Remove additional pieces from old genome index system.

buildbot_setup.sh

@@ -52,12 +52,9 @@ shed_tool_data_table_conf.xml.sample
 migrated_tools_conf.xml.sample
 data_manager_conf.xml.sample
 shed_data_manager_conf.xml.sample
-tool-data/shared/ensembl/builds.txt.sample
 tool-data/shared/igv/igv_build_sites.txt.sample
-tool-data/shared/ncbi/builds.txt.sample
 tool-data/shared/rviewer/rviewer_build_sites.txt.sample
 tool-data/shared/ucsc/builds.txt.sample
-tool-data/shared/ucsc/publicbuilds.txt.sample
 tool-data/shared/ucsc/ucsc_build_sites.txt.sample
 "
 

cron/get_ensembl.py

@@ -1,23 +0,0 @@
-from galaxy import eggs
-import pkg_resources
-pkg_resources.require("SQLAlchemy >= 0.4")
-pkg_resources.require("MySQL_python")
-from sqlalchemy import *
-
-
-engine = create_engine( 'mysql://anonymous@ensembldb.ensembl.org:5306', pool_recycle=3600 )
-conn = engine.connect()
-dbs = conn.execute( "SHOW DATABASES LIKE 'ensembl_website_%%'" )
-builds = {}
-lines = []
-for res in dbs:
-    dbname = res[0]
-    release = dbname.split('_')[-1]
-    genomes = conn.execute( "SELECT RS.assembly_code, S.name, S.common_name, %s FROM ensembl_website_%s.release_species RS LEFT JOIN ensembl_website_%s.species S on RS.species_id = S.species_id" % ( release, release, release ) )
-    for genome in genomes:
-        builds[genome[0]] = dict( release=genome[3], species='%s (%s/%s)' % ( genome[1], genome[2], genome[0] ) )
-for build in builds.items():
-    if build[0]:
-        lines.append( '\t'.join( [ build[0], '%d' % build[1]['release'], build[1]['species'] ] ) )
-    
-print '\n'.join( lines )

cron/get_ncbi.py

@@ -1,93 +0,0 @@
-import urllib, pkg_resources, os
-pkg_resources.require( 'elementtree' )
-from elementtree import ElementTree, ElementInclude
-from xml.parsers.expat import ExpatError as XMLParseErrorThing
-import sys
-
-import pkg_resources
-
-class GetListing:
-    def __init__( self, data ):
-        self.tree = ElementTree.parse( data )
-        self.root = self.tree.getroot()
-        ElementInclude.include(self.root)
-        
-    def xml_text(self, name=None):
-        """Returns the text inside an element"""
-        root = self.root
-        if name is not None:
-            # Try attribute first
-            val = root.get(name)
-            if val:
-                return val
-            # Then try as element
-            elem = root.find(name)
-        else:
-            elem = root
-        if elem is not None and elem.text:
-            text = ''.join(elem.text.splitlines())
-            return text.strip()
-        # No luck, return empty string
-        return ''
-
-def dlcachefile( webenv, querykey, i, results ):
-    url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehistory=y&term=nuccore_assembly[filter]%20AND%20refseq[filter]'
-    fp = urllib.urlopen( url )
-    search = GetListing( fp )
-    fp.close()
-    webenv = search.xml_text( 'WebEnv' )
-    querykey = search.xml_text( 'QueryKey' )
-    url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=nuccore&WebEnv=%s&query_key=%s&retstart=%d&retmax=%d' % ( webenv, querykey, i, results )
-    fp = urllib.urlopen( url )
-    cachefile = os.tmpfile()
-    for line in fp:
-        cachefile.write( line )
-    fp.close()
-    cachefile.flush()
-    cachefile.seek(0)
-    return cachefile
-    
-
-url = 'http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&usehistory=y&term=nuccore_assembly[filter]%20AND%20refseq[filter]'
-fp = urllib.urlopen( url )
-results = GetListing( fp )
-fp.close()
-
-webenv = results.xml_text( 'WebEnv' )
-querykey = results.xml_text( 'QueryKey' )
-counts = int( results.xml_text( 'Count' ) )
-results = 10000
-found = 0
-
-for i in range(0, counts + results, results):
-    rets = dict()
-    cache = dlcachefile( webenv, querykey, i, results )
-    try:
-        xmldoc = GetListing( cache )
-    except (IOError, XMLParseErrorThing):
-        cache = dlcachefile( webenv, querykey, i, results )
-        try:
-            xmldoc = GetListing( cache )
-        except (IOError, XMLParseErrorThing):
-            cache.close()
-            exit()
-        pass
-    finally:
-        cache.close()
-    entries = xmldoc.root.findall( 'DocSum' )
-    for entry in entries:
-        dbkey = None
-        children = entry.findall('Item')
-        for item in children:
-            rets[ item.get('Name') ] = item.text
-        if not rets['Caption'].startswith('NC_'):
-            continue
-            
-        for ret in rets['Extra'].split('|'):
-            if not ret.startswith('NC_'):
-                continue
-            else:
-                dbkey = ret
-                break
-        if dbkey is not None:
-            print '\t'.join( [ dbkey, rets['Title'] ] )

