dimer.tamu.edu

Manatee on genomics03

jimhu@tamu.edu(Jim Hu) — Wed, 03 Sep 2008 20:02:54 -0500

# adjust httpd.conf sudo -s emacs /etc/apache2/httpd.conf insert the following near beginning (above #Serverroot)

#manatee extras 
setenv WEBSERVER_TMP /tmp 
ScriptAlias /tigr-scripts/ "/Library/WebServer/CGI-Executables/" 
Alias /webserver_tmp/ "/tmp/" 
<Directory "/tmp"> 
   Allow from all 
</Directory>

apachectl restart On genomics02 in /Downloads make tgz for manatee already modified scp manatee_mac.tgz genomics03.bio.tamu.edu: On genomics03 copy back to /Downloads untar ./install_perl.pl in phpmyadmin, create manatee user configure failed - need Date:Manip install from CPAN ./configure HTTPD_SERVER_CONFIG_FILE=/etc/apache2/httpd.conf HTTPD_DOC_HOME=/Library/WebServer/Documents make make install #install demo db On genomics02, scp database_install_mac.tgz to genomics03 copy to /Downloads untar cd into itc ./install_demo /usr/local/mysql/data/ /usr/local/search_data mysql5 Not working... reinstall 32 bit mySQL over 64 bit version 5.0.67 cd to ~jimhu/.cpan/build/DBD-xxx perl Makefile.PL --testuser= --testpassword= --mysql_config=/usr/local/mysql/bin/mysql_config make make test make install

chado version of Manatee

jimhu@tamu.edu(Jim Hu) — Wed, 27 Aug 2008 09:46:53 -0500

Move and install files in CGI-executables and Documents/tdb for chado_prok_manatee Put data in /usr/local/manatee/data symlink: sudo ln -s /usr/bin/perl perl

Install Manatee demo dbs for class iMacs

jimhu@tamu.edu(Jim Hu) — Wed, 27 Aug 2008 01:27:47 -0500

History: 173 cd database_install 174 ls -G 175 ./install_demo /usr/local/mysql/data/ /usr/local/search_data mysql5 176 cd /usr/local/mysql/data/ 177 ls -lG 178 chown -R _mysql * Seems to work!

Manatee on class imacs

jimhu@tamu.edu(Jim Hu) — Wed, 27 Aug 2008 01:10:10 -0500

Starting on genomics02 Edit the httpd.conf restart apache: apachectl restart curl -o ftp://ftp.tigr.org/pub/data/manatee/database_installation/database_install.tgz failed. Transferred from my laptop using scp Check for expat - need it. transferred from laptop, installed with ./configure, make. make install. copy and unpack manatee source distro ./install_perl.pl - installs needed modules (I hope). edit configure line 1455 MYSQLSERVER=`ps -ax | grep '$MYSQLD'` also added a semicolon after line 1459 to give: MYSQL_ISRUNNING=1; install_src (remove final slashes) cp -R $SRCDIR $DESTDIR Manatee.conf in both euk and prok Manatee GZCAT=/usr/bin/zcat GUNZIP=/usr/bin/gunzip bash-3.2# ./configure HTTPD_SERVER_CONFIG_FILE=/etc/apache2/httpd.conf HTTPD_DOC_HOME=/Library/WebServer/Documents HTTPD_SCRIPT_HOME=/Library/WebServer/CGI-Executables previously, had extra spaces around '=' http://genomics02.bio.tamu.edu/tdb/prok_manatee/ redirects correctly!! whoop! Now need to install demo db and chado db

genomics04, genomics05

jimhu@tamu.edu(Jim Hu) — Mon, 25 Aug 2008 20:47:21 -0500

cd to /Downloads sudo -s install libgd without freetype perl -MCPAN -e shell install Bundle::CPAN install LWP::Simple force install GD oops, forgot to adjust the path

