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Initially you will find the "Systems
Requirements Sheet"
and I have begun the "build database" for the first version of the
bioinformatics-installer (by whatever name we eventually give to
it).
I
use the WebMin package
for server administration
(old
news pages are here for their notes and other content)
Bioinformatics Server Appliance Software installation
(my running "blah, blah" log of what is or has occurred in
this process)
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##########################################
#
# Please note this address and
# consider the future use of such a system when we can implement it
#
# http://jakarta.apache.org/gump/
#
#===========================================
# This is the dependencies lists for all the packages,
# excluding all the normal OS foundational packages
#
#
# a commented out package means it is in place,
# although it may still require configuration or updating
##########################################
note: the best ftp directories I have found
so far
- ftp://ftp.ebi.ac.uk/pub/
- ftp://ftp.ebi.ac.uk/pub/contrib/
- ftp://ftp.ncbi.nih.gov/
I have just opted for the following package upgrade, and it will
look obvious why I did so when you consider the following list
that this bundled package from sun.com provides.
#Java(TM) Web Services Developer Pack 1.0_01
<SalesPitch>
<Topic>
Web Services
</Topic>
The Java Web Services Developer Pack v1.0_01 includes the following:
# Java XML Pack which includes the following:
# Java API for XML Messaging (JAXM) v1.1_01
# Java API for XML Processing (JAXP) v1.2_01 (with XML Schema support)
# Java API for XML Registries (JAXR) v1.0_02
# Java API for XML-based RPC (JAX-RPC) v1.0_01
# SOAP with Attachments API for Java (SAAJ) v1.1_02
# JavaServer PagesTM Standard Tag Library (JSTL) v1.0.1
# Java WSDP Registry Server v1.0_02
# Web Application Deployment Tool
# Ant Build Tool 1.4.1
# Apache Tomcat 4.1.2 container
This release of the Java Web Services Developer Pack has been tested with various configurations with the Java 2 SDK,
Standard Edition version 1.3.1_04, 1.4, and 1.4.0_01 on the following platforms:
RedHat Linux 7.2, et al
I have now installed the above and the 1.4.0_01 SDK on RedHat 8.0
</SalesPitch>
+++++++++++++++++++++++++++++++++++
# Packages not on your original list were
# likely dependencies that I have found are
# required or suggested for optimal use
# of another package
+++++++++++++++++++++++++++++++++++
THE MAIN PACKAGE LIST, as it currently stands
AceDB
- http://www.acedb.org/
- http://www.acedb.org/Software/Downloads/
- http://www.acedb.org/Cornell/
AcePerl
- http://stein.cshl.org/AcePerl/index.html
- http://www.acedb.org/Software/Interfaces/AcePerl/
AceBrowser
- http://stein.cshl.org/AcePerl/AceBrowser/
#ADOdb
# - web directory readable
#Apache Ant
# - a JAXP-compliant XML parser installed and available on your classpath.
# - a JDK installed on your system, version 1.1 or later.
#Apache Axis
# - JAXP 1.1 XML compliant parser of your choice. .
# - Tomcat 4.x and Java1.4
Apache AxKit - Perl Module
from
this URL I gleaned the below message - http://maclux-rz.uibk.ac.at/~maillists/axkit-users/msg02739.shtml
AxKit
is not compatible with mod_perl 2.0 (or Apache 2.0). We'll work on it, but it
will take some time.
so I force installed mod_perl-1.99_05-3.i386.rpm
#Apache Tomcat
# - Download and install a Java Development Kit 1.4 or later
# - Install Apache Ant 1.5.1
# - Download a binary distribution of Xalan 2
#Apache Web Server
# - already init
# - ANSI-C Compiler and Build System
# - Perl 5 interpreter
Apache XML - see Axis, Batik, Cocoon, Forrest, SOAP, Xalan, Xerces
Batik
# - Java Virtual Machine A Java 1.3 or greater
Cocoon
# - Java Virtual Machine A Java 1.2 or later compatible virtual machine
# - Servlet Engine A Servlet 2.2 compliant servlet engine must be present
FOP
- comes with the Cocoon package free gratis
Forrest
# - Java Virtual Machine -a Java virtual machine must be present.
- You need to retrieve Forrest from its CVS repository
- there are no binary, nor source, nor snapshot distributions yet.