cron/parse_publicbuilds.py

@@ -1,57 +0,0 @@
-#!/usr/bin/env python
-
-"""
-Connects to the URL specified and outputs builds available at that
-DSN in tabular format.  USCS Test gateway is used as default.
-build   description
-"""
-
-import sys
-import urllib
-if sys.version_info[:2] >= ( 2, 5 ):
-    import xml.etree.ElementTree as ElementTree
-else:
-    from galaxy import eggs
-    import pkg_resources; pkg_resources.require( "elementtree" )
-    from elementtree import ElementTree
-
-URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
-
-def getbuilds(url):
-    try:
-        page = urllib.urlopen(URL)
-    except:
-        print "#Unable to open " + URL
-        print "?\tunspecified (?)"
-        sys.exit(1)
-
-    text = page.read()
-    try:
-        tree = ElementTree.fromstring(text)
-    except:
-        print "#Invalid xml passed back from " + URL
-        print "?\tunspecified (?)"
-        sys.exit(1)
-
-    print "#Harvested from http://genome.cse.ucsc.edu/cgi-bin/das/dsn"
-    print "?\tunspecified (?)"
-    for dsn in tree:
-        build = dsn.find("SOURCE").attrib['id']
-        description = dsn.find("DESCRIPTION").text.replace(" - Genome at UCSC","").replace(" Genome at UCSC","")
-        
-        fields = description.split(" ")
-        temp = fields[0]
-        for i in range(len(fields)-1):
-            if temp == fields[i+1]:
-                fields.pop(i+1)
-            else:
-                temp = fields[i+1]
-        description = " ".join(fields)
-        yield [build,description]
-
-if __name__ == "__main__":
-    if len(sys.argv) > 1:
-        URL = sys.argv[1]
-    for build in getbuilds(URL):
-        print build[0]+"\t"+build[1]+" ("+build[0]+")"
-

cron/updateensembl.sh.sample

@@ -1,42 +0,0 @@
-#!/bin/sh 
-#
-# Script to update Ensembl shared data tables.  The idea is to update, but if
-# the update fails, not replace current data/tables with error
-# messages.
-
-# Edit this line to refer to galaxy's path:
-GALAXY=/path/to/galaxy
-PYTHONPATH=${GALAXY}/lib
-export PYTHONPATH
-
-# setup directories
-echo "Creating required directories."
-DIRS="
-${GALAXY}/tool-data/shared/ensembl
-${GALAXY}/tool-data/shared/ensembl/new
-"
-for dir in $DIRS; do
-    if [ ! -d $dir ]; then
-        echo "Creating $dir"
-        mkdir $dir
-    else
-        echo "$dir already exists, continuing."
-    fi
-done
-
-date
-echo "Updating Ensembl shared data tables."
-
-# Try to build "builds.txt"
-echo "Updating builds.txt"
-python ${GALAXY}/cron/get_ensembl.py > ${GALAXY}/tool-data/shared/ensembl/new/builds.txt
-if [ $? -eq 0 ]
-then
-    diff ${GALAXY}/tool-data/shared/ensembl/new/builds.txt ${GALAXY}/tool-data/shared/ensembl/builds.txt > /dev/null 2>&1
-    if [ $? -ne 0 ]
-    then
-        cp -f ${GALAXY}/tool-data/shared/ensembl/new/builds.txt ${GALAXY}/tool-data/shared/ensembl/builds.txt
-    fi
-else
-    echo "Failed to update builds.txt" >&2
-fi

cron/updatencbi.sh.sample

@@ -1,42 +0,0 @@
-#!/bin/sh 
-#
-# Script to update NCBI shared data tables.  The idea is to update, but if
-# the update fails, not replace current data/tables with error
-# messages.
-
-# Edit this line to refer to galaxy's path:
-GALAXY=/path/to/galaxy
-PYTHONPATH=${GALAXY}/lib
-export PYTHONPATH
-
-# setup directories
-echo "Creating required directories."
-DIRS="
-${GALAXY}/tool-data/shared/ncbi
-${GALAXY}/tool-data/shared/ncbi/new
-"
-for dir in $DIRS; do
-    if [ ! -d $dir ]; then
-        echo "Creating $dir"
-        mkdir $dir
-    else
-        echo "$dir already exists, continuing."
-    fi
-done
-
-date
-echo "Updating NCBI shared data tables."
-
-# Try to build "builds.txt"
-echo "Updating builds.txt"
-python ${GALAXY}/cron/get_ncbi.py > ${GALAXY}/tool-data/shared/ncbi/new/builds.txt
-if [ $? -eq 0 ]
-then
-    diff ${GALAXY}/tool-data/shared/ncbi/new/builds.txt ${GALAXY}/tool-data/shared/ncbi/builds.txt > /dev/null 2>&1
-    if [ $? -ne 0 ]
-    then
-        cp -f ${GALAXY}/tool-data/shared/ncbi/new/builds.txt ${GALAXY}/tool-data/shared/ncbi/builds.txt
-    fi
-else
-    echo "Failed to update builds.txt" >&2
-fi

cron/updateucsc.sh.sample

@@ -28,20 +28,6 @@ done
 date
 echo "Updating UCSC shared data tables."
 