Bioperl and gbrowse

jimhu@tamu.edu(Jim Hu) — Mon, 25 Aug 2008 19:51:45 -0500

on genomics02 Do Bioperl from svn $ svn co svn://code.open-bio.org/bioperl/bioperl-live/trunk bioperl-live ./Build ./Build test ./Build install then do the net install script fails due to GD problem. Try this on genomics03, which hasn't had fink stuff. install Bundle::CPAN to make sure we're up to date install LWP::Simple install GD need to do libpng and libgd apparently. do installations ./configure, make, make install force install GD on cpan ---- back to 02 export PATH=/usr/local/bin:$PATH seems to solve GD problem... sort of... but gbrowse still not working... Can't locate object method "Tiny" via package "GD::Font" ---- Solution: recompile libgd without freetype ./configure --without-freetype

MAKER continued

jimhu@tamu.edu(Jim Hu) — Thu, 07 Aug 2008 22:26:23 -0500

check the CPAN prereqs *URI:Escape *threads v1.71 or higher (only needed for mpi_maker, otherwise ignore this) Have these already mpi_maker http://www.mcs.anl.gov/research/projects/mpich2/ install with ./configure --enable-sharedlibs=osx-gcc done.. now what?

Exonerate - needed for MAKER

jimhu@tamu.edu(Jim Hu) — Thu, 07 Aug 2008 22:26:03 -0500

http://www.ebi.ac.uk/~guy/exonerate/ ./configure failed - needs glib2 http://www.gtk.org/download.html Is this it? Not exactly. Need subversion checkout svn checkout http://svn.gnome.org/svn/glib/trunk glib No... http://ftp.gnome.org/pub/GNOME/sources/glib/2.16/ Looks better.. but now I need something else... http://www.freedesktop.org/software/pkgconfig/ Installing pkgconfig seemed to go OK. Now I need http://www.gnu.org/software/gettext/gettext.html Found at Texas mirror http://gnu.inetbridge.net/gettext/ OK, exonerate installed Downloaded v 017 The installation of this takes a long time, it seems! OK, now I can do glib2 I think these worked, but I'm not sure...

Repeatmasker

jimhu@tamu.edu(Jim Hu) — Thu, 07 Aug 2008 20:20:48 -0500

This is needed for MAKER Has prereq TRF http://tandem.bu.edu/trf/trf.download.html Downloaded the leopard version. placed in /usr/local/TRF symlinked Repeatmasker config seems to have worked...

MAKER

jimhu@tamu.edu(Jim Hu) — Thu, 07 Aug 2008 20:09:35 -0500

let's also try to set up Mark Yandell's MAKER on my laptop. Install wu-blast in /usr/local/wu-blast download SNAP from http://homepage.mac.com/iankorf/ make. moved to usr/local/snap export ZOE=/usr/local/snap/Zoe That's it? Test with:

./snap HMM/thale DNA/thale.dna.gz 
scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done 
scoring.....decoding.10.20.30.40.50.60.70.80.90.100 done 
>At1g01040.0 
Einit 1007 1954 + 85.269 0 0 1 At1g01040.0-snap.1 
Exon 2024 2137 + 8.926 0 0 1 At1g01040.0-snap.1 
Exon 2234 2444 + 20.788 0 1 1 At1g01040.0-snap.1 
Exon 2523 2917 + 35.162 2 0 1 At1g01040.0-snap.1 
Exon 3006 3225 + 34.428 0 1 2 At1g01040.0-snap.1 
Exon 3307 3479 + 14.790 2 0 2 At1g01040.0-snap.1 
Exon 3563 3685 + 4.678 0 0 1 At1g01040.0-snap.1 
Exon 3774 3934 + 10.179 0 2 2 At1g01040.0-snap.1 
Exon 4025 4258 + 25.991 1 2 2 At1g01040.0-snap.1 
Exon 4344 4506 + 4.289 1 0 0 At1g01040.0-snap.1 
Exon 4581 4763 + 28.696 0 0 2 At1g01040.0-snap.1 
Exon 4854 5015 + 15.217 0 0 2 At1g01040.0-snap.1 
Exon 5100 5195 + 23.205 0 0 2 At1g01040.0-snap.1 
Eterm 5285 5917 + 45.878 0 0 1 At1g01040.0-snap.1 
Einit 6086 6144 + 6.596 0 2 1 At1g01040.0-snap.2 
Exon 6190 6287 + 22.495 1 1 1 At1g01040.0-snap.2 
Exon 6372 6562 + 17.809 2 0 1 At1g01040.0-snap.2 
Exon 6642 6803 + 16.407 0 0 2 At1g01040.0-snap.2 
Exon 6828 7547 + 69.159 0 0 2 At1g01040.0-snap.2 
Exon 7629 7793 + 40.262 0 0 2 At1g01040.0-snap.2 
Exon 7892 8298 + 46.310 0 2 1 At1g01040.0-snap.2 
Eterm 8384 8561 + 17.079 1 0 2 At1g01040.0-snap.2

I guess that's good... Repeatmasker: http://www.repeatmasker.org/RMDownload.html Wow, the latest release is from today! Finding the libraries on the GIRI site was a bit nonobvious... they're in the RepBase section: http://www.girinst.org/server/RepBase/index.php Getting this requires registration, which is reviewed - takes 1-2 days... I guess I'll see if I can get the other stuff in the meantime.

Manatee - what breaks now

jimhu@tamu.edu(Jim Hu) — Thu, 07 Aug 2008 11:36:08 -0500

Tried to search protein name for "hsp70" got blank result. Clicked on gene_name and got a crash http://localhost/cgi-bin/tigr-scripts/prok_manatee/search_ident.cgi?db=gvc&sortby=gene_name&search_str=hsp70&search_type=gene%20name

[Thu Aug 07 11:32:01 2008] [error] [client ::1] [Thu Aug 7 11:32:01 2008] search_ident.cgi: could not find ParserDetails.ini in /Library/Perl/5.8.8/XML/SAX, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/search_ident.cgi [Thu Aug 07 11:32:02 2008] [error] [client ::1] Can't use an undefined value as an ARRAY reference at shared/Coati/Sorters.pm line 32., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/search_ident.cgi [Thu Aug 07 11:32:02 2008] [error] [client ::1] Premature end of script headers: search_ident.cgi, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/search_ident.cgi

This looks like a validation bug, actually.

Manatee - current status

jimhu@tamu.edu(Jim Hu) — Thu, 07 Aug 2008 11:33:30 -0500

Needed new MySQL Patches to configure may not have been sufficient, but basic core works after copying prok-manatee to CGI-executables and tweaking the files. Mostly had to adjust the more than 100 places where the cgi-bin was missing from a file path. Had to adjust permissions on /tmp Still need to do some path adjustment - would help to understand where the paths are kept.

some are specified by some xml files
others are hard-coded

Some solutions may be in: http://manatee.sourceforge.net/troubleshooting.shtml Modifying httpd.conf gets the ORF view to work. Modified permissions on the manatee directory in /usr/local to see the data files. Changed conf to correct gzcat /usr/bin/gzcat, not /usr/local/bin/gzcat Wondering if there is a way to test all without manually clicking every link...

Manatee installation - progress!

jimhu@tamu.edu(Jim Hu) — Thu, 07 Aug 2008 10:56:29 -0500

It looks like there was a problem with some Perl module and the version of MySQL I had (mysql-standard-5.0.24-osx10.3-powerpc, presumably runningin emulation mode). Installed 5.0.51b and moved the data directory. After this, login.cgi redirected to gateway.cgi, but the URL is wrong. Correcting it by hand gave a Manatee welcome screen. I also did cpan upgrade to make sure all modules were up to date. But... all this worked before I left work and it's failing from home.

