# for emacs: -*- mode: sh; -*-

 
# This file describes building the browser database for the archaeal
# species Methanosarcina acetivorans.

# DOWNLOAD SEQUENCE FROM GENBANK (DONE 8/05)

    ssh eieio
    mkdir /cluster/store5/archae/metAce1
    ln -s /cluster/store5/archae/metAce1 /cluster/data/metAce1
    cd /cluster/data/metAce1
    wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Methanosarcina_acetivorans/NC_003552.fna
    mv NC_003552.fna chr.fa
    # Edit header of chr.fa to '> metAce1'

# CREATE DATABASES AND A BUNCH OF INITIAL STUFF (DONE 8/05)

    ssh hgwdev
    echo 'create database metAce1' | hgsql ''
    cd /cluster/data/metAce1
    faToNib chr.fa nib/chr.nib
    hgNibSeq metAce1 /cluster/data/metAce1/nib chr.fa
    faSize -detailed chr.fa > chrom.sizes
    mkdir -p /gbdb/metAce1/nib
    echo "create table grp (PRIMARY KEY(NAME)) select * from hg16.grp" \
	    | hgsql metAce1
    echo 'INSERT INTO dbDb \
        (name, description, nibPath, organism, \
                defaultPos, active, orderKey, genome, scientificName, \
                htmlPath, hgNearOk) values \
        ("metAce1", "April 2002", "/gbdb/metAce1/nib", "Methanosarcina acetivorans", \
               "chr:500000-550000", 1, 205, "Methanosarcina acetivorans", \
                "Methanosarcina acetivorans C2A", "/gbdb/metAce1/html/description.html", \
                0);' \
      | hgsql hgcentraltest
    echo 'INSERT INTO defaultDb (genome, name) values ("Methanosarcina acetivorans", "metAce1");' \
      | hgsql hgcentraltest
    echo 'INSERT INTO genomeClade (genome, clade, priority) values ("Methanosarcina acetivorans", "archaea",85);'  \
      | hgsql hgcentraltest

    cd ~/kent/src/hg/makeDb/trackDb
    # edit the trackDb makefile

    # add the trackDb directories
    mkdir -p archae/metAce1
    cvs add archae
    cvs add archae/metAce1
    cvs commit

# GC 20 BASE WIGGLE TRACK (DONE 8/13/05)

    mkdir /cluster/data/metAce1/bed/gc20Base
    cd /cluster/data/metAce1/bed/gc20Base
    mkdir wigData20 dataLimits20
    hgGcPercent -chr=chr -file=stdout -win=20 -overlap=19 metAce1 ../../nib | grep -w GC | \
    awk '
{
    bases = $3 - $2
    perCent = $5/10.0
    printf "%d\t%.1f\n", $2+1, perCent
}' | wigAsciiToBinary -dataSpan=1 -chrom=chr \
	-wibFile=wigData20/gc20Base_1 -name=1 stdin > dataLimits20/chr
    hgLoadWiggle metAce1 gc20Base wigData20/*.wig
    mkdir /gbdb/metAce1/wib
    ln -s `pwd`/wigData20/*.wib /gbdb/metAce1/wib
    #	the trackDb entry

# CONTIG TRACK 
    # reformat is a Todd Lowe program
    for num in `seq 746 946`; do   
       curl -o ${num}.gbk "http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?txt=on&val=AE009${num}.1"
       reformat fasta ${num}.gbk >> contigs.fa
    done
    blat /cluster/data/metAce1/chr.fa contigs.fa -minIdentity=100 contigs.psl
    perfectBlatBed4 contigs.psl contigs.bed
    mkdir /cluster/data/metAce1/bed/metAce1Contigs
    cp contigs.bed /cluster/data/metAce1/bed/metAce1Contigs
    cd /cluster/data/metAce1/bed/metAce1Contigs
    hgLoadBed metAce1 metAce1Contigs contigs.bed
    # the trackDb entry: 
track metAce1Contigs
shortLabel Contigs
longLabel Contigs deposited in Genbank
group map
priority 0.5
visibility pack
url http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=nucleotide&cmd=search&term=$$
type bed 4 .


