cb
> GENEX_CGIDIR =3D /var/www/cgi-bin/genex
> GENEX_CGI_URL =3D http://linux-104.weizmann.ac.il/cgi-bin/genex
> GENEX_CONNECT =3D $Bio::Genex::LOCAL =3D 1;
> GENEX_CURATOR =3D shi...@we...
> GENEX_CUR_TOOL_DIR =3D /var/www/cgi-bin/genex/curation-tool
> GENEX_DBMS =3D Pg
> GENEX_DB_USERSEC =3D geL8TEYU5FBEI
> GENEX_DIR =3D genex
> GENEX_EXAMPLE_DIR =3D /var/www/cgi-bin/genex/samples
> GENEX_EXP_CACHE_DIR =3D /usr/local/genex/cache/db2xml/exp
> GENEX_EXTRALIBS =3D use lib q[/usr/local/lib/perl5];
> use lib q[/usr/local/lib/perl5];
> =

> GENEX_GRAPHICS_URL =3D http://linux-104.weizmann.ac.il/genex/graphics
> GENEX_HOST =3D localhost
> GENEX_HTM_URL =3D http://linux-104.weizmann.ac.il/genex
> GENEX_INSTALLSITE =3D /usr/local/lib/perl5
> GENEX_LOCAL =3D 1
> GENEX_MAN1 =3D /usr/local/genex/man/man1
> GENEX_MAN3 =3D /usr/local/genex/man/man3
> GENEX_PORT =3D 5432
> GENEX_QUERY_DIR =3D /var/www/cgi-bin/genex/gxquery
> GENEX_RO_PASSWORD =3D
> GENEX_RO_USER =3D readonly
> GENEX_SECRET =3D Sun May 20 15:03:54 2001
> GENEX_SERVER_INSTALLED_BY =3D ron...@we...
> GENEX_SUBMISSION_HOME =3D /usr/local/genex/submission
> GENEX_SU_PASSWORD =3D
> GENEX_SU_USER =3D genex
> GENEX_URL_CUR_TOOL =3D http://linux-104.weizmann.ac.il/cgi-bin/genex/cu=
ration-tool
> GENEX_URL_EXAMPLE =3D http://linux-104.weizmann.ac.il/cgi-bin/genex/sam=
ples
> GENEX_URL_QUERY =3D http://linux-104.weizmann.ac.il/cgi-bin/genex/gxque=
ry
> GNUCUT =3D /bin/cut
> GNUINSTALL =3D /usr/bin/install
> GNUMKDIR =3D /bin/mkdir
> GNUPLOT =3D /usr/bin/gnuplot
> GNUSORT =3D /bin/sort
> GNUTAIL =3D /usr/bin/tail
> GNUTAR =3D /bin/tar
> GRAPHICS_DIR =3D genex/graphics
> GS =3D /usr/bin/gs
> GXQUERY_DIR =3D genex/gxquery
> HTMLDIR =3D /var/www/html
> HTMLTMPDIR =3D /var/www/html/genex/tmp
> HTML_ROOT_URL =3D http://linux-104.weizmann.ac.il
> HTTP_ERR_LOG =3D /var/log/httpd/error_log
> INCLUDE_DIR =3D genex/include
> JAR =3D
> LOCAL_BIN =3D /usr/local/genex/bin
> LOCAL_LIB =3D /usr/local/genex/lib
> LOCAL_ROOT =3D /usr/local/genex
> LOCAL_SHARE =3D /usr/local/genex/share
> LOCAL_VAR =3D /usr/local/genex/var
> LOGIN_DIR =3D genex/login
> MAX_SYSTMP_SIZE =3D 15
> MAX_TMPFILE_AGE =3D 24
> MERGEM_DIR =3D genex/mergem
> MPAGE =3D /usr/bin/mpage
> PATH =3D /usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/sbin=
:/sbin:/usr/sbin:/bin:/usr/bin:/usr/X11R6/bin:/root/bin
> PREFIX =3D /usr/local/lib/perl5
> R =3D /usr/bin/R
> RCLUSTER_PERL_LIB =3D /usr/local/lib/perl5/RCluster
> RCLUST_DIR =3D genex/rcluster
> RCluster_Demo_DIR =3D genex/RCluster-Demo
> R_VERSION =3D R 1.2.3 (2001-04-26).
> SENDMAIL =3D /usr/sbin/sendmail
> START_PERL =3D #!/usr/local/bin/perl
> SYSTMP =3D /tmp/genex
> TOP_LEVEL_DIR =3D genex/top_level
> VERSION_STRING =3D $Id: install-all.pl,v 1.82 2001/03/02 19:23:13 jes E=
xp $
> VNCSERVER =3D /usr/bin/vncserver
> WWWHOST =3D linux-104.weizmann.ac.il
> XCLUSTER =3D
> XCLUSTER_DIR =3D genex/xcluster
> XGOBI =3D
> XGOBID =3D /usr/local/src/xgobi
> XGVIS =3D
> XML_WRITER =3D /usr/local/genex/bin/db2xml.pl
> =

