User talk:Darek Kedra/sandbox 21: Difference between revisions
Darek Kedra (talk | contribs) |
Darek Kedra (talk | contribs) |
||
Line 181: | Line 181: | ||
install S/SM/SMUELLER/PathTools-3.31.tar.gz | install S/SM/SMUELLER/PathTools-3.31.tar.gz | ||
# // closest with ver. number from 1000genomes.org list | # // closest with ver. number from 1000genomes.org list | ||
install Template::Plugin::Number::Format | |||
# Template-Plugin-Number-Format-1.02.tar.gz | # Template-Plugin-Number-Format-1.02.tar.gz | ||
install Time::HiRes | |||
# Time-HiRes-1.9721.tar.gz | |||
install XML::DOM | |||
# XML-DOM-1.44.tar.gz | |||
install XML::RSS | |||
# XML-RSS-1.48.tar.gz | |||
install Compress::Bzip2 | |||
# Compress-Bzip2-2.09.tar.gz | |||
</pre> | </pre> | ||
These modules were missing when starting httpd with ENSEMBL's httpd.conf | These modules were missing when starting httpd with ENSEMBL's httpd.conf: | ||
<pre> | <pre> | ||
Line 196: | Line 204: | ||
install JSON | install JSON | ||
# JSON-2.21.tar.gz | # JSON-2.21.tar.gz | ||
</pre> | </pre> | ||
Revision as of 07:22, 8 May 2010
ENSEMBL Install
=web server
Perl
http://www.perl.org/get.html got perl-5.12.0
cd perl-5.12.0 cd perl-5.12.0/ CFLAGS='-m64 -mtune=nocona' ./Configure -des -A ccflags=-fPIC -Dprefix=/home/ensembl_usr/local/ make make test make install
The "CFLAGS" line is required on 64-bit Linux system to compile mod_perl. See relevant section
Apache httpd
http://httpd.apache.org/download.cgi got httpd-2.2.15.tar.gz
installation:
./configure --enable--deflate --enable--headers --enable--expires --prefix=/home/ensembl_usr/local/apache2 make make test make install
checking what is build in:
/home/ensembl_usr/local/apache2/bin/apachectl -t -D DUMP_MODULES
my output:
core_module (static) authn_file_module (static) authn_default_module (static) authz_host_module (static) authz_groupfile_module (static) authz_user_module (static) authz_default_module (static) auth_basic_module (static) include_module (static) filter_module (static) log_config_module (static) env_module (static) setenvif_module (static) version_module (static) mpm_prefork_module (static) http_module (static) mime_module (static) status_module (static) autoindex_module (static) asis_module (static) cgi_module (static) negotiation_module (static) dir_module (static) actions_module (static) userdir_module (static) alias_module (static) so_module (static) perl_module (shared)
mod_per 4 apache2.x
http://perl.apache.org/download/index.html got mod_perl-2.0.4
cd mod_perl-2.0.4 perl Makefile.PL MP_APXS=/home/ensembl_usr/local/apache2/bin/apxs make make test make install
Perl modules required by ENSEMBL
Assumes that you installed Perl in /home/ensembl_usr/local/ and got perl binary in /home/ensembl_usr/local/bin/
Check the list of modules here i.e: http://browser.1000genomes.org/info/docs/webcode/install/non-ensembl-code.html
There are several versions of this list of modules, but ultimately you may be missing several not listed modules, and you will get their names (one by one) after trying to start your ENSEMBL site.
Despite the advise of installing always the newest module versions there is one important exception: LWP. LWP version 5.812 is required by latest (2.57) ParallelUserAgent. This will be covered in a separate section of this page.
Also some modules do not install (at least on my machine) from perls CPAN shell. These may require installation by hand from sources (described later).