# TANDEM REPEAT MASKER (DONE)

    ssh hgwdev
    mkdir -p /cluster/data/metAce1/bed/simpleRepeat
    cd /cluster/data/metAce1
    trfBig chr.fa /dev/null -bedAt=/cluster/data/metAce1/bed/simpleRepeat/chr.bed
    cd /cluster/data/metAce1/bed/simpleRepeat
    vi chr.bed and replace metAce1 with chr
    hgLoadBed metAce1 simpleRepeat *.bed -sqlTable=~kent/src/hg/lib/simpleRepeat.sql

# DESCRIPTION PAGE (DONE)

    ssh hgwdev
    # Write ~/kent/src/hg/makeDb/trackDb/archae/metAce1/description.html
    chmod a+r ~/kent/src/hg/makeDb/trackDb/archae/metAce1/description.html
    # Check it in.
    mkdir /gbdb/metAce1/html
    ln -s /cluster/data/metAce1/html/description.html /gbdb/metAce1/html/

# GENBANK PROTEIN-CODING GENES (DONE)

    ssh hgwdev
    mkdir /cluster/data/metAce1/genbank
    cd /cluster/data/metAce1/genbank
    wget ftp://ftp.ncbi.nlm.nih.gov/genomes/Bacteria/Methanosarcina_acetivorans/NC_003552.gbk
    mv NC_003552.gbk metAce1.gbk
    # Create 3 files to assist parsing of the genbank
    # 1. for a genePred file

echo 'locus_tag
chr
strand
start
end
start
end
1
start
end
lineNumber
gene
cmpl
cmpl
0' > metAce1-params-gp.txt
    # 2. for the peptide parts
    echo 'locus_tag
translation' > metAce1-params-pep.txt
    # 3. for the other gene information
    echo 'locus_tag
gene
product
note
protein_id
db_xref
EC_number
db_xref2' > metAce1-params-xra.txt
    # Now extract the genes and information:
    gbArchaeGenome metAce1.gbk metAce1-params-gp.txt metAce1-genbank-cds.gp
    gbArchaeGenome metAce1.gbk metAce1-params-pep.txt metAce1-genbank-cds.pep
    gbArchaeGenome metAce1.gbk metAce1-params-xra.txt metAce1-genbank-cds.xra
    hgsql metAce1 < /cluster/home/baertsch/kent/src/hg/lib/pepPred.sql
    hgsql metAce1 < /cluster/home/baertsch/kent/src/hg/lib/minGeneInfo.sql
    echo rename table pepPred to gbProtCodePep | hgsql metAce1
    echo rename table minGeneInfo to gbProtCodeXra | hgsql metAce1
    echo load data local infile \'metAce1-genbank-cds.pep\' into table gbProtCodePep | hgsql metAce1
    echo load data local infile \'metAce1-genbank-cds.xra\' into table gbProtCodeXra | hgsql metAce1
    ldHgGene metAce1 refSeq metAce1.gp -predTab -genePredExt

# COG STUFF
  awk 'NR>3{OFS="\t";print $6,$8,$7}' /projects/lowelab/db/Bacteria/Methanosarcina_acetivorans/NC_003552.ptt  > COG
  hgsql metAce1 < /cluster/home/baertsch/kent/src/hg/lib/cogs.sql
  echo "load data local infile 'COG' into table COG" | hgsql metAce1
# load cog codes
 hgsql metAce1 < /cluster/data/metAce1/genbank/COGXra.sql


# GENBANK rRNA GENES (NOT QUITE DONE)
    ssh hgdev
    cd /cluster/data/metAce1/genbank
    gbArchaeGenome -kind=rRNA metAce1.gbk metAce1-params-bed.txt metAce1-rrnas.bed
    echo 'gene product NA' > metAce1-params-rrna-xra.txt
    gbArchaeGenome -kind=rRNA metAce1.gbk metAce1-params-rrna-xra.txt metAce1-rrnas-xra.txt
    hgLoadBed metAce1 gbRRNA metAce1-rrnas.bed
    hgsql metAce1 < ~/kent/src/hg/lib/minGeneInfo.sql
    echo rename table minGeneInfo to gbRRNAXra | hgsql metAce1
    echo load data local infile \'metAce1-rrnas-xra.txt\' into table gbRRNAXra | hgsql metAce1


# TODD LOWE tRNA GENES ()

    # This one is a bed 6+ file created by hand of 46 tRNAs and 1 pseudo tRNA by Todd
    # Lowe.  See ~/kent/src/hg/lib/loweTrnaGene.as for a description of the fields.
    # **Showing the tRNAScanSE instructions would be nice in the future.  
    ssh hgwdev
    mkdir /cluster/data/metAce1/bed/loweTrnaGene
    cd /cluster/data/metAce1/bed/loweTrnaGene
    hgLoadBed -tab metAce1 loweTrnaGene metAce1-lowe-trnas.bed -sqlTable=~/kent/src/hg/lib/loweTrnaGene.sql