-# Try to build "publicbuilds.txt"
-echo "Updating publicbuilds.txt"
-python ${GALAXY}/cron/parse_publicbuilds.py > ${GALAXY}/tool-data/shared/ucsc/new/publicbuilds.txt
-if [ $? -eq 0 ]
-then
-    diff ${GALAXY}/tool-data/shared/ucsc/new/publicbuilds.txt ${GALAXY}/tool-data/shared/ucsc/publicbuilds.txt > /dev/null 2>&1
-    if [ $? -ne 0 ]
-    then
-        cp -f ${GALAXY}/tool-data/shared/ucsc/new/publicbuilds.txt ${GALAXY}/tool-data/shared/ucsc/publicbuilds.txt
-    fi
-else
-    echo "Failed to update publicbuilds.txt" >&2
-fi
-
 # Try to build "builds.txt"
 echo "Updating builds.txt"
 python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt

doc/Makefile

@@ -17,22 +17,9 @@ ALLSPHINXOPTS   = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) sou
 # the i18n builder cannot share the environment and doctrees with the others
 I18NSPHINXOPTS  = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source
 
-# Galaxy Local variables
-
-TOOLDATASHAREDDIR  = ../tool-data/shared
-TOOLDATABUILDFILES = $(TOOLDATASHAREDDIR)/ensembl/builds.txt \
-                     $(TOOLDATASHAREDDIR)/ncbi/builds.txt \
-                     $(TOOLDATASHAREDDIR)/ucsc/publicbuilds.txt
-
 .PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext updaterst
 
 
-# Sphinx wants the build files to be there;  Copy the sample files into
-# place if we don't already have the build files.
-$(TOOLDATABUILDFILES) : 
-	/bin/cp $@.sample $@
-
-
 help:
 	@echo "Please use \`make <target>' where <target> is one of"
 	@echo "  html       to make standalone HTML files"

lib/galaxy/util/__init__.py

@@ -842,39 +842,6 @@ def read_dbnames(filename):
     return db_names
 
 
-def read_ensembl( filename, ucsc ):
-    """ Read Ensembl build names from file """
-    ucsc_builds = []
-    for build in ucsc:
-        ucsc_builds.append( build[0] )
-    ensembl_builds = list()
-    try:
-        for line in open( filename ):
-            if line[0:1] in [ '#', '\t' ]:
-                continue
-            fields = line.replace("\r", "").replace("\n", "").split("\t")
-            if fields[0] in ucsc_builds:
-                continue
-            ensembl_builds.append( dict( dbkey=fields[0], release=fields[1], name=fields[2].replace( '_', ' ' ) ) )
-    except Exception, e:
-        print "ERROR: Unable to read builds file:", e
-    return ensembl_builds
-
-
-def read_ncbi( filename ):
-    """ Read NCBI build names from file """
-    ncbi_builds = list()
-    try:
-        for line in open( filename ):
-            if line[0:1] in [ '#', '\t' ]:
-                continue
-            fields = line.replace("\r", "").replace("\n", "").split("\t")
-            ncbi_builds.append( dict( dbkey=fields[0], name=fields[1] ) )
-    except Exception, e:
-        print "ERROR: Unable to read builds file:", e
-    return ncbi_builds
-
-
 def read_build_sites( filename, check_builds=True ):
     """ read db names to ucsc mappings from file, this file should probably be merged with the one above """
     build_sites = []
@@ -1161,12 +1128,8 @@ galaxy_root_path = os.path.join(__path__[0], "..", "..", "..")
 
 # The dbnames list is used in edit attributes and the upload tool
 dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) )
-ucsc_names = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "publicbuilds.txt" ) )
-ensembl_names = read_ensembl( os.path.join( galaxy_root_path, "tool-data", "shared", "ensembl", "builds.txt" ), ucsc_names )
-ncbi_names = read_ncbi( os.path.join( galaxy_root_path, "tool-data", "shared", "ncbi", "builds.txt" ) )
 ucsc_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "ucsc_build_sites.txt" ) )
 gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) )
-dlnames = dict(ucsc=ucsc_names, ensembl=ensembl_names, ncbi=ncbi_names)
 
 
 def galaxy_directory():

lib/galaxy/web/framework/__init__.py

@@ -1259,18 +1259,6 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ):
         # FIXME: This method should be removed
         return self.app.genome_builds.get_genome_build_names( trans=self )
 
