Difference between revisions of "Software Life Cycle: 1. Updating The Development Server"
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| − | This is a quick description of how to update the development server with a new release of the database. | + | This is a quick description of how to update the development server with a new release of the database. In general, the development process involves mirroring a large number of files from Sanger, unpacking, and in many cases, massaging into a format suitable for driving the website. |
== Development Server == | == Development Server == | ||
| Line 11: | Line 11: | ||
The update pipeline code is available in the WormBase admin module: | The update pipeline code is available in the WormBase admin module: | ||
| − | brie3 | + | brie3> svn co svn+ssh://brie3.cshl.org/usr/local/svn/admin |
| − | + | ||
Change into the development directory: | Change into the development directory: | ||
| − | brie3 | + | brie3> cd admin/update/development |
| − | + | ||
The contents are: | The contents are: | ||
| Line 30: | Line 30: | ||
A single shell script fires off all steps of the process. | A single shell script fires off all steps of the process. | ||
| − | brie3 | + | brie3> ./update.sh |
| − | The steps it performs are: | + | The steps it performs are: |
| − | * Purge disk space | + | *Purge disk space |
| − | * Create necessary directories | + | *Create necessary directories |
| − | * Mirror and unpack ACeDB from Sanger | + | *Mirror and unpack ACeDB from Sanger |
| − | * Mirror ontology files from Sanger | + | *Mirror ontology files from Sanger |
| − | * Compile ontology resources for the site | + | *Compile ontology resources for the site |
| − | * Create BLAST databases for available species | + | *Create BLAST databases for available species |
| − | * Create BLAT database for available species | + | *Create BLAT database for available species |
| − | * Create ePCR databases for select species | + | *Create ePCR databases for select species |
| − | * Load genomic GFF databases for available species | + | *Load genomic GFF databases for available species |
| − | * Build and load GFF patches | + | *Build and load GFF patches |
| − | * Convert GFF3 into GFF3 | + | *Convert GFF3 into GFF3 |
| − | * Create a GBrowse-driven genetic map | + | *Create a GBrowse-driven genetic map |
| − | * Create a GBrowse-drive physical map | + | *Create a GBrowse-drive physical map |
| − | * Create dump files of common datasets | + | *Create dump files of common datasets |
| − | * Load the CLUSTALW database | + | *Load the CLUSTALW database |
| − | * Mirror annotation files from Sanger to the FTP site | + | *Mirror annotation files from Sanger to the FTP site |
| − | Each step is described below. | + | Each step is described below. |
| − | == Update Steps == | + | == Update Steps == |
| − | === Purge Disk Space === | + | === Purge Disk Space === |
| − | Remove obsolete files from the (staging) FTP site. | + | Remove obsolete files from the (staging) FTP site. These have already been mirrored to the production FTP site and do not need to be maintained on the development server. |
| − | Usage : ./steps/purge_disk_space.pl | + | Usage : ./steps/purge_disk_space.pl |
| + | |||
| − | === Create necessary directories == | + | === Create necessary directories == |
| − | Create staging directories for the update process. | + | Create staging directories for the update process. |
| − | Usage : ./steps/create_directories.pl {WSRELEASE} | + | Usage : ./steps/create_directories.pl {WSRELEASE} |
| + | |||
| − | === Mirror and unpack ACeDB from Sanger ==== | + | === Mirror and unpack ACeDB from Sanger = === |
| − | Mirror and unpack the new release of the database from Sanger. | + | Mirror and unpack the new release of the database from Sanger. |
| − | Usage : ./steps/create_directories.pl {WSRELEASE} | + | Usage : ./steps/create_directories.pl {WSRELEASE} |
| + | |||
| − | ''Note: | + | ''Note: This can take a *long* time. You might to run this in a screen:'' |
| − | brie3 | + | brie3> screen |
| − | brie3 | + | brie3> ./steps/mirror_acedb.pl WS198 |
| − | brie3 | + | brie3> ^D |
(to resume) | (to resume) | ||
| − | brie3 | + | brie3> screen -r |
