mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Ross Lazarus
6c7570a8cb
These are potentially useful to keep private software development sites under local control...
254 lines
8.5 KiB
Plaintext
254 lines
8.5 KiB
Plaintext
# ---- HTTP Server ----------------------------------------------------------
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[server:main]
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use = egg:Paste#http
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port = 8080
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host = 127.0.0.1
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use_threadpool = true
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threadpool_workers = 10
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# ---- Galaxy Web Interface -------------------------------------------------
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[app:main]
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# Specifies the factory for the universe WSGI application
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paste.app_factory = galaxy.web.buildapp:app_factory
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log_level = DEBUG
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# Should jobs be tracked through the database, rather than in memory
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## track_jobs_in_database = true
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# Number of concurrent jobs to run (local runner)
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job_queue_workers = 5
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# Job scheduling policy to be used.
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# module/package name and classname should be in "module:classname" format.
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# Comment / uncomment the following policies depending upon which is to be used.
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#job_scheduler_policy = FIFO
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job_scheduler_policy = galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin
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# Job queue cleanup interval in minutes. Currently only used by RoundRobin
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job_queue_cleanup_interval = 30
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# Database connection
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database_file = database/universe.sqlite
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# You may use a SQLAlchemy connection string to specify an external database instead
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## database_connection = postgres:///galaxy_test
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# Where dataset files are saved
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file_path = database/files
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# Temporary storage for additional datasets, this should be shared through the cluster
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new_file_path = database/tmp
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# Tools
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tool_config_file = tool_conf.xml
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tool_path = tools
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# Datatype converters
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datatype_converters_config_file = datatype_converters_conf.xml
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datatype_converters_path = %(here)s/lib/galaxy/datatypes/converters
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# Session support (beaker)
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use_beaker_session = True
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session_type = file
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session_data_dir = %(here)s/database/beaker_sessions
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session_key = galaxysessions
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session_secret = changethisinproduction
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# Configuration for debugging middleware
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debug = true
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use_lint = false
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# NEVER enable this on a public site (even test or QA)
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use_interactive = true
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# Admin Password
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admin_pass = "galaxy"
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# path to sendmail
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sendmail_path = /usr/sbin/sendmail
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# Address to join mailing list
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mailing_join_addr = galaxy-user-join@bx.psu.edu
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# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!)
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## use_heartbeat = True
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# Profiling middleware (cProfile based)
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## use_profile = True
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# Mail
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smtp_server = coltrane.bx.psu.edu
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error_email_to = galaxy_bugs@bx.psu.edu
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# Use the new iframe / javascript based layout
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use_new_layout = true
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# Comma separated list of UCSC / gbrowse browsers to use for viewing
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ucsc_display_sites = main,test,archaea
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gbrowse_display_sites = wormbase,flybase
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# Serving static files (needed if running standalone)
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static_enabled = True
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static_cache_time = 360
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static_dir = %(here)s/static/
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static_images_dir = %(here)s/static/images
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static_favicon_dir = %(here)s/static/favicon.ico
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static_scripts_dir = %(here)s/static/scripts/
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static_style_dir = %(here)s/static/june_2007_style/blue
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## Leave these commented out for the defaults at the main galaxy site
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## Uncomment and adjust these to change locally configurable items in the masthead
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## for a local mirror where you are doing private software development
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##
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## Brand: appends "/[brand]" to the "Galaxy" text in the masthead
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## wiki_url: replaces the default galaxy main wiki
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## bugs_email: replaces the default galaxy bugs email list
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#brand = Private local mirror
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#wiki_url=/path/to/my/local/wiki
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#bugs_email=mailto:bugmaster@this.site.com
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# ---- Datatypes ------------------------------------------------------------
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[galaxy:datatypes]
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ab1 = galaxy.datatypes.images:Ab1,application/octet-stream
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axt = galaxy.datatypes.sequence:Axt
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bed = galaxy.datatypes.interval:Bed
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binseq.zip = galaxy.datatypes.images:Binseq,application/zip
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customtrack = galaxy.datatypes.interval:CustomTrack
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data = galaxy.datatypes.data:Data,application/octet-stream
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fasta = galaxy.datatypes.sequence:Fasta
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gbrowsetrack = galaxy.datatypes.interval:GBrowseTrack
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gff = galaxy.datatypes.interval:Gff
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gff3 = galaxy.datatypes.interval:Gff3
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gif = galaxy.datatypes.images:Image,image/gif
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gmaj.zip = galaxy.datatypes.images:Gmaj,application/zip
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html = galaxy.datatypes.images:Html,text/html
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interval = galaxy.datatypes.interval:Interval
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jpg = galaxy.datatypes.images:Image,image/jpeg
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laj = galaxy.datatypes.images:Laj
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lav = galaxy.datatypes.sequence:Lav
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maf = galaxy.datatypes.sequence:Maf
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pdf = galaxy.datatypes.images:Image,application/pdf
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png = galaxy.datatypes.images:Image,image/png
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scf = galaxy.datatypes.images:Scf,application/octet-stream