-    @property
-    def ucsc_builds( self ):
-        return util.dlnames['ucsc']
-
-    @property
-    def ensembl_builds( self ):
-        return util.dlnames['ensembl']
-
-    @property
-    def ncbi_builds( self ):
-        return util.dlnames['ncbi']
-
     @property
     def user_ftp_dir( self ):
         identifier = self.app.config.ftp_upload_dir_identifier

scripts/common_startup.sh

@@ -26,10 +26,7 @@ SAMPLES="
     job_metrics_conf.xml.sample
     universe_wsgi.ini.sample
     lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml.sample
-    tool-data/shared/ncbi/builds.txt.sample
-    tool-data/shared/ensembl/builds.txt.sample
     tool-data/shared/ucsc/builds.txt.sample
-    tool-data/shared/ucsc/publicbuilds.txt.sample
     tool-data/shared/ucsc/ucsc_build_sites.txt.sample
     tool-data/shared/igv/igv_build_sites.txt.sample
     tool-data/shared/rviewer/rviewer_build_sites.txt.sample

tool-data/shared/ensembl/builds.txt.sample

@@ -1,164 +0,0 @@
-MEDAKA1	67	Oryzias_latipes (Medaka/MEDAKA1)
-Myoluc2.0	67	Myotis_lucifugus (Microbat/Myoluc2.0)
-anoCar1	67	Anolis_carolinensis (Anole lizard/anoCar1)
-WS220	67	Caenorhabditis_elegans (C.elegans/WS220)
-WS180	67	Caenorhabditis_elegans (C.elegans/WS180)
-MICROBAT1	67	Myotis_lucifugus (Microbat/MICROBAT1)
-loxAfr3	67	Loxodonta_africana (Elephant/loxAfr3)
-AgamP3	67	Anopheles_gambiae (Mosquito/AgamP3)
-DROM3	67	Drosophila_melanogaster (Fly/DROM3)
-LatCha1	67	Latimeria_chalumnae (Coelacanth/LatCha1)
-vicPac1	67	Vicugna_pacos (Alpaca/vicPac1)
-COMMON_SHREW1	67	Sorex_araneus (Shrew/COMMON_SHREW1)
-MGSC3	67	Mus_musculus (Mouse/MGSC3)
-MGSC1	67	Mus_musculus (Mouse/MGSC1)
-JGI4.1	67	Xenopus_tropicalis (Xenopus/JGI4.1)
-RGSC1	67	Rattus_norvegicus (Rat/RGSC1)
-RGSC2	67	Rattus_norvegicus (Rat/RGSC2)
-gadMor1	67	Gadus_morhua (Atlantic cod/gadMor1)
-CSAV2.0	67	Ciona_savignyi (C.savignyi/CSAV2.0)
-oryCun2	67	Oryctolagus_cuniculus (Rabbit/oryCun2)
-ZFISH6	67	Danio_rerio (Zebrafish/ZFISH6)
-ZFISH7	67	Danio_rerio (Zebrafish/ZFISH7)
-ZFISH4	67	Danio_rerio (Zebrafish/ZFISH4)
-ZFISH5	67	Danio_rerio (Zebrafish/ZFISH5)
-ZFISH2	67	Danio_rerio (Zebrafish/ZFISH2)
-ZFISH3	67	Danio_rerio (Zebrafish/ZFISH3)
-MOZ2a	67	Anopheles_gambiae (Mosquito/MOZ2a)
-EquCab2	67	Equus_caballus (Horse/EquCab2)
-AMEL1.1	67	Apis_mellifera (Honeybee/AMEL1.1)
-MMUL_1	67	Macaca_mulatta (Macaque/MMUL_1)
-dasNov2	67	Dasypus_novemcinctus (Armadillo/dasNov2)
-choHof1	67	Choloepus_hoffmanni (Sloth/choHof1)
-lamPac1	50	Lama_pacos (Alpaca/lamPac1)
-OANA5	67	Ornithorhynchus_anatinus (Platypus/OANA5)
-CEL160	67	Caenorhabditis_elegans (C.elegans/CEL160)
-WBcel215	67	Caenorhabditis_elegans (C.elegans/WBcel215)
-gorGor3	67	Gorilla_gorilla (Gorilla/gorGor3)
-SQUIRREL	67	Spermophilus_tridecemlineatus (Ground Squirrel/SQUIRREL)
-gorGor1	67	Gorilla_gorilla (Gorilla/gorGor1)
-pteVam1	67	Pteropus_vampyrus (Flying fox/pteVam1)
-SGD1	67	Saccharomyces_cerevisiae (S.cerevisiae/SGD1)