Easy things first:
export PATH=/home/ensembl_usr/local/bin/:$PATH which perl # ~/local/bin/perl perl -MCPAN -e shell #<snip> #commit: wrote '/home/ensembl_usr/local/lib/perl5/5.12.0/CPAN/Config.pm' install Cache::Memcached # Cache-Memcached-1.28.tar.gz install CGI # CGI.pm-3.49.tar.gz install CGI::Ajax # CGI-Ajax-0.707.tar.gz install CGI::Session # CGI-Session-4.42.tar.gz install Class::Accessor # Class::Accessor is up to date (0.34). // checked after installation of all modules install Class::Data::Inheritable # Class::Data::Inheritable is up to date (0.08). // checked after inst. of all modules install Class::Std # Class-Std-0.011.tar.gz install Class::DBI::Sweet # Class-DBI-Sweet-0.10.tar.gz install Class::Std::Utils # Class-Std-Utils-v0.0.3.tar.gz install Compress::Zlib # Compress::Zlib is up to date (2.027). install Compress::Raw::Zlib # Compress-Raw-Zlib-2.027.tar.gz install SHLOMIF/Config-IniFiles-2.57.tar.gz #// i /Config::Inifiles/ lists 3 modules, this one is the only one which version is close to the one listed on 1000genomes.org web page (see above) install DBI #DBI-1.611.tar.gz install DB_File # DB_File is up to date (1.820). // day 2, after installation of other modules install Devel::StackTrace # Devel-StackTrace-1.22.tar.gz install GD #GD-2.45.tar.gz install Data::UUID #Data-UUID-1.203.tar.gz install Digest::MD5 #Digest::MD5 is up to date (2.39). install Exception::Class # Exception-Class-1.30.tar.gz install install Hash::Merge # Hash-Merge-0.12.tar.gz install Storable #Storable is up to date (2.22). install SOAP::Lite # SOAP-Lite-0.711.tar.gz install XML::Parser # XML::Parser is up to date (2.36). install XML::Simple # XML-Simple-2.18.tar.gz install Parse::RecDescent # Parse-RecDescent-1.965001.tar.gz install PDF::API2 # PDF-API2-0.73.tar.gz install Spreadsheet::WriteExcel # Spreadsheet-WriteExcel-2.37.tar.gz install OLE::Storage_Lite # OLE::Storage_Lite is up to date (0.19) install Time::HiRes # Time-HiRes-1.9721.tar.gz install HTML::Template # HTML-Template-2.9.tar.gz install File::Temp # File::Temp is up to date (0.22) install Mail::Mailer # MailTools-2.06.tar.gz install Math::Bezier # Math-Bezier-0.01.tar.gz install IO::String # IO-String-1.08.tar.gz install Image::Size # Image-Size-3.221.tar.gz install K/KM/KMACLEOD/libxml-perl-0.08.tar.gz # // OK install List::MoreUtils #List-MoreUtils-0.22.tar.gz install Log::Log4perl # Log-Log4perl-1.28.tar.gz install Number::Format # Number-Format-1.73.tar.gz install DCONWAY/Parse-RecDescent-1.965001.tar.gz # // closest with ver. number from 1000genomes.org list install S/SM/SMUELLER/PathTools-3.31.tar.gz # // closest with ver. number from 1000genomes.org list install Template::Plugin::Number::Format # Template-Plugin-Number-Format-1.02.tar.gz install Time::HiRes # Time-HiRes-1.9721.tar.gz install XML::DOM # XML-DOM-1.44.tar.gz install XML::RSS # XML-RSS-1.48.tar.gz install Compress::Bzip2 # Compress-Bzip2-2.09.tar.gz
These modules were missing when starting httpd with ENSEMBL's httpd.conf:
install BSD::Resource # BSD-Resource-1.2904.tar.gz install Sys::Hostname::Long # Sys-Hostname-Long-1.4.tar.gz install JSON # JSON-2.21.tar.gz
Problems:
- Template::Toolkit
Used by BioMart http://www.cpan.org/modules/by-module/Template/Template-Toolkit-2.15.tar.gz
- install DBD::mysql -> problem... on a machine without mysql