[Wed Aug 06 23:27:43 2008] [error] [client ::1] Died with 'Invalid username/password/db access %%Database login%%The database server [hu-pismo.tamu.edu] denied access to the username [manatee].  Please check the username/password and confirm you have permissions to access the [gvc] database%%Can't connect to MySQL server on 'hu-pismo.tamu.edu' (60)%%gvc

I suspect something weird with hostnames - off the tamu network, I suspect that hu-pismo.tamu.edu doesn't mean anything. Changed to localhost - seems to get the Welcome screen back. Searching from there gives a bad URL. Searched for "/tigr-scripts and replaced with "/cgi-bin/tigr-scripts in 106 places... but that didn't fix things. I think the docs want me to do a redirect in the apache conf file... which I'd rather avoid. OK, repeating the search replace with single quotes helps. But its not enough. ORF_infopage.cgi?db=gvc&orf=ORFA00901 can't find the png file.

Manatee - source install continued

jimhu@tamu.edu(Jim Hu) — Tue, 05 Aug 2008 15:39:47 -0500

edit config file src/prok_manatee/conf/Manatee.conf: GZCAT=/usr/bin/zcat GUNZIP=/usr/bin/gunzip # both conffiles will have the full hostname of the local machine as db server # other optional settings in both: CLUSTALW, SIGNAL_P paths, IPRSCAN_DIR

Weirdness:

bash-3.2# make Converting perl path where needed to /usr/bin/perl bash-3.2# make install make: `install' is up to date.

based on http://cygwin.com/ml/cygwin-xfree/2001-q3/msg01084.html

bash-3.2# mv INSTALL INSTALL2
bash-3.2# make install
Found content directory
Installing euk_manatee scripts
usage: touch [-acfm] [-r file] [-t [[CC]YY]MMDDhhmm[.SS]] file ...
Installing euk_manatee content
Saving previous script install to /Library/WebServer/Documents/tdb/euk_manatee.old
Installing prok_manatee scripts
usage: touch [-acfm] [-r file] [-t [[CC]YY]MMDDhhmm[.SS]] file ...
Installing prok_manatee content
Saving previous script install to /Library/WebServer/Documents/tdb/prok_manatee.old


--------------------------------------------------
**The euk_manatee configuration file resides at 

/euk_manatee/conf/Manatee.conf 

Please confirm settings in the configuration file before continuing.
**The prok_manatee configuration file resides at 

/prok_manatee/conf/Manatee.conf 

Please confirm settings in the configuration file before continuing.
--------------------------------------------------
After configuration is complete, enter the following URLs to begin using Manatee
For eukaryotic databases
http://SERVER:PORT/tdb/euk_manatee/
For prokaryotic databases
http://SERVER:PORT/tdb/prok_manatee/

See http://manatee.sourceforge.net/installation.html for more installation information

But this is still hosed. Nothing got copied to cgi-bin, and the redirect doesn't have cgi-bin in the path. Manually copy prok_manatee to CGI-executables, and navigate to: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi I get a login screen. Tried to login using manatee:manatee and common as db. White screen -> error log: [Tue Aug 05 15:34:49 2008] [error] [client ::1] dyld: lazy symbol binding failed: Symbol not found: _mysql_server_init, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:34:49 2008] [error] [client ::1] Referenced from: /Library/Perl/5.8.8/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:34:49 2008] [error] [client ::1] Expected in: dynamic lookup, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:34:49 2008] [error] [client ::1] , referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:34:49 2008] [error] [client ::1] dyld: Symbol not found: _mysql_server_init, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:34:49 2008] [error] [client ::1] Referenced from: /Library/Perl/5.8.8/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:34:49 2008] [error] [client ::1] Expected in: dynamic lookup, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:34:49 2008] [error] [client ::1] , referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi added -w flag to login.cgi:

[Tue Aug 05 15:38:25 2008] [error] [client ::1] "my" variable $ipr_obj masks earlier declaration in same scope at Manatee/GetInterPro.pm line 185., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:25 2008] [error] [client ::1] Subroutine search_properties_by_name redefined at Manatee.pm line 1648., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:25 2008] [error] [client ::1] Subroutine search_properties_by_role redefined at Manatee.pm line 1676., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:25 2008] [error] [client ::1] Subroutine search_properties_by_GO redefined at Manatee.pm line 1704., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:25 2008] [error] [client ::1] "my" variable $ev_type masks earlier declaration in same scope at Manatee.pm line 2575., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:25 2008] login.cgi: Odd number of elements in hash assignment at Coati/Logger.pm line 89., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: "my" variable $url masks earlier declaration in same scope at /Library/WebServer/CGI-Executables/tigr-scripts/prok_manatee/shared/login.cgi line 135., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: Useless use of reference constructor in void context at ..//Manatee/ProkManateeDB.pm line 159., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: "my" variable $query masks earlier declaration in same scope at ..//Manatee/ProkManateeDB.pm line 347., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: "my" variable $ret masks earlier declaration in same scope at ../shared/Coati/Coati/ProkCoatiDB.pm line 316., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: Subroutine get_gene_id_to_frameshifts redefined at ../shared/Coati/Coati/ProkCoatiDB.pm line 632., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: Subroutine get_db_to_roles redefined at ../shared/Coati/Coati/ProkCoatiDB.pm line 1015., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: "my" variable $query masks earlier declaration in same scope at ../shared/Coati/Coati/ProkCoatiDB.pm line 1688., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: Use of uninitialized value in concatenation (.) or string at Manatee.pm line 69., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: Use of uninitialized value in concatenation (.) or string at Manatee.pm line 69., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:26 2008] [error] [client ::1] [Tue Aug 5 15:38:26 2008] login.cgi: Use of uninitialized value in concatenation (.) or string at Manatee.pm line 69., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] [Tue Aug 5 15:38:27 2008] login.cgi: Use of uninitialized value in string ne at ..//Manatee/GetManateeTemplate.pm line 76., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] [Tue Aug 5 15:38:27 2008] login.cgi: Use of uninitialized value in string ne at ..//Manatee/GetManateeTemplate.pm line 88., referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] dyld: lazy symbol binding failed: Symbol not found: _mysql_server_init, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] Referenced from: /Library/Perl/5.8.8/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] Expected in: dynamic lookup, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] , referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] dyld: Symbol not found: _mysql_server_init, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] Referenced from: /Library/Perl/5.8.8/darwin-thread-multi-2level/auto/DBD/mysql/mysql.bundle, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] Expected in: dynamic lookup, referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi [Tue Aug 05 15:38:27 2008] [error] [client ::1] , referer: http://localhost/cgi-bin/tigr-scripts/prok_manatee/shared/login.cgi

Manatee - source install again continued

jimhu@tamu.edu(Jim Hu) — Tue, 05 Aug 2008 15:05:09 -0500

Change correction from double quotes to single quotes MYSQLSERVER=`ps -ax | grep '$MYSQLD'` also added a semicolon after line 1459 to give: MYSQL_ISRUNNING=1;