-micMur1	67	Microcebus_murinus (Mouse lemur/micMur1)
-proCap1	67	Procavia_capensis (Rock hyrax/proCap1)
-NCBIM30	67	Mus_musculus (Mouse/NCBIM30)
-NCBIM33	67	Mus_musculus (Mouse/NCBIM33)
-NCBIM32	67	Mus_musculus (Mouse/NCBIM32)
-NCBIM35	67	Mus_musculus (Mouse/NCBIM35)
-AaegL1	67	Aedes_aegypti (A.aegypti/AaegL1)
-NCBIM37	67	Mus_musculus (Mouse/NCBIM37)
-NCBIM36	67	Mus_musculus (Mouse/NCBIM36)
-EF2	67	Saccharomyces_cerevisiae (S.cerevisiae/EF2)
-EF3	67	Saccharomyces_cerevisiae (S.cerevisiae/EF3)
-EF4	67	Saccharomyces_cerevisiae (S.cerevisiae/EF4)
-BDGP5.4	67	Drosophila_melanogaster (Fly/BDGP5.4)
-PPYG2	67	Pongo_abelii (Orangutan/PPYG2)
-CEL150	67	Caenorhabditis_elegans (C.elegans/CEL150)
-AMEL2.0	67	Apis_mellifera (Honeybee/AMEL2.0)
-WASHUC1	67	Gallus_gallus (Chicken/WASHUC1)
-WASHUC2	67	Gallus_gallus (Chicken/WASHUC2)
-Btau_3.1	67	Bos_taurus (Cow/Btau_3.1)
-gorGor3.1	67	Gorilla_gorilla (Gorilla/gorGor3.1)
-CEL130	67	Caenorhabditis_elegans (C.elegans/CEL130)
-Zv9	67	Danio_rerio (Zebrafish/Zv9)
-BROADS1	67	Gasterosteus_aculeatus (Stickleback/BROADS1)
-BROADD2	67	Canis_familiaris (Dog/BROADD2)
-BROADD1	67	Canis_familiaris (Dog/BROADD1)
-pika	67	Ochotona_princeps (Pika/pika)
-ZFISH08	67	Danio_rerio (Zebrafish/ZFISH08)
-ZFISH06	67	Danio_rerio (Zebrafish/ZFISH06)
-calJac3	67	Callithrix_jacchus (Marmoset/calJac3)
-CHIMP2.1.4	67	Pan_troglodytes (Chimp/CHIMP2.1.4)
-JGI2	67	Ciona_intestinalis (C.intestinalis/JGI2)
-JGI3	67	Xenopus_tropicalis (Xenopus/JGI3)
-UCSC	67	Homo_sapiens (Human/UCSC)
-Zv8	67	Danio_rerio (Zebrafish/Zv8)
-JGI4	67	Xenopus_tropicalis (Xenopus/JGI4)
-CEL140	67	Caenorhabditis_elegans (C.elegans/CEL140)
-HEDGEHOG	67	Erinaceus_europaeus (Hedgehog/HEDGEHOG)
-callJacc3	67	Callithrix_jacchus (Marmoset/callJacc3)
-WS210	67	Caenorhabditis_elegans (C.elegans/WS210)
-BDGP4	67	Drosophila_melanogaster (Fly/BDGP4)
-BDGP5	67	Drosophila_melanogaster (Fly/BDGP5)
-CHIMP1	67	Pan_troglodytes (Chimp/CHIMP1)
-OtoGar3	67	Otolemur_garnettii (Bushbaby/OtoGar3)
-MOZ2	67	Anopheles_gambiae (Mosquito/MOZ2)
-FUGU4	67	Takifugu_rubripes (Fugu/FUGU4)
-MOZ1	67	Anopheles_gambiae (Mosquito/MOZ1)
-GUINEAPIG	67	Cavia_porcellus (Guinea Pig/GUINEAPIG)
-BROADE1	67	Loxodonta_africana (Elephant/BROADE1)
-RABBIT	67	Oryctolagus_cuniculus (Rabbit/RABBIT)
-TETRAODON7	67	Tetraodon_nigroviridis (Tetraodon/TETRAODON7)
-TETRAODON8	67	Tetraodon_nigroviridis (Tetraodon/TETRAODON8)
-gorGor2	67	Gorilla_gorilla (Gorilla/gorGor2)
-SGD1.01	67	Saccharomyces_cerevisiae (S.cerevisiae/SGD1.01)
-ailMel1	67	Ailuropoda_melanoleuca (Panda/ailMel1)
-Sscrofa9	67	Sus_scrofa (Pig/Sscrofa9)
-cavPor3	67	Cavia_porcellus (Guinea Pig/cavPor3)
-Orenil1.0	67	Oreochromis_niloticus (Nile tilapia/Orenil1.0)
-BDGP4.2	67	Drosophila_melanogaster (Fly/BDGP4.2)
-BDGP4.3	67	Drosophila_melanogaster (Fly/BDGP4.3)
-Petromyzon_marin	64	Petromyzon_marinus (Lamprey/Petromyzon_marin)
-RGSC3.4	67	Rattus_norvegicus (Rat/RGSC3.4)
-Pmarinus_7.0	67	Petromyzon_marinus (Lamprey/Pmarinus_7.0)