# TODD LOWE snoRNA GENES ()
    # This is a bed 6 file created by hand.
    ssh hgwdev
    mkdir /cluster/data/metAce1/bed/loweSnoGene
    cd /cluster/data/metAce1/bed/loweSnoGene
    hgLoadBed -tab metAce1 loweSnoGene metAce1-snos.bed

# TIGR GENES (DONE)
    # First go to http://www.tigr.org/tigr-scripts/CMR2/gene_attribute_form.dbi
    # and fill out the web form as follows:
    #   - Pick "Retrieve attributes for the specified DNA feature within a specific 
    #     organism and/or a specific role category".
    #       * Pick "Pyrobaculum aerophilum IM2", and "Primary and TIGR annotation ORFs" 
    #         from the 1st and 3rd box.
    #       * Select everything from "Choose TIGR Annotation Gene Attributes"
    #       * Select "Primary Locus Name" from "Choose Primary Annotation Gene Attributes"
    #       * Select everything from "Choose Other Gene Attributes"
    #   - Click submit, and click save as tab-delimited file.
    ssh hgwdev
    mkdir /cluster/data/metAce1/bed/tigrCmrORFs
    cp metAce1-tigr.tab /cluster/data/metAce1/bed/tigrCmrORFs
    cd /cluster/data/metAce1/bed/tigrCmrORFs
    /projects/lowelab/users/aamp/bin/i386/tigrCmrToBed metAce1-tigr.tab metAce1-tigr.bed
    hgLoadBed -tab metAce1 tigrCmrORFs metAce1-tigr.bed -sqlTable=~/kent/src/hg/lib/tigrCmrGene.sql

###########################################################
#mulitz pHMM conservation track for 3 Methosarcina species#
###########################################################
## DONE: 8/14/05 (baertsch)

cd /cluster/data/metAce1/bed
mkdir conservation
cd conservation
cp /cluster/data/pyrFur2/bed/conservation/HoxD55.q .

#get fastas
cp ../../chr.fa metAce1.chr
cp /projects/lowelab/db/blastdb/Meth_maze.fa metMaz1.fa
wget ftp://ftp.jgi-psf.org/pub/JGI_data/Microbial/methanosarcina/031109/2351479_fasta.screen.contigs
mv 2351479_fasta.screen.contigs metBak0.chr
ftp://ftp.jgi-psf.org/pub/JGI_data/Microbial/methanococcoides_burtonii/041112/2662199.fsa
mv 2662199.fsa metBur0.chr
#edit > lines to say metAce1.chr, metBak0.contigN, and metMaz1.chr

#make nibs and 2bits
/cluster/bin/i386/faToNib metAce1.chr metAce1.chr.nib
/cluster/bin/i386/faToNib metMaz1.chr metMaz1.chr.nib
/cluster/bin/i386/faToTwoBit metBak0.chr metBak0.2bit
/cluster/bin/i386/faToTwoBit metBur0.chr metBur0.2bit


#chrom sizes
faSize -detailed *.chr > chrom.sizes

#blastz
blastz metAce1.chr metBak0.chr Q=HoxD55.q > metAce1-metBak0.lav
blastz metAce1.chr metMaz1.chr Q=HoxD55.q > metAce1-metMaz1.lav
blastz metAce1.chr metBur0.chr Q=HoxD55.q > metAce1-metBur0.lav
/cluster/bin/i386/lavToAxt metAce1-metBak0.lav . metBak0.2bit metAce1-metBak0.axt
/cluster/bin/i386/lavToAxt metAce1-metMaz1.lav . . metAce1-metMaz1.axt
/cluster/bin/i386/lavToAxt metAce1-metBur0.lav . metBur0.2bit metAce1-metBur0.axt

axtBest metAce1-metBak0.axt metAce1.chr -winSize=500 -minScore=5000 metAce1-metBak0-best.axt
axtBest metAce1-metMaz1.axt metAce1.chr -winSize=500 -minScore=5000 metAce1-metMaz1-best.axt
axtBest metAce1-metBur0.axt metAce1.chr -winSize=500 -minScore=5000 metAce1-metBur0-best.axt
axtToMaf metAce1-metBak0-best.axt chrom.sizes chrom.sizes metAce1-metBak0.maf
axtToMaf metAce1-metMaz1-best.axt chrom.sizes chrom.sizes metAce1-metMaz1.maf
axtToMaf metAce1-metBur0-best.axt chrom.sizes chrom.sizes metAce1-metBur0.maf