bash-3.2# ./configure HTTPD_SERVER_CONFIG_FILE = /etc/apache2/httpd.conf HTTPD_DOC_HOME = /Library/WebServer/Documents HTTPD_SCRIPT_HOME = /Library/WebServer/CGI-Executables
configure: WARNING: you should use --build, --host, --target
./configure: line 597: =: command not found
export DISPLAY="/tmp/launch-R7t2bC/:0"
export EDITOR="emacs"
export HOME="/Users/jimhu"
export LOGNAME="root"
export OLDPWD
export PATH="/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/user/local/graphviz/bin"
export PWD="/Users/jimhu/genomics installs/manatee"
export SHELL="/bin/sh"
export SHLVL="2"
export SSH_AUTH_SOCK="/tmp/launch-X8zHv0/Listeners"
export SUDO_COMMAND="/bin/bash"
export SUDO_GID="501"
export SUDO_UID="501"
export SUDO_USER="jimhu"
export TERM="xterm-color"
export USER="root"
export __CF_USER_TEXT_ENCODING="0x1F5:0:0"
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: /etc/apache2/httpd.conf
configure: WARNING: you should use --build, --host, --target
./configure: line 597: =: command not found
export DISPLAY="/tmp/launch-R7t2bC/:0"
export EDITOR="emacs"
export HOME="/Users/jimhu"
export LOGNAME="root"
export OLDPWD
export PATH="/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/user/local/graphviz/bin"
export PWD="/Users/jimhu/genomics installs/manatee"
export SHELL="/bin/sh"
export SHLVL="2"
export SSH_AUTH_SOCK="/tmp/launch-X8zHv0/Listeners"
export SUDO_COMMAND="/bin/bash"
export SUDO_GID="501"
export SUDO_UID="501"
export SUDO_USER="jimhu"
export TERM="xterm-color"
export USER="root"
export __CF_USER_TEXT_ENCODING="0x1F5:0:0"
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: /Library/WebServer/Documents
configure: WARNING: you should use --build, --host, --target
./configure: line 597: =: command not found
export DISPLAY="/tmp/launch-R7t2bC/:0"
export EDITOR="emacs"
export HOME="/Users/jimhu"
export LOGNAME="root"
export OLDPWD
export PATH="/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/user/local/graphviz/bin"
export PWD="/Users/jimhu/genomics installs/manatee"
export SHELL="/bin/sh"
export SHLVL="2"
export SSH_AUTH_SOCK="/tmp/launch-X8zHv0/Listeners"
export SUDO_COMMAND="/bin/bash"
export SUDO_GID="501"
export SUDO_UID="501"
export SUDO_USER="jimhu"
export TERM="xterm-color"
export USER="root"
export __CF_USER_TEXT_ENCODING="0x1F5:0:0"
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: /Library/WebServer/CGI-Executables
checking for perl... /usr/bin/perl
checking for httpd... /usr/sbin/httpd
checking for /private/etc/apache2/httpd.conf... yes
   60 ??         0:11.48 /usr/sbin/httpd -D FOREGROUND
   63 ??         0:23.55 /usr/sbin/httpd -D FOREGROUND
  219 ??         0:20.31 /usr/sbin/httpd -D FOREGROUND
 4719 ??         0:20.16 /usr/sbin/httpd -D FOREGROUND
10922 ??         0:24.35 /usr/sbin/httpd -D FOREGROUND
10924 ??         0:16.75 /usr/sbin/httpd -D FOREGROUND
10925 ??         0:24.30 /usr/sbin/httpd -D FOREGROUND
15864 ttys000    0:00.00 grep /usr/sbin/httpd
checking for mysql... /usr/local/mysql/bin/mysql
checking for safe_mysqld... /usr/local/mysql/bin/safe_mysqld
configure: WARNING: /usr/local/mysql/bin/safe_mysqld is running on this server. Saving default mysql host  hu-pismo.tamu.edu  in conf/Manatee.conf
checking for perl module CGI... yes
checking for perl module DBI... yes
checking for perl module DBD::mysql... yes
checking for perl module XML::Parser... yes
checking for perl module XML::Twig... yes
checking for perl module XML::Simple... yes
checking for perl module XML::Writer... yes
checking for perl module HTML::Template... yes
checking for perl module Tree::DAG_Node... yes
checking for perl module File::Spec... yes
checking for perl module GD... yes
checking for perl module GD::Text... yes
checking for perl module GD::Graph... yes
checking for perl module Storable... yes
checking for perl module Date::Manip... yes
checking for perl module IO::Tee... yes
checking for perl module Log::Log4perl... yes
checking for perl module MLDBM... yes
checking for perl module DBD::Sybase... no
checking for src/euk_manatee/conf/Manatee.conf... yes
checking for src/prok_manatee/conf/Manatee.conf... yes
configure: creating ./config.status
config.status: creating stamp-h
config.status: creating Makefile
bash-3.2#