-RGSC3.1	67	Rattus_norvegicus (Rat/RGSC3.1)
-BDGP5.25	67	Drosophila_melanogaster (Fly/BDGP5.25)
-ARMA	67	Dasypus_novemcinctus (Armadillo/ARMA)
-CINT1.95	67	Ciona_intestinalis (C.intestinalis/CINT1.95)
-Btau_1.0	67	Bos_taurus (Cow/Btau_1.0)
-JGI_4.2	67	Xenopus_tropicalis (Xenopus/JGI_4.2)
-CEL116	67	Caenorhabditis_elegans (C.elegans/CEL116)
-BUSHBABY1	67	Otolemur_garnettii (Bushbaby/BUSHBABY1)
-Sscrofa10.2	67	Sus_scrofa (Pig/Sscrofa10.2)
-BDGP3.2.1	67	Drosophila_melanogaster (Fly/BDGP3.2.1)
-taeGut3.2.4	67	Taeniopygia_guttata (Zebra finch/taeGut3.2.4)
-KH	67	Ciona_intestinalis (C.intestinalis/KH)
-JGI4_1	67	Xenopus_tropicalis (Xenopus/JGI4_1)
-spetri2	67	Spermophilus_tridecemlineatus (Ground Squirrel/spetri2)
-Btau_4.0	67	Bos_taurus (Cow/Btau_4.0)
-UMD2	67	Meleagris_gallopavo (Turkey/UMD2)
-NCBI28	67	Homo_sapiens (Human/NCBI28)
-NCBI29	67	Homo_sapiens (Human/NCBI29)
-Btau_2.0	67	Bos_taurus (Cow/Btau_2.0)
-NCBI26	67	Homo_sapiens (Human/NCBI26)
-CAT	67	Felis_catus (Cat/CAT)
-TENREC	67	Echinops_telfairi (Tenrec/TENREC)
-WS200	67	Caenorhabditis_elegans (C.elegans/WS200)
-AnoCar1.0	67	Anolis_carolinensis (Anole lizard/AnoCar1.0)
-Nleu1.0	67	Nomascus_leucogenys (Gibbon/Nleu1.0)
-Meug_1.0	67	Macropus_eugenii (Wallaby/Meug_1.0)
-C_jacchus3.2.1	67	Callithrix_jacchus (Marmoset/C_jacchus3.2.1)
-CHIMP2.1	67	Pan_troglodytes (Chimp/CHIMP2.1)
-WS190	67	Caenorhabditis_elegans (C.elegans/WS190)
-dipOrd1	67	Dipodomys_ordii (Kangaroo rat/dipOrd1)
-AnoCar2.0	67	Anolis_carolinensis (Anole lizard/AnoCar2.0)
-ACME0.1	67	None (None/ACME0.1)
-CEL95	67	Caenorhabditis_elegans (C.elegans/CEL95)
-CEL93	67	Caenorhabditis_elegans (C.elegans/CEL93)
-DEVIL7.0	67	Sarcophilus_harrisii (Tasmanian Devil/DEVIL7.0)
-CEL98	67	Caenorhabditis_elegans (C.elegans/CEL98)
-CEL102	67	Caenorhabditis_elegans (C.elegans/CEL102)
-TREESHREW	67	Tupaia_belangeri (Tree Shrew/TREESHREW)
-NCBI31	67	Homo_sapiens (Human/NCBI31)
-NCBI30	67	Homo_sapiens (Human/NCBI30)
-NCBI33	67	Homo_sapiens (Human/NCBI33)
-NCBI35	67	Homo_sapiens (Human/NCBI35)
-NCBI34	67	Homo_sapiens (Human/NCBI34)
-turTru1	67	Tursiops_truncatus (Bottlenose dolphin/turTru1)
-NCBI36	67	Homo_sapiens (Human/NCBI36)
-UMD3.1	67	Bos_taurus (Cow/UMD3.1)
-speTri1	67	Spermophilus_tridecemlineatus (Ground Squirrel/speTri1)
-GRCh37	67	Homo_sapiens (Human/GRCh37)
-CHIMP1A	67	Pan_troglodytes (Chimp/CHIMP1A)
-WB170	67	Caenorhabditis_elegans (C.elegans/WB170)
-FUGU1	67	Takifugu_rubripes (Fugu/FUGU1)
-FUGU2	67	Takifugu_rubripes (Fugu/FUGU2)
-NCBIM34	67	Mus_musculus (Mouse/NCBIM34)
-DROM3A	67	Drosophila_melanogaster (Fly/DROM3A)
-tarSyr1	67	Tarsius_syrichta (Tarsier/tarSyr1)
-CBR25	67	Caenorhabditis_briggsae (C.briggsae/CBR25)
-BROADO5	67	Monodelphis_domestica (Opossum/BROADO5)
-BROADO2	67	Monodelphis_domestica (Opossum/BROADO2)
-BROADO3	67	Monodelphis_domestica (Opossum/BROADO3)
-BDGP5.13	67	Drosophila_melanogaster (Fly/BDGP5.13)
-MMUL_0_1	67	Macaca_mulatta (Macaque/MMUL_0_1)