SOAP - Client-Side Instructions
Your classpath must contain /foo/soap-2_3/lib/soap.jar and the following:
# mail.jar from JavaMail
# activation.jar from JavaBeans Activation Framework
# a JAXP compatible, namespace-aware XML parser such as Apache Xerces (v1.1.2 or later).
# Xalan # installed c binaries - Xalan-Java - To use Xalan-Java, you need the following:
# The JDK or JRE 1.2.2, or 1.3.x
# xalan.jar
# xml-apis.jar
# xercesImpl.jar, or another XML Parser
# - Xalan-C++ - just the download it seems
# Xerces # installed c binaries
- Xerces - Java 2 # - Ant, if building from source code download
# - Xerces
- C++ - to compile the source code using Ant or build the distributions,
# - the contents of Xerces-J-tools.2.2.1.zip on your classpath;
i.e., you will need access to a version of;
# - ant
# - xalan
# - StyleBook
# - XML parser such as xerces
# - the recommendation is extracting Xerces-J-tools.2.2.1.zip in your xerces root
directory
ArgoUML
# - Java 2 JRE or JDK
#Berkeley DB
- already init, without a source directory
BioPerl
# - Bundle::BioPerl is a special bundle they built to include all necessary PERL modules, is retrievable by CPAN
# - The free graphical debugger ptkdb (available as Devel::ptkdb from CPAN) is highly recommended
# - Data::Dumper
# For accessing remote databases you will need: File-Temp-0.09 and IO-String-1.01
what is an Ace DB? For accessing Ace databases you will need: AcePerl-1.68
# For remote blast searches you will need:
libwww-perl-5.48 Digest-MD5-2.12 HTML-Parser-3.13 libnet-1.0703 MIME-Base64-2.11 URI-1.09 IO-stringy-1.216
# For xml parsing you will need:
libxml-perl-0.07 XML-Parser-2.30 XML-Twig-2.02 XML-Writer-0.4 Soap-Lite-0.52 XML-DOM-1.37
# expat-1.95.1 from http://sourceforge.net/projects/expat/
For more current and additional information on external modules required by bioperl, check
http://bioperl.org/Core/external.shtml
Bioperl C extensions & external bioinformatics programs
Bioperl also uses several C programs for sequence alignment and local blast searching.
# To use these features of bioperl you will need an ANSI C or Gnu C compiler
as well as the actual program available from sources such as:
for Smith-Waterman alignments- bioperl-ext-0.6 from http://bioperl.org/Core/external.shtml
for clustalw alignments- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/ http://www.ebi.ac.uk/FTP/
for tcoffee alignments- http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
for local blast searching- ftp://ftp.ncbi.nlm.nih.gov/blast/server/current_release/
for EMBOSS applications - http://www.hgmp.mrc.ac.uk/Software/EMBOSS/download.html
- Blast ftp://ftp.ebi.ac.uk/pub/software/unix/
#Bonnie++
- none listed
Clustal
- It uses the Vibrant multi-platform user interface development library,
developed by the National Center for Biotechnology Information as part of
their NCBI SOFTWARE DEVELOPMENT TOOLKIT
#cURL and libcurl
- already init
- can be configured and built with openSSL support if already available to it
DbDesigner
- nothing special noted, until I tried to configure it, when first It threw me an error
cc1plus: warning: as it has already been specified as a non-system directory
It wouldn't configure until I did:
- http://www.redhat.com/mailing-lists/redhat-devel-list/msg09843.html
- it still states that it cannot find and needs >=Qt2.2.2 libraries
- even though it has Version 3.0.5-17 from the RedHat 8.0 install
- which I tried to work around by giving all of the lib folders for Qt an entry into the pathmunge
- then that didn't work and I found
- http://www.linuxquestions.org/questions/history/36827
- ftp://ftp.trolltech.com/qt/source/qt-embedded-2.2.2.tar.gz
for QT install see INSTALL doc
http://mail.nl.linux.org/xchat-discuss/2001-07/msg00030.html
was getting this error after an upgrade of PERL5 while using the CPAN choked on
mod_perl
perl: error while loading shared libraries: libperl.so: cannot open shared object file: No such file or directory
so I... Put directory listings for all lib folders in /etc/ld.so.conf and ran ldconfig
and I put those same entries in a LD_LIBRARY_PATH environment variable
AND I still needed to install the qt source for 2.2.2 to satisfy the hard-coded
dependency in the DbDesigner makefile
(or maybe I can alter the configure script for DbDesigner)
Lines 4934 through 4938 of the file /usr/local/DbDesigner/configure gave me a clue as to where the script was looking
(I can either make a symlink or change the script, I think, but the QTDIR
environment variable didn't seem to work)
4934 if test $kde_qtver = 2; then
4935 kde_qt_dirs="$QTDIR /usr/lib/qt2 /usr/lib/qt"
4936 else
4937 kde_qt_dirs="$QTDIR /usr/lib/qt"
