295b9dbab341deac96c7f6166bea56f0fc7fa770 max Fri Feb 12 05:38:32 2021 -0800 changes after code review, refs #26951. Since all README files were merged into mirrorManual.txt in 2016, to avoid further confusion, I am removing them now. I manually merged all changes made since then (just 3-4 changes) into mirrorManual.txt now. mirrorManual.txt is automatically converted to https://genome.ucsc.edu/goldenPath/help/mirrorManual.html by the makefile in mirrorDocs. This makes sure that we have installation instructions that can be read with vi or less and at the same time we have a nice html file that is easy to read, looks like official documentation and is indexed by Google well. The big no.1 advantage of mirrorManual.txt is that the sections have an order in increasing complexity and the user knows where to start. The old README files had no order at all and the names were misleading (e.g. quickstart was not about a quickstart) diff --git src/product/README.trackDb src/product/README.trackDb deleted file mode 100644 index 80c85f2..0000000 --- src/product/README.trackDb +++ /dev/null @@ -1,150 +0,0 @@ -README.trackDb - -Creating tracks in the browser. - -See also: -http://genome.ucsc.edu/goldenPath/help/trackDb/trackDbDoc.html -http://genomewiki.ucsc.edu/index.php/Local_tracks_at_mirror_sites - -A track needs two items to make it exist in the browser: - -1. A database table with the track data -2. An entry in a database table: trackDb_localTracks - Built from track specifications in your trackDb.ra file. - Please note the description of trackDb.ra entries in the - source tree: src/hg/makeDb/trackDb/README - The correspondence between the database table and the trackDb.ra - definition is in the name used on the 'track' line in the - trackDb.ra file. Your database table name is used on the 'track' - definition line. - -Almost all of the database tables have specific loader -programs to load the track data. The loader programs -also verify the data before it is added to the table, -and they create the proper indexes on the table to allow -efficient display by the genome browser. - -By far the most common format of track data is the BED format. -See also: http://genome.ucsc.edu/FAQ/FAQformat.html#format1 -for a description of BED file formats. - -A typical BED file format is loaded into a database table with -the loader: hgLoadBed -For example, to load the data from the file: data.bed into -the table named: bedExample - -$ hgLoadBed hg17 bedExample data.bed - -There are a variety of file formats: GFF, GTF, PSL, WIG, MAF as well as -a variety of specialized data types. All the loader programs can be seen -in the source tree as subdirectories in: src/hg/makeDb/ - -$ cd src/hg/makeDb -$ ls -d hg* - -The build instructions for the browser code do not include -instructions for building all of the loaders, or other utilities -in the kent source tree. This is because there are literally -hundreds of utilities, 345 at last count, that are not needed -for ordinary browser development. In most cases a developer will -need only a couple of the loaders and utilities. Since the libraries -were built for the CGI binaries, to build any utility or -loader, simply go into its directory and run a 'make' - -For our purposes here, we need for example, for BED format tracks: -1. hgLoadBed -2. hgTrackDb -3. hgFindSpec - -To build the three loaders mentioned, go to the three directories: -src/hg/makeDb/hgTrackDb/ -src/hg/makeDb/hgFindSpec/ -src/hg/makeDb/hgLoadBed/ - -And run a 'make' in each one. The resulting binary is placed -in: $HOME/bin/$MACHTYPE -This binary directory should be in your PATH, or make this directory -be a symlink to some binary directory that is in your PATH -and you have write permission to. - -With those three loader programs built, you can now load BED -format tracks, and build the trackDb_localTracks table as -mentioned next. - -The hgTrackDb and hgFindSpec loaders are used to build the trackDb and -hgFindSpec tables in the database. Older instructions used to mention -using the trackDb file hierarchy in the source tree. This is no longer -necessary and is not recommended. You can certainly obtain example -trackDb entries from the source tree hierarchy: src/hg/makeDb/trackDb/ -in any of the *.ra files. And you will need to refer to the README -file in that directory for information about options you can use with -each track type. To work independently of the UCSC source tree, -establish your own trackDb.ra files outside the UCSC source tree in -a directory of your choice under your control. Then, to load them -into the database, run the hgTrackDb command with this -simple makefile in the directory where your .ra file exists: - -trackDbSql=/path/to/kent/source/tree/src/hg/lib/trackDb.sql -DB=hg19 - -all:: - hgTrackDb . ${DB} trackDb_localTracks ${trackDbSql} . - -This hgTrackDb command reads your trackDb.ra file and converts it -into row entries for each track specified in it into row contents -in this new table trackDb_localTracks. - -The DB= specification is your database of interest, this example: hg19 -This loads your local specific table trackDb_localTracks in the database. -This name trackDb_localTracks is not special, just different than -the ordinary trackDb table. It should have some meaning to anyone -in your environment and not be the same name as any UCSC database -table. The two '.' arguments in the command above refer -to directory names. Since you have no hierarchy of levels in this -single directory, unlike in the source tree trackDb hierarchy, the -'.' arguments refer to the current directory. - -To direct the genome browser to this table to use as extra trackDb -definitions, add to the specification in your cgi-bin/hg.conf file: - -db.trackDb=trackDb_localTracks,trackDb - -Beware of the specified order of the tables if there are tracks -by the same name in each table. Any definitions for tracks -in trackDb_localTracks will override any definitions for the -same named tracks in trackDb. You could thus override the -standard definitions for tracks from the trackDb table. -Your usual case will be that your tracks are unique to your -local installation. - -======================================================================== -Extra Credit: - -See also: new assistant scripts as of March 2010 in the ./scripts/ - directory here to fetch and build the source tree. - -Older instructions about building the source tree remain valid: - -If you really do want to build all the utilities and all database -loaders, perform the following 'make' commands in your source tree: - -$ cd src -$ make clean -$ make libs -$ cd hg -$ make -$ cd ../utils -$ make - -This builds everything cleanly, all CGI binaries, all database -loaders, all utilities. Perform this sequence each time you -do a 'git pull' on your source tree. The 'make clean' step -is especially important since the makefile hierarchy does not -have built in dependencies and will not rebuild items that -depend upon each other. The traditional dependency on the -source tree libraries is taken care of because a make in any -directory that produces a binary will always re-link the -binary every time, thus always picking up any potentially new -library. - -====================================================================