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.cram src/product/README.cram deleted file mode 100644 index 2336431..0000000 --- src/product/README.cram +++ /dev/null @@ -1,54 +0,0 @@ - -Activating CRAM support for the Genome Browser. - -The UCSC Genome Browser is capable of displaying tracks from both the BAM and -CRAM file formats. While BAM tracks provide all of the required data within -the file, however, CRAM tracks depend on external "reference sequence" files -(see http://www.ebi.ac.uk/ena/software/cram-toolkit for more information about -the CRAM format). A bit of information on how the Browser works with these -files is included below. For installation instructions, skip to the numbered -steps at the end of this file. - -The directory that Genome Browser CGIs check for CRAM reference files is set -with the cramRef setting in hg.conf. For example, the following setting is -used on our production servers: - -cramRef=/userdata/cramCache - -When loading tracks from the CRAM file format, CGIs will look for reference -sequences in that directory. The filename of each reference sequence should be -the MD5 or SHA1 checksum of the reference sequence as described at -http://www.ebi.ac.uk/ena/software/cram-reference-registry. If a CGI is unable -to find the reference sequence file for a CRAM track, it will next check the -cramRef/pending/ directory to see if a request for that reference sequence has -already been made, and the cramRef/error/ directory to see if a previous -attempt at downloading that reference sequence resulted in an error. If none -of those files are found, the CGI will then create a request file in the -cramRef/pending/ directory. The name of the request file will be the MD5 or -SHA1 sequence checksum, as specified in the CRAM data file. The contents of -the request file will be the URL to download that reference sequence. A -separate tool can then be used to download reference sequences listed in the -pending/ directory and place them into cramRef/. - -Steps to set up CRAM track support: - -1. Add the hg.conf setting cramRef. The value should be the path (relative - or absolute) to a directory where CRAM reference sequences are stored. - -2. Inside the cramRef directory create subdirectories called "pending" and - "error". The apache user must have read/write permissions for the pending/ - directory, and at least read permissions for the cramRef/ and error/ - directories. - -If you plan to manually load all CRAM reference sequences for your tracks into -the cramRef directory, track support is now complete. If you prefer to -have reference sequences automatically downloaded and placed in that directory -(e.g., for user-submitted custom tracks), continue to step 3. - -3. Add a cron job to run a script that parses files in the cramRef/pending/ - directory, downloads the corresponding reference sequence files, and places - those sequence files in cramRef/. Error messages during file retrieval - should be placed in cramRef/error/. An example script is provided in this - repository at kent/src/product/scripts/fetchCramReference.sh. The account - that runs this script must have read/write permissions for the cramRef/, - cramRef/pending/, and cramRef/error/ directories.