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tabular = galaxy.datatypes.tabular:Tabular
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txt = galaxy.datatypes.data:Text
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txtseq.zip = galaxy.datatypes.images:Txtseq,application/zip
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wig = galaxy.datatypes.interval:Wiggle
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#EMBOSS TOOLS
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acedb = galaxy.datatypes.data:Text
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asn1 = galaxy.datatypes.data:Text
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btwisted = galaxy.datatypes.data:Text
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cai = galaxy.datatypes.data:Text
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charge = galaxy.datatypes.data:Text
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checktrans = galaxy.datatypes.data:Text
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chips = galaxy.datatypes.data:Text
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clustal = galaxy.datatypes.data:Text
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codata = galaxy.datatypes.data:Text
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codcmp = galaxy.datatypes.data:Text
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coderet = galaxy.datatypes.data:Text
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compseq = galaxy.datatypes.data:Text
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cpgplot = galaxy.datatypes.data:Text
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cpgreport = galaxy.datatypes.data:Text
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cusp = galaxy.datatypes.data:Text
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cut = galaxy.datatypes.data:Text
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dan = galaxy.datatypes.data:Text
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dbmotif = galaxy.datatypes.data:Text
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diffseq = galaxy.datatypes.data:Text
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digest = galaxy.datatypes.data:Text
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dreg = galaxy.datatypes.data:Text
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einverted = galaxy.datatypes.data:Text
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embl = galaxy.datatypes.data:Text
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epestfind = galaxy.datatypes.data:Text
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equicktandem = galaxy.datatypes.data:Text
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est2genome = galaxy.datatypes.data:Text
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etandem = galaxy.datatypes.data:Text
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excel = galaxy.datatypes.data:Text
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feattable = galaxy.datatypes.data:Text
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fitch = galaxy.datatypes.data:Text
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freak = galaxy.datatypes.data:Text
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fuzznuc = galaxy.datatypes.data:Text
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fuzzpro = galaxy.datatypes.data:Text
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fuzztran = galaxy.datatypes.data:Text
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garnier = galaxy.datatypes.data:Text
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gcg = galaxy.datatypes.data:Text
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geecee = galaxy.datatypes.data:Text
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genbank = galaxy.datatypes.data:Text
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helixturnhelix = galaxy.datatypes.data:Text
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hennig86 = galaxy.datatypes.data:Text
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hmoment = galaxy.datatypes.data:Text
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ig = galaxy.datatypes.data:Text
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isochore = galaxy.datatypes.data:Text
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jackknifer = galaxy.datatypes.data:Text
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jackknifernon = galaxy.datatypes.data:Text
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markx10 = galaxy.datatypes.data:Text
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markx1 = galaxy.datatypes.data:Text
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markx0 = galaxy.datatypes.data:Text
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markx3 = galaxy.datatypes.data:Text
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markx2 = galaxy.datatypes.data:Text
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match = galaxy.datatypes.data:Text
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mega = galaxy.datatypes.data:Text
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meganon = galaxy.datatypes.data:Text
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motif = galaxy.datatypes.data:Text
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msf = galaxy.datatypes.data:Text
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nametable = galaxy.datatypes.data:Text
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ncbi = galaxy.datatypes.data:Text
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needle = galaxy.datatypes.data:Text
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newcpgreport = galaxy.datatypes.data:Text
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newcpgseek = galaxy.datatypes.data:Text
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nexus = galaxy.datatypes.data:Text
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nexusnon = galaxy.datatypes.data:Text
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noreturn = galaxy.datatypes.data:Text
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pair = galaxy.datatypes.data:Text
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palindrome = galaxy.datatypes.data:Text
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pepcoil = galaxy.datatypes.data:Text
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pepinfo = galaxy.datatypes.data:Text
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pepstats = galaxy.datatypes.data:Text
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phylip = galaxy.datatypes.data:Text
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phylipnon = galaxy.datatypes.data:Text
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pir = galaxy.datatypes.data:Text
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polydot = galaxy.datatypes.data:Text
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preg = galaxy.datatypes.data:Text
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prettyseq = galaxy.datatypes.data:Text
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primersearch = galaxy.datatypes.data:Text
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regions = galaxy.datatypes.data:Text
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score = galaxy.datatypes.data:Text
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selex = galaxy.datatypes.data:Text
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seqtable = galaxy.datatypes.data:Text
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showfeat = galaxy.datatypes.data:Text
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showorf = galaxy.datatypes.data:Text
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simple = galaxy.datatypes.data:Text
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sixpack = galaxy.datatypes.data:Text
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srs = galaxy.datatypes.data:Text
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srspair = galaxy.datatypes.data:Text
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staden = galaxy.datatypes.data:Text
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strider = galaxy.datatypes.data:Text
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supermatcher = galaxy.datatypes.data:Text
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swiss = galaxy.datatypes.data:Text
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syco = galaxy.datatypes.data:Text
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table = galaxy.datatypes.data:Text
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textsearch = galaxy.datatypes.data:Text
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vectorstrip = galaxy.datatypes.data:Text
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wobble = galaxy.datatypes.data:Text
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wordcount = galaxy.datatypes.data:Text
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tagseq = galaxy.datatypes.data:Text
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# ---- Data Type Sniff Order --------------------------------------------------
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[galaxy:sniff_order]
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05 = galaxy.datatypes.sequence:Maf
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10 = galaxy.datatypes.sequence:Lav
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15 = galaxy.datatypes.sequence:Fasta
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20 = galaxy.datatypes.interval:Wiggle
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25 = galaxy.datatypes.images:Html
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30 = galaxy.datatypes.sequence:Axt
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35 = galaxy.datatypes.interval:Bed
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40 = galaxy.datatypes.interval:CustomTrack
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45 = galaxy.datatypes.interval:Gff
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50 = galaxy.datatypes.interval:Gff3
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55 = galaxy.datatypes.interval:Interval
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