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[Gmod-schema-cmts] schema/chado INSTALL,1.16,1.17 TODO,1.15,1.16
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From: Scott C. <sco...@us...> - 2004-03-26 19:19:22
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Update of /cvsroot/gmod/schema/chado In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv2702 Modified Files: INSTALL TODO Log Message: doc updating Index: TODO =================================================================== RCS file: /cvsroot/gmod/schema/chado/TODO,v retrieving revision 1.15 retrieving revision 1.16 diff -C2 -d -r1.15 -r1.16 *** TODO 25 Mar 2004 21:10:06 -0000 1.15 --- TODO 26 Mar 2004 19:08:20 -0000 1.16 *************** *** 3,8 **** Done! - test load_gff.pl Done! - roll yeast gff3 file into distribution ! - add a make target to remove ontology lock files ! - change tmp space for ontologies to $GMOD_ROOT/tmp Done! - update AutoDBI.PLS Done! - fix the prepdb thing (are the inserts that fail generic or specific to --- 3,8 ---- Done! - test load_gff.pl Done! - roll yeast gff3 file into distribution ! Done! - add a make target to remove ontology lock files ! Done! - change tmp space for ontologies to $GMOD_ROOT/tmp Done! - update AutoDBI.PLS Done! - fix the prepdb thing (are the inserts that fail generic or specific to *************** *** 31,35 **** For the next release: ! - fix Makefile.PL to install scripts in $GMOD_ROOT/bin - add documentation for creating Class::DBI classes for an existing schema-- this will no doubt be necessary for future upgrade paths (I'm thinking the way --- 31,35 ---- For the next release: ! - fix Makefile.PL to install scripts in $GMOD_ROOT/bin (i'm not convinced I want this; I think /usr/local/bin is fine sc-3/26/04) - add documentation for creating Class::DBI classes for an existing schema-- this will no doubt be necessary for future upgrade paths (I'm thinking the way *************** *** 38,45 **** - add documentation for loading ontologies when the files are already present locally. - - create pre-created Class::DBI classes for a 'default' install, eliminating - the need for S::T. - - either make Term::ProgressBar optional or submit a patch to give back a - default width when the XS module fails to find a terminal width (or both). - remove hard coded passwords and other conf stuff from Class::DBI classes. - integrate Apollo --- 38,41 ---- Index: INSTALL =================================================================== RCS file: /cvsroot/gmod/schema/chado/INSTALL,v retrieving revision 1.16 retrieving revision 1.17 diff -C2 -d -r1.16 -r1.17 *** INSTALL 15 Mar 2004 18:58:32 -0000 1.16 --- INSTALL 26 Mar 2004 19:08:20 -0000 1.17 *************** *** 98,101 **** --- 98,113 ---- used by Chado and its associated tools: + * Use the simple install (uses default database schema) [Y] + + Answering yes skips questions about what exensions to use, and + eliminates the need to have SQL::Translator installed. This + is recomended. + + * Use values in '/home/scott/schema/chado/build.conf'? [Y] + + If `perl Makefile.PL` has been run before, answering yes to this + will cause Makefile.PL to use the configuration options from the + previous build. + * What database server will you be using? [PostgreSQL] *************** *** 123,126 **** --- 135,142 ---- Port of the database daemon. + * Where shall downloaded ontologies go? [./tmp] + + The directory where ontology files and there lock files will be stored + * Available extensions to the core schema: [1] sequence/gff-bridge/sequence-gff-views.sql *************** *** 166,199 **** specialized needs of a MOD. * make Creates necessary files for the rest of the build process. * make load_schema Creates database, installs schema. Note that it will wipe out any database with the same name in the process! * make prepdb Inserts a few useful items into fundamental Chado tables. It ! uses load/etc/initialize.sql and when organism information is ! needed, it uses human as an example. This file can be edited ! to use any organism. Also note that if you did not select ! all of the optional exentions when you executed perl Makefile.PL ! you may get some errors at this stage and that is normal (they ! result from trying to insert data into tables that don't ! exist). * make ontologies Gets and installs various ontologies. Requires a network connection. Note retrieved ontology files are stored ! in /tmp/chado_load/. In order to do a repeat installation, ! lock files need to be removed to allow reinstallation of ! ontologies. Those lock files are located in subdirectories ! of /tmp/chado_load and are suffixed with '_chado'. For ! example, the Sequence Ontology lock files are located in ! /tmp/chado_load/song and are called so.definition_chado ! and so.ontology_chado. Alternatively, deleting everything ! in /tmp/chado_load will force the re-downloading of the ! ontology data from their respective sources. Also note that ! loading a large ontology like the Gene Ontology will take several minutes (perhaps as long as an hour). --- 182,220 ---- specialized needs of a MOD. + * make Creates necessary files for the rest of the build process. + * make load_schema Creates database, installs schema. Note that it will wipe out any database with the same name in the process! + * make prepdb Inserts a few useful items into fundamental Chado tables. It ! uses load/etc/initialize.sql. It contains information for several ! common organisms and source databases (eg, genbank). This file ! can be edited to add any organism or source database, using the ! INSERT statements for the examples as a template. Also note that ! if you did not select all of the optional exentions when you executed ! perl Makefile.PL you may get some errors at this stage and that is ! normal (they result from trying to insert data into tables that don't ! exist). Note also that the prepdb target needs to be executed ! before the ontologies target, but it can be executed again later, ! if more insert statements are added (for instance to add a new ! organism or database). ! * make ontologies Gets and installs various ontologies. Requires a network connection. Note retrieved ontology files are stored ! in the directory specified when perl Makefile.PL was run (the default ! is ./tmp). In order to do a repeat installation, lock files need to be ! removed to allow reinstallation of ontologies. Those lock files ! can be removed by executing `make rm_locks`. Alternatively, ! deleting everything in the temporary directory will force the ! re-downloading of the ontology data from their respective sources. ! Also note that loading a large ontology like the Gene Ontology will take several minutes (perhaps as long as an hour). *************** *** 204,226 **** modules to perl lib directories. ! * gmod_load_gff3.pl --organism fruitfly \ ! --srcdb DB:genbank \ ! --gfffile dat/AE003644.gbk.gff.bp (note that the '\' is included to allow cutting and pasting to a unix command line.) ! Loads GFF file. Note that this command will fail unless you add ! fruitfly to the organism table. See `gmod_load_gff3.pl --help` for ! details. In summary, execute this command in the psql shell for the ! database: ! ! chado=# insert into organism (abbreviation, genus, species, common_name) ! chado-# values ('D.melanogaster','Drosophila','melanogaster','fruitfly'); ! to add fruitfly to the organism table. The loading script requires ! GFF3 as it has tighter control of the syntax and requires the use of a ! controlled vocabulary (SOFA), allowing mapping to the relational schema. ! GFF3 files can be generated either from the included gmod_genbank2gff3.pl ! script: $ gmod_genbank2gff3.pl <genbank file> > <gff file> --- 225,255 ---- modules to perl lib directories. ! With that, the installation of the schema is complete. The easiest way ! to load data into the database is to use a GFF3 file and the script ! gmod_load_gff3.pl. Located in the dat directory is a compressed ! GFF3 file for S. cerevisiae called yeast.gff3.bz2. First, uncompress ! the file with bzip2: ! ! bzip2 -d dat/yeast.gff3.bz2 ! ! Then execute gmod_load_gff3.pl: ! ! gmod_load_gff3.pl --organism yeast \ ! --srcdb DB:SGD \ ! --gfffile dat/yeast.gff3 (note that the '\' is included to allow cutting and pasting to a unix command line.) ! This loads the GFF3 file. The loading script requires GFF3 as it has ! tighter control of the syntax and requires the use of a controlled ! vocabulary (SOFA), allowing mapping to the relational schema. In ! addition to supplying the location of the file with the --gfffile flag, ! the --orgainism tag uses the common name from the organism table and ! --srcdb uses the database name from the db table. See ! `perldoc gmod_load_gff.pl` for more information on adding other ! organisms and databases, as well as other available commandline flags. ! GFF3 files can also be generated either from the included ! gmod_genbank2gff3.pl script: $ gmod_genbank2gff3.pl <genbank file> > <gff file> *************** *** 236,241 **** development is ongoing to provide better translation. ! * install Generic-Genome-Browser. ! $ tar -zxvf Generic-Genome-Browser-1.58.tar.gz ! $ cd Generic-Genome-Browser-1.58.tar.gz and follow the instruction in the INSTALL documentation. --- 265,275 ---- development is ongoing to provide better translation. ! ! Finally, to browse the data in chado, install the Generic Genome Browser, ! GBrowse. To do this execute the following commands (substituting the ! version number for the 'x's): ! ! $ tar -zxvf Generic-Genome-Browser-x.xx.tar.gz ! $ cd Generic-Genome-Browser-x.xx.tar.gz and follow the instruction in the INSTALL documentation. + |