4938 fi
AND BEYOND
#Dia
- already init
# - Dia needs Gtk+ at least version 1.2.0 installed.
It can be found at:
ftp://ftp.gtk.org/pub/gtk/v1.2/
Binaries available at:
ftp://ftp.gtk.org/pub/gtk/binary/devel/RPMS/
# - As of version 0.30 Dia also needs libxml (aka gnome-xml).
It is recommended that you get a fairly recent version, but not version 1.8.0
It can be found here:
ftp://ftp.gnome.org/pub/GNOME/stable/sources/gnome-xml/
# - As of version 0.40 Dia needs gdk_imlib, at least version 1.8.2.
It can be found here:
ftp://ftp.gnome.org/pub/GNOME/stable/sources/imlib/
# - As of version 0.86, Dia requires either gdk_imlib (version 1.8.2 or newer) or gdk-pixbuf (version 0.7.0 or newer).
Older versions of Dia used gdk_imlib only. Gdk_imlib will probably be phased out after a while.
Gdk-pixbuf can be found here:
ftp://ftp.gnome.org/pub/GNOME/unstable/sources/gdk-pixbuf/
Gdk_imlib can be found here:
ftp://ftp.gnome.org/pub/GNOME/stable/sources/imlib/
DoubleChocoLatte
- Now built as part of GNUenterprise
Emboss - these packages from download
- EMBOSS-1.0.0.tar.gz
- PHYLIP-3.573c.tar.gz
- MSE-0.0.4.tar.gz
- TOPO-0.1.tar.gz
#GCC Compiler
- already init
GeneX
#- Apache Web Server - already init
#- Required Perl modules
# - Perl 5.005
# - DBI
# - DBB::Pg
# - Class::ObjectTemplate::DB 0.24 Required by all Bio::Genex modules
# - Class::ObjectTemplate 0.4 Required by Class::ObjectTemplate::DB
# - XML::DOM n/a Required for XML I/O
# - XML::Parser n/a Required by XML::DOM
# - Digest::MD5 n/a Required by LoginUtils.pm
# - CGI n/a Required by most CGI scripts
# - Term::ReadKey
- R stats pkg
# - you need a means of compliing C and Fortran 77
# - PERL up to date
# - makeinfo version 4 or later
# - readline library
# - zlib version 1.1.3 or later
# - jpeg 6b or later, libpng 1.2.3 or later
# - ghostscript
# - bzip2 for libbzip2
# - PCRE - ftp://ftp.csx.cam.ac.uk/pub/software/programming/pcre/
# - Tcl/Tk
- BLAS
- http://cran.r-project.org/src/base/R-1.6.1.tgz
- xgobi/xgvis
- none noted yet
# - GNU SW tools
- no special SW noted just the entire library
J-Express
# - JAVA Virtual Machine version 1.3.1 or above
- Stanford xcluster
- cannot locate the download at
- http://genome-www.stanford.edu/~sherlock/cluster.html
GNUe
- you will need to install Python2.1 and the Python2.1-devel package
- http://www.gnuenterprise.org/docs/redhat_install.html
- Go to the dependencies web page. Grab the wx* files. Then grab the mx.DateTime package and install
... but here is no such download
found this
http://goats.gnue.org/~dneighbo/projects.php
which also takes you to a dead link for the deps
GSoap
- none noted yet
#Hmmer
- none noted yet, built and installed and choked on putting the docs where they were supposed to go
because it could not find the folder "documentation/man" from where it was running the install
and the files it can't stat to cp in the documentation/man dir are not in the directory to be copied to anywhere
and the documentation states that if you have trouble installing that you can do a simple file copy
of the docs and binaries if need be
#Java 2
# - JDK
#KDE - already init
KDevelop-Project
- Required:
# g++ 2.7.2/g++ 2.8.1/egcs 1.1 (or compatible), available at http://www.gnu.org
# GNU make (or compatible), available at http://www.gnu.org
# perl 5.004, available at http://www.perl.com
# automake 1.2, available at http://www.gnu.org
# flex 2.5.4
# GNU gettext, available at http://www.gnu.org
# Qt 1.42, available at http://www.troll.no
# KDE 1.1.x, available at http://www.kde.org
Optional:
enscript for printing support
# ghostview or kghostview for printing preview
glimpse 4.0 for the search index, available at http://glimpse.cs.arizona.edu
sgmltools 1.0, available at http://www.sgmltools.org
KDE-SDK (KDE Software Development Kit), which includes KDoc, KSgml2Html, KTranslator
(available at http://developer.kde.org)
# KDbg, available at http://members.telecom.at/~johsixt/kdbg.html
# KIconEdit (available at http://www.kde.org)
#Koffice
- can be installed with it
libpqxx
- none noted yet
Mono
- a C compiler
- glib2
- libgc
- mcs
- gc6
#MySQL
- already init
ncbi-toolkit
- none noted yet
NIH Image (ImageJ, is Java version)
- This installation includes Sun's Java Runtime Environment 1.3.1 and the complete ImageJ source code
OpenMosix
- What does matter is that the kernel is at least on 2.4 level, and that your network-cards are configured correctly,
- next to that you`ll need a healthy space of swap
#OpenOffice
- already init
OpenVRML
- This distribution includes LookAt, a sample viewer program that uses GLUT
- ANTLR
# - zlib
- OpenGL/Mesa
# - GLUT
# - libpng
# - libjpeg
- SpiderMonkey
# - Sun Java Development Kit
# - Doxygen
PgAccess
- download and install a Tcl/Tk package from http://www.scriptics.com
(8.0.x or greater)
- install PgAccess package
- install the libpgtcl package
#PHP
- already init
php_lib_login
- none noted yet, except php of course
PhpGroupWare
#- You will need PHP compiled and installed on your system.