#multiz: v10 has new parameter (3rd par), 0=2 seqs not align to ref, else 1.
# stick with v8 for now.
multiz metAce1-metBak0.maf metAce1-metMaz1.maf - > metAce1-metBak0-metMaz1.maf


#phyloHMM
/cluster/bin/phast/msa_view -i MAF -M metAce1.chr -o SS metAce1-metBak0-metMaz1.maf > metAce1.ss
/cluster/bin/phast/phyloFit -i SS metAce1.ss -t "(metAce1,(metBak0,metMaz1))" 
/cluster/bin/phast/msa_view -i SS metAce1.ss --summary-only
#descrip.                      A          C          G          T        G+C     length   all_gaps  some_gaps
#metAce1.ss               0.2892     0.2088     0.2089     0.2931     0.4177    6057454          0     580625
/cluster/bin/phast/phastCons metAce1.ss phyloFit.mod --gc 0.4177 \
 --target-coverage 0.5 --estimate-trees met-tree \
 --expected-lengths 7 --no-post-probs --ignore-missing \
 --nrates 1,1
/cluster/bin/phast/phastCons metAce1.ss \
 met-tree.cons.mod,met-tree.noncons.mod \
 --target-coverage 0.5 --expected-lengths 75 \
 --viterbi metAce-elements.bed --score \
 --require-informative 0 --seqname chr > cons.dat
wigEncode cons.dat phastCons.wig phastCons.wib

#phlyloHmmm new

multiz metAce1-metMaz1.maf metAce1-metBak0.maf - > metAce1-metMaz1-metBak0.maf
/cluster/bin/phast/msa_view -i MAF -M metAce1.chr -o SS metAce1-metMaz1-metBak0.maf > metAce1new.ss
/cluster/bin/phast/phyloFit -i SS metAce1new.ss -t "(metBak0,(metAce1,metMaz1))" -o Ma1Mz1Mb0
/cluster/bin/phast/msa_view -i SS metAce1new.ss --summary-only 
#descrip.                      A          C          G          T        G+C     length   all_gaps  some_gaps
#metAce1new.ss            0.2892     0.2088     0.2090     0.2930     0.4178    6057224          0     579124
/cluster/bin/phast/phastCons metAce1new.ss Ma1Mz1Mb0.mod --gc 0.4177 \
 --target-coverage 0.7 --estimate-trees met-tree2 \
 --expected-lengths 7 --no-post-probs --ignore-missing \
 --nrates 1,1
/cluster/bin/phast/phastCons metAce1new.ss \
 met-tree2.cons.mod,met-tree2.noncons.mod \
 --target-coverage 0.7 --expected-lengths 75 \
 --viterbi metAce-elements2.bed --score \
 --require-informative 0 --seqname chr > cons2.dat
wigEncode cons2.dat phastCons2.wig phastCons2.wib


#move data
mkdir wib
mv phastCons.wib wib/phastCons.wib
mv phastCons.wig wib/phastCons.wig
ln -s /cluster/data/metAce1/bed/conservation/wib/phastCons.wib /gbdb/metAce1/wib
mkdir /gbdb/metAce1/pwMaf
mkdir -p otherMet/metBak0 otherMet/metMaz1
mv metAce1-metBak0.maf otherMet/metBak0/chr.maf
mv metAce1-metMaz1.maf otherMet/metMaz1/chr.maf
ln -s /cluster/data/metAce1/bed/conservation/otherMet/metBak0 /gbdb/metAce1/pwMaf/metBak0_pwMaf
ln -s /cluster/data/metAce1/bed/conservation/otherMet/metMaz1 /gbdb/metAce1/pwMaf/metMaz1_pwMaf
mkdir multiz
mv metAce1-metBak0-metMaz1.maf multiz/chr.maf
ln -s /cluster/data/metAce1/bed/conservation/multiz /gbdb/metAce1/multizMa1Mb1Mz1