> Following are the Application Paths you set or allowed to be set:
> R =3D /usr/bin/R
> cut =3D /bin/cut
> dtd2html =3D /usr/local/bin/dtd2html
> gnuplot =3D /usr/bin/gnuplot
> gs =3D /usr/bin/gs
> install =3D /usr/bin/install
> jar =3D
> mkdir =3D /bin/mkdir
> mpage =3D /usr/bin/mpage
> sendmail =3D /usr/sbin/sendmail
> sort =3D /bin/sort
> tail =3D /usr/bin/tail
> tar =3D /bin/tar
> vncserver =3D /usr/bin/vncserver
> xcluster =3D
> xgobi =3D
> xgvis =3D
> =

> Following are the ENVIRONMENT VARIABLES you set or allowed to be set:
> ENV_HOME =3D /tmp/genex
> PATH =3D /usr/local/sbin:/usr/sbin:/sbin:/usr/local/bin:/usr/local/sbin=
:/sbin:/usr/sbin:/bin:/usr/bin:/usr/X11R6/bin:/root/bin
> XGOBID =3D /usr/local/src/xgobi
> =

> **Find on xgvis
> =

> /usr/local/lib/R/library/xgobi/help/xgvis
> /usr/local/src/xgobi/src/xgvis
> /usr/local/src/xgobi/help/xgvis
> /usr/local/genex/lib/R/library/xgobi/help/xgvis
> =

> **List path of java ( where I put the jre 1.3)
> =

> /usr/local/java/:
> =AF----------------CHANGES
> =AF----------------ControlPanel.html
> =AF----------------COPYRIGHT
> =AF----------------LICENSE
> =AF----------------LICENSE.fr
> =AF----------------README
> =AF---------------Welcome.html
> =3D=3D=3D=3D=3D=3D=3D=3D=3D/bin:
> =AF--------------------awt_robot*
> =AF--------------------ControlPanel*
> =3D=3D=3D=3D=3D=3D=3D=3D=3Di386/
> =AF-------------------java@
> =AF-------------------keytool@
> =AF-------------------policytool@
> =AF-------------------realpath*
> =AF-------------------rmid@
> =AF-------------------rmiregistry@
> =AF-------------------tnameserv@
> =

> /usr/local/java/bin/i386:
> =AF-------------------green_threads/
> =AF-------------------native_threads/
> =AF-------------------realpath*
> =

> /usr/local/java/bin/i386/green_threads:
> =AF--------------------------------------------appletviewer*
> =AF--------------------------------------------extcheck*
> =AF--------------------------------------------idlj*
> =AF--------------------------------------------jar*
> =AF--------------------------------------------jarsigner*
> =AF--------------------------------------------java*
> =AF--------------------------------------------javac*
> =AF--------------------------------------------javadoc*
> =AF--------------------------------------------javah*
> =AF--------------------------------------------javap*
> =AF--------------------------------------------jdb*
> =AF--------------------------------------------keytool*
> =AF--------------------------------------------native2ascii*
> =AF--------------------------------------------oldjava*
> =AF--------------------------------------------oldjavac*
> =AF--------------------------------------------oldjdb*
> =AF--------------------------------------------policytool*
> =AF--------------------------------------------rmic*
> =AF--------------------------------------------rmid*
> =AF--------------------------------------------rmiregistry*
> =AF--------------------------------------------serialver*
> =AF--------------------------------------------tnameserv*
> =

> /usr/local/java/bin/i386/native_threads:
> =AF--------------------------------------------java*
> =AF--------------------------------------------java_vm*
> =AF--------------------------------------------keytool*
> =AF--------------------------------------------policytool*
> =AF--------------------------------------------rmid*
> =AF--------------------------------------------rmiregistry*
> =AF--------------------------------------------tnameserv*
> =

> /usr/local/java/lib:
> ----------------applet/
> -----------------audio/
> -----------------cmm/
> content-types.properties
> =AF----------------ext/
> flavormap.properties
> font.properties
> font.properties.ja
> font.properties.zh
> fonts/
> i18n.jar
> i386/
> images/
> javaplugin.jar
> jvm.cfg
> jvm.hprof.txt
> jvm.jcov.txt
> locale/
> psfontj2d.properties
> psfont.properties.ja
> rt.jar
> security/
> sunrsasign.jar
> tzmappings
> =