This is still throwing warnings, but detecting mysqld is a step in the right direction. I'm concerned about the one for line 597

Manatee - source install (again)

jimhu@tamu.edu(Jim Hu) — Tue, 05 Aug 2008 14:59:50 -0500

I've done this before, but need to try it again... From manatee expanded archive, modify notes at: http://sourceforge.net/forum/forum.php?thread_id=1562985&forum_id=394634

hack configure script line 1457 to use ps ax | grep ... | grep -v grep and quote the variable, so it detects mysqld running.

This seems to be line 1455 in the current release. Changed to MYSQLSERVER=`ps -ax | grep "$MYSQLD"`

hack install_src: change cp -R $SRCDIR/ ... to ... $SRCDIR ... (OS X cp -R is like rsync) mv INSTALL INSTALL.txt # Makefile target... ./configure MYSQLD=/sw/bin/mysqld_safe HTTPD=/sw/sbin/httpd (don't let it use apache1 /usr/sbin/httpd)

I read that as saying remove the final / after SRCDIR and DESTDIR: cp -R $SRCDIR $DESTDIR From shell: ./configure HTTPD_SERVER_CONFIG_FILE = /etc/apache2/httpd.conf HTTPD_DOC_HOME = /Library/WebServer/Documents HTTPD_SCRIPT_HOME = /Library/WebServer/CGI-Executables

