2012-02-23: import and UCSC GENCODE group process of GENCODE V11 (markd)
    # Due to UCSC Genome Browser using the NC_001807 mitochondrial genome sequence
    # (chrM) and GENCODE annotating the NC_012920 mitochondrial sequence, the
    # GENCODE mitochondrial sequences are not loaded

    # download files
    mkdir -p /hive/groups/encode/dcc/data/gencodeV11/release
    cd /hive/groups/encode/dcc/data/gencodeV11/release

    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.2wayconspseudos.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.annotation.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.long_noncoding_RNAs.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.pc_transcripts.fa.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.pc_translations.fa.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.polyAs.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.tRNAs.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode11_GRCh37.tgz

    # silly sanity check:
    for f in * ; do zcat $f >/dev/null ; done

    # untar main distribution
    tar -zxf gencode11_GRCh37.tgz

    # obtain transcription support level analysis from UCSC GENCODE group (markd/rachel)
    mkdir -p data
    cp /cluster/home/markd/compbio/ccds/branches/transSupV11.1/modules/gencodeTransSupport/exprs/classDev/runs/2012-02-26/results/gencode.v11.transcriptionSupportLevel.{tab,tsv} data/

    # create Makefile from previous one
    cd /hive/groups/encode/dcc/data/gencodeV11/
    cp ../gencodeV10/Makefile .
    # edit as needed
   
    # on code in the CCDS subversion tree:
    #   svn+ssh://hgwdev.cse.ucsc.edu/projects/compbio/svnroot/hausslerlab/ccds/trunk
    # and markd's python library (it will be moved to the hausslerlab
    # repository soon)
    # may need to update
        ccds2/modules/gencode/src/lib/gencode/data/gencodeGenes.py
    # to add new biotypes, use this command to verify and update as needed
    make checkAttrs

    (time nice make -j 10 mkTables) >&build.out&
    # took ~45 minutes, log below

    ## copy and update trackDb files from previous release
    kent/src/hg/makeDb/trackDb
    cp human/hg19/wgEncodeGencodeV10.ra human/hg19/wgEncodeGencodeV11.ra
    cp human/hg19/wgEncodeGencodeV10.html human/hg19/wgEncodeGencodeV11.html

    ### IMPORTANT: make sure that hgTracks/simpleTracks.c registers
    ### track handler for this version of gencode:
    registerTrackHandlerOnFamily("wgEncodeGencodeV11", gencodeGeneMethods);

------------------------------------------------------------------------------
2012-06-05:

An error was discovered where both gene names and transcript names (not ids) a
version number appended. eg. RP11-513O17.2.1 and RP11-513O17.2-006.  In
total 19958 gene names and 27058 transcript names have been corrected.

Repeat above build in a new directory

    mkdir -p /hive/groups/encode/dcc/data/gencodeV11b/release
    cd /hive/groups/encode/dcc/data/gencodeV11b/release

    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.2wayconspseudos.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.annotation.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.long_noncoding_RNAs.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.pc_transcripts.fa.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.pc_translations.fa.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.polyAs.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode.v11.tRNAs.gtf.gz
    wget -nv ftp://ftp.sanger.ac.uk/pub/gencode/release_11/gencode11_GRCh37.tgz

    # silly sanity check:
    for f in * ; do zcat $f >/dev/null ; done

    # untar main distribution
    tar -zxf gencode11_GRCh37.tgz

    # copy over obtain transcription support level analysis, not affect by change
    cd ..
    mkdir -p data
    cp /cluster/home/markd/compbio/ccds/branches/transSupV11.1/modules/gencodeTransSupport/exprs/classDev/runs/2012-02-26/results/gencode.v11.transcriptionSupportLevel.{tab,tsv} data/

    # keep Makefile from previous V11
    cp ../gencodeV11/Makefile .
   
    (time nice make -j 10 mkTables) >&build.out&
    # took ~45 minutes

    # validate what changed
    (cd ../gencodeV11; md5sum tables/*)> v11.tables.md5

diff -r ../gencodeV11/tables tables >tbl.diff