#load
hgLoadWiggle metAce1 phastCons /cluster/data/metAce1/bed/conservation/wib/phastCons.wig
hgLoadMaf -warn metAce1 multizMa1Mb1Mz1
hgLoadMaf -warn metAce1 metBak0_pwMaf -pathPrefix=/gbdb/metAce1/pwMaf/metBak0_pwMaf
hgLoadMaf -warn metAce1 metMaz1_pwMaf -pathPrefix=/gbdb/metAce1/pwMaf/metMaz1_pwMaf

#trackDb.ra entry
 # track multizMa1Mb1Mz1
 # shortLabel Conservation
 # longLabel Methosarcina  3-way multiz alignments
 # group compGeno
 # priority 10.0
 # visibility pack
 # type wigMaf 0.0 1.0
 # maxHeightPixels 100:40:11
 # wiggle phastCons
 # yLineOnOff Off
 # autoScale Off
 # pairwise pwMaf
 # speciesOrder metBak0 metMaz1
cd ~/kent/src/hg/makeDb/trackDb/archae/metAce1
cvs commit -m "Added multiz track" trackDb.ra

#html page for multizMa1Mb1Mz1
cd ~/kent/src/hg/makeDb/trackDb/archae/metAce1
cvs add multizMa1Mb1Mz1.html
cvs commit -m "Details page for multiz track" multizMa1Mb1Mz1.html

## 4 way
multiz metAce1-metBur0.maf metAce1-metMaz1-metBak0.maf - > metAce1-metMaz1-metBak0-metBur0.maf
/cluster/bin/phast/msa_view -i MAF -M metAce1.chr -o SS metAce1-metMaz1-metBak0-metBur0.maf > metAce4way.ss
/cluster/bin/phast/phyloFit -i SS metAce4way.ss -t "(metBur0,(metBak0,(metAce1,metMaz1)))" -o Ma1Mz1Mbk0Mbr0
/cluster/bin/phast/msa_view -i SS metAce4way.ss --summary-only 
#descrip.                      A          C          G          T        G+C     length   all_gaps  some_gaps
#metAce4way.ss            0.2887     0.2092     0.2094     0.2926     0.4186    6100179          0     710386
/cluster/bin/phast/phastCons metAce4way.ss Ma1Mz1Mbk0Mbr0.mod --gc 0.4186 \
 --target-coverage 0.7 --estimate-trees met-tree4 \
 --expected-lengths 7 --no-post-probs --ignore-missing \
 --nrates 1,1
/cluster/bin/phast/phastCons metAce4way.ss \
 met-tree4.cons.mod,met-tree4.noncons.mod \
 --target-coverage 0.7 --expected-lengths 75 \
 --viterbi metAce-elements2.bed --score \
 --require-informative 0 --seqname chr > cons4.dat
wigEncode cons4.dat phastCons4.wig phastCons4.wib

draw_tree Ma1Mz1Mbk0Mbr0.mod  > tree4.ps
ps2pdf tree4.ps tree4.pdf
#move data
mv phastCons4.wib wib/phastCons4.wib
mv phastCons4.wig wib/phastCons4.wig
ln -s /cluster/data/metAce1/bed/conservation/wib/phastCons4.wib /gbdb/metAce1/wib
mkdir -p otherMet/metBur0 
mv metAce1-metBur0.maf otherMet/metBur0/chr.maf
ln -s /cluster/data/metAce1/bed/conservation/otherMet/metBur0 /gbdb/metAce1/pwMaf/metBur0_pwMaf
mkdir multiz4way
mv metAce1-metMaz1-metBak0-metBur0.maf multiz4way/chr.maf
ln -s /cluster/data/metAce1/bed/conservation/multiz4way /gbdb/metAce1/multizMa1Mz1Mbk0Mbr0

#load
hgLoadWiggle metAce1 phastCons4 /cluster/data/metAce1/bed/conservation/wib/phastCons4.wig
hgLoadMaf -warn metAce1 multizMa1Mz1Mbk0Mbr0
hgLoadMaf -warn metAce1 metBur0_pwMaf -pathPrefix=/gbdb/metAce1/pwMaf/metBur0_pwMaf
   
#trackDb.ra entry
 # track multizMa1Mz1Mbk0Mbr0
 # shortLabel Cons 4way
 # longLabel Methosarcina Acetivorans/Mazei/Bakeri 3-way multiz alignments + Methanobacteriodes Burtonii
 # group compGeno
 # priority 10.0
 # visibility pack
 # type wigMaf 0.0 1.0
 # maxHeightPixels 100:40:11
 # wiggle phastCons
 # yLineOnOff Off
 # autoScale Off
 # pairwise pwMaf
 # speciesOrder metMaz1 metBak0 metBur0