tool-data/shared/ucsc/publicbuilds.txt.sample

@@ -1,96 +0,0 @@
-#Harvested from http://genome.cse.ucsc.edu/cgi-bin/das/dsn
-?	unspecified (?)
-hg19	Human Feb. 2009 (GRCh37/hg19) (hg19)
-hg18	Human Mar. 2006 (NCBI36/hg18) (hg18)
-hg17	Human May 2004 (NCBI35/hg17) (hg17)
-panTro3	Chimp Oct. 2010 (CGSC 2.1.3/panTro3) (panTro3)
-panTro2	Chimp Mar. 2006 (CGSC 2.1/panTro2) (panTro2)
-gorGor3	Gorilla May 2011 (gorGor3.1/gorGor3) (gorGor3)
-ponAbe2	Orangutan July 2007 (WUGSC 2.0.2/ponAbe2) (ponAbe2)
-nomLeu1	Gibbon Jan. 2010 (GGSC Nleu1.0/nomLeu1) (nomLeu1)
-rheMac2	Rhesus Jan. 2006 (MGSC Merged 1.0/rheMac2) (rheMac2)
-calJac3	Marmoset March 2009 (WUGSC 3.2/calJac3) (calJac3)
-calJac1	Marmoset June 2007 (WUGSC 2.0.2/calJac1) (calJac1)
-mm10	Mouse Dec. 2011 (GRCm38/mm10) (mm10)
-mm9	Mouse July 2007 (NCBI37/mm9) (mm9)
-mm8	Mouse Feb. 2006 (NCBI36/mm8) (mm8)
-rn5	Rat Mar. 2012 (RGSC 5.0/rn5) (rn5)
-rn4	Rat Nov. 2004 (Baylor 3.4/rn4) (rn4)
-hetGla1	Naked mole-rat Jul. 2011 (BGI HetGla_1.0/hetGla1) (hetGla1)
-cavPor3	Guinea pig Feb. 2008 (Broad/cavPor3) (cavPor3)
-oryCun2	Rabbit Apr. 2009 (Broad/oryCun2) (oryCun2)
-susScr2	Pig Nov. 2009 (SGSC Sscrofa9.2/susScr2) (susScr2)
-oviAri1	Sheep Feb. 2010 (ISGC Ovis_aries_1.0/oviAri1) (oviAri1)
-bosTau7	Cow Oct. 2011 (Baylor Btau_4.6.1/bosTau7) (bosTau7)
-bosTau6	Cow Nov. 2009 (Bos_taurus_UMD_3.1/bosTau6) (bosTau6)
-bosTau4	Cow Oct. 2007 (Baylor 4.0/bosTau4) (bosTau4)
-equCab2	Horse Sep. 2007 (Broad/equCab2) (equCab2)
-equCab1	Horse Jan. 2007 (Broad/equCab1) (equCab1)
-felCat4	Cat Dec. 2008 (NHGRI/GTB V17e/felCat4) (felCat4)
-felCat3	Cat Mar. 2006 (Broad/felCat3) (felCat3)
-canFam3	Dog Sep. 2011 (Broad CanFam3.1/canFam3) (canFam3)
-canFam2	Dog May 2005 (Broad/canFam2) (canFam2)
-ailMel1	Panda Dec. 2009 (BGI-Shenzhen 1.0/ailMel1) (ailMel1)
-myoLuc2	Microbat Jul. 2010 (Broad Institute Myoluc2.0/myoLuc2) (myoLuc2)
-loxAfr3	Elephant Jul. 2009 (Broad/loxAfr3) (loxAfr3)
-monDom5	Opossum Oct. 2006 (Broad/monDom5) (monDom5)
-monDom4	Opossum Jan. 2006 (Broad/monDom4) (monDom4)
-macEug2	Wallaby Sep. 2009 (TWGS Meug_1.1/macEug2) (macEug2)
-ornAna1	Platypus Mar. 2007 (WUGSC 5.0.1/ornAna1) (ornAna1)
-galGal4	Chicken Nov. 2011 (ICGSC Gallus_gallus-4.0/galGal4) (galGal4)
-galGal3	Chicken May 2006 (WUGSC 2.1/galGal3) (galGal3)
-melGal1	Turkey Dec. 2009 (TGC Turkey_2.01/melGal1) (melGal1)
-taeGut1	Zebra finch Jul. 2008 (WUGSC 3.2.4/taeGut1) (taeGut1)
-anoCar2	Lizard May 2010 (Broad AnoCar2.0/anoCar2) (anoCar2)
-anoCar1	Lizard Feb. 2007 (Broad/anoCar1) (anoCar1)
-chrPic1	Painted turtle Dec. 2011 (v3.0.1/chrPic1) (chrPic1)
-xenTro3	X. tropicalis Nov. 2009 (JGI 4.2/xenTro3) (xenTro3)
-xenTro2	X. tropicalis Aug. 2005 (JGI 4.1/xenTro2) (xenTro2)
-danRer7	Zebrafish Jul. 2010 (Zv9/danRer7) (danRer7)