configure: WARNING: you should use --build, --host, --target
./configure: line 597: =: command not found
export DISPLAY="/tmp/launch-R7t2bC/:0"
export EDITOR="emacs"
export HOME="/Users/jimhu"
export LOGNAME="root"
export OLDPWD
export PATH="/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/user/local/graphviz/bin"
export PWD="/Users/jimhu/genomics installs/manatee"
export SHELL="/bin/sh"
export SHLVL="2"
export SSH_AUTH_SOCK="/tmp/launch-X8zHv0/Listeners"
export SUDO_COMMAND="/bin/bash"
export SUDO_GID="501"
export SUDO_UID="501"
export SUDO_USER="jimhu"
export TERM="xterm-color"
export USER="root"
export __CF_USER_TEXT_ENCODING="0x1F5:0:0"
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: /etc/apache2/httpd.conf
configure: WARNING: you should use --build, --host, --target
./configure: line 597: =: command not found
export DISPLAY="/tmp/launch-R7t2bC/:0"
export EDITOR="emacs"
export HOME="/Users/jimhu"
export LOGNAME="root"
export OLDPWD
export PATH="/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/user/local/graphviz/bin"
export PWD="/Users/jimhu/genomics installs/manatee"
export SHELL="/bin/sh"
export SHLVL="2"
export SSH_AUTH_SOCK="/tmp/launch-X8zHv0/Listeners"
export SUDO_COMMAND="/bin/bash"
export SUDO_GID="501"
export SUDO_UID="501"
export SUDO_USER="jimhu"
export TERM="xterm-color"
export USER="root"
export __CF_USER_TEXT_ENCODING="0x1F5:0:0"
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: /Library/WebServer/Documents
configure: WARNING: you should use --build, --host, --target
./configure: line 597: =: command not found
export DISPLAY="/tmp/launch-R7t2bC/:0"
export EDITOR="emacs"
export HOME="/Users/jimhu"
export LOGNAME="root"
export OLDPWD
export PATH="/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/user/local/graphviz/bin"
export PWD="/Users/jimhu/genomics installs/manatee"
export SHELL="/bin/sh"
export SHLVL="2"
export SSH_AUTH_SOCK="/tmp/launch-X8zHv0/Listeners"
export SUDO_COMMAND="/bin/bash"
export SUDO_GID="501"
export SUDO_UID="501"
export SUDO_USER="jimhu"
export TERM="xterm-color"
export USER="root"
export __CF_USER_TEXT_ENCODING="0x1F5:0:0"
configure: WARNING: you should use --build, --host, --target
configure: WARNING: invalid host type: /Library/WebServer/CGI-Executables
checking for perl... /usr/bin/perl
checking for httpd... /usr/sbin/httpd
checking for /private/etc/apache2/httpd.conf... yes
   60 ??         0:11.46 /usr/sbin/httpd -D FOREGROUND
   63 ??         0:23.55 /usr/sbin/httpd -D FOREGROUND
  219 ??         0:20.31 /usr/sbin/httpd -D FOREGROUND
 4719 ??         0:20.16 /usr/sbin/httpd -D FOREGROUND
10922 ??         0:24.35 /usr/sbin/httpd -D FOREGROUND
10924 ??         0:16.75 /usr/sbin/httpd -D FOREGROUND
10925 ??         0:24.30 /usr/sbin/httpd -D FOREGROUND
15031 ttys000    0:00.00 grep /usr/sbin/httpd
checking for mysql... /usr/local/mysql/bin/mysql
checking for safe_mysqld... /usr/local/mysql/bin/safe_mysqld
./configure: line 1457: test: too many arguments
checking for perl module CGI... yes
checking for perl module DBI... yes
checking for perl module DBD::mysql... yes
checking for perl module XML::Parser... yes
checking for perl module XML::Twig... yes
checking for perl module XML::Simple... yes
checking for perl module XML::Writer... yes
checking for perl module HTML::Template... yes
checking for perl module Tree::DAG_Node... yes
checking for perl module File::Spec... yes
checking for perl module GD... yes
checking for perl module GD::Text... yes
checking for perl module GD::Graph... yes
checking for perl module Storable... yes
checking for perl module Date::Manip... yes
checking for perl module IO::Tee... yes
checking for perl module Log::Log4perl... yes
checking for perl module MLDBM... yes
checking for perl module DBD::Sybase... no
checking for src/euk_manatee/conf/Manatee.conf... yes
checking for src/prok_manatee/conf/Manatee.conf... yes
configure: creating ./config.status
config.status: creating stamp-h
config.status: creating Makefile

I see an error for line 597 and several warnings

Manatee cont. Sample dbs

jimhu@tamu.edu(Jim Hu) — Tue, 05 Aug 2008 16:09:30 -0500

These will get replaced with Chado, but need for testing. Download from ftp://ftp.tigr.org/pub/data/manatee/database_installation/database_install.tgz I don't like the way this installer works - should use SQL dump not filecopy!! sudo ./install_demo /usr/local/mysql /usr/local/manatee mysql5 This is running a long time... wonder what's up...OK, it's back...but the files weren't copied. sudo -s cd /usr/local/mysql/data cp -R ~/genomics installs/database_install/mysql5/* . chown -R _mysql * Note: there is no README file, despite the docs saying to consult it.

Manatee

jimhu@tamu.edu(Jim Hu) — Tue, 05 Aug 2008 14:19:08 -0500

Manatee docs at: http://manatee.sourceforge.net/ not clear if these are up to date. There's no OSX, so let's use Linux as the model. Sections on Apache 2 - got that already GD Graphics Library Installation - got it already Expat XML Parser Installation - need that. Downloaded 2.0.1 from sourceforge. Installed with normal params. Don't know how to test.

testing again

jimhu@tamu.edu(Jim Hu) — Mon, 03 Mar 2008 20:41:47 -0600

another test

test

jimhu@tamu.edu(Jim Hu) — Sat, 26 May 2007 13:55:04 -0500

test