| + | |||
| − | * Mirror ontology files from Sanger | + | *Mirror ontology files from Sanger |
| − | * Compile ontology resources for the site | + | *Compile ontology resources for the site |
| − | * Create BLAST databases for available species | + | *Create BLAST databases for available species |
| − | * Create BLAT database for available species | + | *Create BLAT database for available species |
| − | * Create ePCR databases for select species | + | *Create ePCR databases for select species |
| − | * Load genomic GFF databases for available species | + | *Load genomic GFF databases for available species |
| − | * Build and load GFF patches | + | *Build and load GFF patches |
| − | * Convert GFF3 into GFF3 | + | *Convert GFF3 into GFF3 |
| − | * Create a GBrowse-driven genetic map | + | *Create a GBrowse-driven genetic map |
| − | * Create a GBrowse-drive physical map | + | *Create a GBrowse-drive physical map |
| − | * Create dump files of common datasets | + | *Create dump files of common datasets |
| − | * Load the CLUSTALW database | + | *Load the CLUSTALW database |
| − | * Mirror annotation files from Sanger to the FTP site | + | *Mirror annotation files from Sanger to the FTP site |
Revision as of 19:21, 6 January 2009
This is a quick description of how to update the development server with a new release of the database. In general, the development process involves mirroring a large number of files from Sanger, unpacking, and in many cases, massaging into a format suitable for driving the website.
Contents
Development Server
The current development server is
brie3: brie3.cshl.org / dev.wormbase.org
Update Pipeline Code
The update pipeline code is available in the WormBase admin module:
brie3> svn co svn+ssh://brie3.cshl.org/usr/local/svn/admin
Change into the development directory:
brie3> cd admin/update/development
The contents are:
logs/ -- the logs directory for each step/update README.txt -- nothing steps/ -- Perl scripts that launch each step Update.pm -- the top level module for the update process Update/ -- Perl modules corresponding to each step updatelog.conf -- a configuration file for the update process update.sh -- master script that fires off each step of the pipeline util/ -- various helper scripts for the update process
A single shell script fires off all steps of the process.
brie3> ./update.sh
The steps it performs are:
- Purge disk space
- Create necessary directories
- Mirror and unpack ACeDB from Sanger
- Mirror ontology files from Sanger
- Compile ontology resources for the site
- Create BLAST databases for available species
- Create BLAT database for available species
- Create ePCR databases for select species
- Load genomic GFF databases for available species
- Build and load GFF patches
- Convert GFF3 into GFF3
- Create a GBrowse-driven genetic map
- Create a GBrowse-drive physical map
- Create dump files of common datasets
- Load the CLUSTALW database
- Mirror annotation files from Sanger to the FTP site
Each step is described below.
Update Steps
Purge Disk Space
Remove obsolete files from the (staging) FTP site. These have already been mirrored to the production FTP site and do not need to be maintained on the development server.
Usage : ./steps/purge_disk_space.pl
= Create necessary directories
Create staging directories for the update process.
Usage : ./steps/create_directories.pl {WSRELEASE}
Mirror and unpack ACeDB from Sanger =
Mirror and unpack the new release of the database from Sanger.
Usage : ./steps/create_directories.pl {WSRELEASE}
Note: This can take a *long* time. You might to run this in a screen:
brie3> screen brie3> ./steps/mirror_acedb.pl WS198 brie3> ^D (to resume) brie3> screen -r
- Mirror ontology files from Sanger
- Compile ontology resources for the site
- Create BLAST databases for available species
- Create BLAT database for available species
- Create ePCR databases for select species
- Load genomic GFF databases for available species
- Build and load GFF patches
- Convert GFF3 into GFF3
- Create a GBrowse-driven genetic map
- Create a GBrowse-drive physical map
- Create dump files of common datasets
- Load the CLUSTALW database
- Mirror annotation files from Sanger to the FTP site