## re-run with 25 expected length parameter
/cluster/bin/phast/phastCons metAce4way.ss Ma1Mz1Mbk0Mbr0.mod --gc 0.4186 \
 --target-coverage 0.7 --estimate-trees met-tree4.25 \
 --expected-lengths 25 --no-post-probs --ignore-missing \
 --nrates 1,1
/cluster/bin/phast/phastCons metAce4way.ss \
 met-tree4.25.cons.mod,met-tree4.25.noncons.25.mod \
 --target-coverage 0.7 --expected-lengths 25 \
 --viterbi metAce-elements.25.bed --score \
 --require-informative 0 --seqname chr > cons4.25.dat

wigEncode cons4.25.dat phastCons4.25.wig phastCons4.25.wib
mkdir wib
mv phastCons4.25.wib wib/phastCons4.25.wib
mv phastCons4.25.wig wib/phastCons4.25.wig
ln -s /cluster/data/metAce1/bed/conservation/wib/phastCons.wib /gbdb/metAce1/wib
hgLoadWiggle metAce1 phastCons4_25 /cluster/data/metAce1/bed/conservation/phastCons4.25.wig

# 3 states, 2 conserved , 1 nonconserved
nice /cluster/bin/phast/phastCons metAce4way.ss Ma1Mz1Mbk0Mbr0.mod --gc 0.4186 \
 --target-coverage 0.7 --estimate-trees met-tree4.25.3state  \
 --expected-lengths 25 --no-post-probs --ignore-missing  \
 --nrates 2,1 

/cluster/bin/phast/phastCons metAce4way.ss \
 met-tree4.25.cons1.mod,met-tree4.25.cons2.mod,met-tree4.25.3state.noncons.25.mod \
 --target-coverage 0.7 --expected-lengths 25 \
 --viterbi metAce-elements.3state.25.bed --score \
 --require-informative 0 --seqname chr > cons4.25.3state.dat

#FINISH UP MULTIZ TRACK (4way) 
# DONE (10/9/05), kpollard

    cd /cluster/data/metAce1/bed/conservation/
    #move data
    cp tree4.jpg /usr/local/apache/htdocs/images/metAce1-tree.jpg
    cd wib
    mv phastCons.wib phastCons3.wib
    mv phastCons.wig phastCons3.wig
    cp phastCons4.25.wib phastCons.wib
    cp phastCons4.25.wig phastCons.wig
    ln -s /cluster/data/metAce1/bed/conservation/wib/phastCons.wib /gbdb/metAce1/wib
    #drop tables so can reload with new data
    hgLoadWiggle metAce1 phastCons /cluster/data/metAce1/bed/conservation/wib/phastCons.wig
    hgLoadMaf -warn metAce1 multizMa1Mz1Mbk0Mbr0
    hgLoadMaf -warn metAce1 metBak0_pwMaf -pathPrefix=/gbdb/metAce1/pwMaf/metBak0_pwMaf
    hgLoadMaf -warn metAce1 metBur0_pwMaf -pathPrefix=/gbdb/metAce1/pwMaf/metBur0_pwMaf
    hgLoadMaf -warn metAce1 metMaz1_pwMaf -pathPrefix=/gbdb/metAce1/pwMaf/metMaz1_pwMaf
    hgLoadBed metAce1 phastConsElements metAce-elements.25.bed 
    #trackDb
    cd ~/kent/src/hg/makeDb/trackDb/archae/metAce1
    #trackDb.ra entry
    # track multizMa1Mz1Mbk0Mbr0
    # shortLabel Cons 4way
    # longLabel Methosarcina 4-way multiz alignments
    # group compGeno
    # priority 10.0
    # visibility pack
    # type wigMaf 0.0 1.0
    # maxHeightPixels 100:40:11
    # wiggle phastCons
    # yLineOnOff Off
    # autoScale Off
    # pairwise pwMaf
    # speciesOrder metMaz1 metBak0 metBur0
    cvs commit -m "New multiz track" trackDb.ra
    #html page
    mv multizMa1Mb1Mz1.html multizMa1Mz1Mbk0Mbr0.html
    cvs remove multizMa1Mb1Mz1.html
    cvs add multizMa1Mz1Mbk0Mbr0.html
    cvs commit -m "Details page for multiz track" multizMa1Mz1Mbk0Mbr0.html