> /usr/local/java/lib/applet:
> =

> /usr/local/java/lib/audio:
> soundbank.gm
> =

> /usr/local/java/lib/cmm:
> CIEXYZ.pf
> GRAY.pf
> LINEAR_RGB.pf
> PYCC.pf
> sRGB.pf
> =

> /usr/local/java/lib/ext:
> =

> /usr/local/java/lib/fonts:
> fonts.dir
> LucidaBrightDemiBold.ttf
> LucidaBrightDemiItalic.ttf
> LucidaBrightItalic.ttf
> LucidaBrightRegular.ttf
> LucidaSansDemiBold.ttf
> LucidaSansDemiOblique.ttf
> LucidaSansOblique.ttf
> LucidaSansRegular.ttf
> LucidaTypewriterBoldOblique.ttf
> LucidaTypewriterBold.ttf
> LucidaTypewriterOblique.ttf
> LucidaTypewriterRegular.ttf
> =

> /usr/local/java/lib/i386:
> classic/
> client/
> green_threads/
> hotspot@
> libagent.so*
> libawt.so*
> libcmm.so*
> libdcpr.so*
> libfontmanager.so*
> libhprof.so*
> libioser12.so*
> libjavaplugin_jni.so*
> libjava.so*
> libjawt.so*
> libjcov.so*
> libJdbcOdbc.so*
> libjpeg.so*
> libjsound.so*
> libmlib_image.so*
> libnet.so*
> libpreemptive_close.so*
> libverify.so*
> libzip.so*
> native_threads/
> server/
> =

> /usr/local/java/lib/i386/classic:
> libjvm.so*
> Xusage.txt
> =

> /usr/local/java/lib/i386/client:
> libjvm.so*
> Xusage.txt
> =

> /usr/local/java/lib/i386/green_threads:
> libhpi.so*
> =

> /usr/local/java/lib/i386/native_threads:
> libhpi.so*
> =

> /usr/local/java/lib/i386/server:
> libjvm.so*
> Xusage.txt
> =

> /usr/local/java/lib/images:
> cursors/
> =

> /usr/local/java/lib/images/cursors:
> cursors.properties
> invalid32x32.gif
> motif_CopyDrop32x32.gif
> motif_CopyNoDrop32x32.gif
> motif_LinkDrop32x32.gif
> motif_LinkNoDrop32x32.gif
> motif_MoveDrop32x32.gif
> motif_MoveNoDrop32x32.gif
> =

> /usr/local/java/lib/locale:
> de/
> es/
> fr/
> it/
> ja/
> ko/
> ko.UTF-8/
> sv/
> zh/
> zh.GBK/
> zh_TW/
> zh_TW.BIG5/
> =

> /usr/local/java/lib/locale/de:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/de/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/es:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/es/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/fr:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/fr/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/it:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/it/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/ja:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/ja/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/ko:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/ko/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/ko.UTF-8:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/ko.UTF-8/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/sv:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/sv/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/zh:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/zh/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/zh.GBK:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/zh.GBK/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/zh_TW:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/zh_TW/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/locale/zh_TW.BIG5:
> LC_MESSAGES/
> =

> /usr/local/java/lib/locale/zh_TW.BIG5/LC_MESSAGES:
> sunw_java_plugin.mo
> =

> /usr/local/java/lib/security:
> cacerts
> java.policy
> java.security
> =

> /usr/local/java/man:
> ja@
> ja_JP.eucJP/
> man1/
> =

> /usr/local/java/man/ja_JP.eucJP:
> man1/
> =

> /usr/local/java/man/ja_JP.eucJP/man1:
> java.1
> keytool.1
> rmid.1
> rmiregistry.1
> tnameserv.1
> =

> /usr/local/java/man/man1:
> java.1
> keytool.1
> rmid.1
> rmiregistry.1
> tnameserv.1
> =

> /usr/local/java/plugin:
> i386/
> =

> /usr/local/java/plugin/i386:
> ns4/
> ns600/
> =

> /usr/local/java/plugin/i386/ns4:
> javaplugin.so*
> =

> /usr/local/java/plugin/i386/ns600:
> libjavaplugin_oji.so*
> =

> Many thanks for your help,
> =

>   ---------------------------------------------------------------------=
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>                Name: TEXT.htm
>    TEXT.htm    Type: Hypertext Markup Language (TEXT/HTML)
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-- =

Cheers,
Harry

Harry J Mangalam -- (949) 856 2847 (v&f) -- hj...@nc... || mangalam@home=
=2Ecom