#- You will also need MySQL or PostgreSQL setup.
#- If you are planning on using the email system,
you will need to have an IMAP server installed and IMAP support compiled into PHP
phpPgAdmin
#- PostgreSQL
#- PHP
PhpWebSite
#- DB and PHP
Phylip
- none noted yet
#PostgreSQL
- The following prerequisites exist for building PostgreSQL:
# - GNU make is required
# - You need an ISO/ANSI C compiler
# - gzip
# - The GNU Readline
# - GNU Flex
# - GNU Bison
PyPgSQL
#- These instructions assume you have Python 2.0 (or later) and PostgreSQL
- If you are going to use the DB-API 2.0 compliant module,
- you must also install the mxDateTime module from http://starship.python.net/~lemburg/mxDateTime.html
#Python
- already init
#Quixote
#- Python 2.0 and 2.1 only - http://www.mems-exchange.org/software/quixote/doc/
RPM-update
- none noted yet
#Samba
- already init
#Sendmail
- already init
Subversion
- libsvn_ra_dav: accesses a networked repository using WebDAV http://www.webdav.org
# - libsvn_ra_local: accesses a local repository using Berkeley DB
- If you want Subversion to build the APR libraries from source code as part of the Subversion build process,
you can put their source code into the "./apr" and "./apr-util" directories.
- The Subversion tarball comes with copies of the libraries' source code stored in
these subdirectories which you could copy or link to.
- To be safe, however, you should check out the latest version from the Apache CVS repository,
since the latest Subversion may well rely on the latest changes to APR and APRUTIL.
# - autoconf 2.50 or newer
# - libtool 1.4 or newer
# - bison or yacc
- Neon library 0.23.5 - http://www.webdav.org/neon/neon-0.23.5.tar.gz
# - Berkeley DB 4.0.14 - http://www.sleepycat.com/
# - Apache Web Server 2.0.42 or newer
# - Python 2.0
# - A gnu-like diff and diff3
# - OpenSSL
# - zlib
# - Texinfo. We are in the process of migrating all texinfo files to DocBook Lite. The online documentation for texinfo is at
http://www.gnu.org/manual/texinfo-4.0/html_chapter/texinfo_toc.html
- Depending on exactly which doc targets you make, you'll need one or more of:
# - the `makeinfo' program from the latest texinfo package in
ftp://ftp.gnu.org/pub/gnu/texinfo/
# - the `texi2dvi' or `texi2html' programs
- the `dvipdf' script from Ghostscript (pipes dvi | ps | Ghostscript)
T-COFFEE
- http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
#TOra - for Oracle DB - already init
WebMail
- may not be needed
# - JDK 1.4 or greater (get it at http://java.sun.com)
# - a mailserver for sending (SMTP) and receiving (IMAP) mails; by default, JWebMail will use "localhost" for both
# - a webapp capable servlet container (e.g. Apache Tomcat, preferably >= 4.1,
http://jakarta.apache.org
#Wget
- already init
XML-DBMS
- XML-DBMS, PERL version 1.03
- none noted yet
- XML-DBMS, Java version 1.01
# - JDK (Java Development Kit) 1.1.x or 1.2.x Download: http://java.sun.com/products/jdk/1.1/index.html
# - A relational database such as Oracle, DB2, Informix, MS Access, or MySQL
- A JDBC driver for your database http://industry.java.sun.com/products/jdbc/drivers
# - postgresql-jdbc installed
# - An XML parser written in Java http://www.xmlsoftware.com/parsers/
dead link
# - A DOM level 1 implementation written in Java http://www.docuverse.com/
# - SAX (Simple API for XML) version 1 http://www.megginson.com/SAX/index.html
#YUM - yum uses a relatively standard ./configure ; make ; make install to work,
and installs itself as a service
although it is recommended that you install an RPM as yum requires that it be installed as an RPM.
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