-danRer6	Zebrafish Dec. 2008 (Zv8/danRer6) (danRer6)
-tetNig2	Tetraodon Mar. 2007 (Genoscope 8.0/tetNig2) (tetNig2)
-tetNig1	Tetraodon Feb. 2004 (Genoscope 7/tetNig1) (tetNig1)
-fr3	Fugu Oct. 2011 (FUGU5/fr3) (fr3)
-fr2	Fugu Oct. 2004 (JGI 4.0/fr2) (fr2)
-gasAcu1	Stickleback Feb. 2006 (Broad/gasAcu1) (gasAcu1)
-oryLat2	Medaka Oct. 2005 (NIG/UT MEDAKA1/oryLat2) (oryLat2)
-petMar1	Lamprey Mar. 2007 (WUGSC 3.0/petMar1) (petMar1)
-aplCal1	Sea hare Sept. 2008 (Broad 2.0/aplCal1) (aplCal1)
-braFlo1	Lancelet Mar. 2006 (JGI 1.0/braFlo1) (braFlo1)
-ci2	C. intestinalis Mar. 2005 (JGI 2.1/ci2) (ci2)
-ci1	C. intestinalis Dec. 2002 (JGI 1.0/ci1) (ci1)
-strPur2	S. purpuratus Sep. 2006 (Baylor 2.1/strPur2) (strPur2)
-strPur1	S. purpuratus Apr. 2005 (Baylor 1.1/strPur1) (strPur1)
-ce10	C. elegans Oct. 2010 (WS220/ce10) (ce10)
-ce6	C. elegans May 2008 (WS190/ce6) (ce6)
-ce4	C. elegans Jan. 2007 (WS170/ce4) (ce4)
-caePb2	C. brenneri Feb. 2008 (WUGSC 6.0.1/caePb2) (caePb2)
-caePb1	C. brenneri Jan. 2007 (WUGSC 4.0/caePb1) (caePb1)
-cb3	C. briggsae Jan. 2007 (WUGSC 1.0/cb3) (cb3)
-cb1	C. briggsae July 2002 (WormBase cb25.agp8/cb1) (cb1)
-caeRem3	C. remanei May 2007 (WUGSC 15.0.1/caeRem3) (caeRem3)
-caeRem2	C. remanei Mar. 2006 (WUGSC 1.0/caeRem2) (caeRem2)
-caeJap1	C. japonica Mar. 2008 (WUGSC 3.0.2/caeJap1) (caeJap1)
-priPac1	P. pacificus Feb. 2007 (WUGSC 5.0/priPac1) (priPac1)
-dm3	D. melanogaster Apr. 2006 (BDGP R5/dm3) (dm3)
-dm2	D. melanogaster Apr. 2004 (BDGP R4/dm2) (dm2)
-droSim1	D. simulans Apr. 2005 (WUGSC mosaic 1.0/droSim1) (droSim1)
-droSec1	D. sechellia Oct. 2005 (Broad/droSec1) (droSec1)
-droYak2	D. yakuba Nov. 2005 (WUGSC 7.1/droYak2) (droYak2)
-droYak1	D. yakuba Apr. 2004 (WUGSC 1.0/droYak1) (droYak1)
-droEre1	D. erecta Aug. 2005 (Agencourt prelim/droEre1) (droEre1)
-droAna2	D. ananassae Aug. 2005 (Agencourt prelim/droAna2) (droAna2)
-droAna1	D. ananassae July 2004 (TIGR/droAna1) (droAna1)
-dp3	D. pseudoobscura Nov. 2004 (FlyBase 1.03/dp3) (dp3)
-dp2	D. pseudoobscura Aug. 2003 (Baylor freeze1/dp2) (dp2)
-droPer1	D. persimilis Oct. 2005 (Broad/droPer1) (droPer1)
-droVir2	D. virilis Aug. 2005 (Agencourt prelim/droVir2) (droVir2)
-droVir1	D. virilis July 2004 (Agencourt prelim/droVir1) (droVir1)
-droMoj2	D. mojavensis Aug. 2005 (Agencourt prelim/droMoj2) (droMoj2)
-droMoj1	D. mojavensis Aug. 2004 (Agencourt prelim/droMoj1) (droMoj1)
-droGri1	D. grimshawi Aug. 2005 (Agencourt prelim/droGri1) (droGri1)
-anoGam1	A. gambiae Feb. 2003 (IAGEC MOZ2/anoGam1) (anoGam1)
-apiMel2	A. mellifera Jan. 2005 (Baylor 2.0/apiMel2) (apiMel2)
-apiMel1	A. mellifera July 2004 (Baylor 1.2/apiMel1) (apiMel1)
-sacCer3	S. cerevisiae Apr. 2011 (SacCer_Apr2011/sacCer3) (sacCer3)
-sacCer2	S. cerevisiae June 2008 (SGD/sacCer2) (sacCer2)