diff --git a/Bein/BeinClient.hs b/Bein/BeinClient.hs
new file mode 100644
--- /dev/null
+++ b/Bein/BeinClient.hs
@@ -0,0 +1,39 @@
+module Main where
+
+import Control.Monad
+import Network.Socket
+import System.Environment (getArgs)
+import System.Exit (exitSuccess)
+import System.IO (hPutStrLn, hGetLine, hFlush, Handle, IOMode(ReadWriteMode), hSetBuffering, BufferMode(LineBuffering), stdin, stdout)
+
+help :: IO a
+help = putStrLn "Usage: MutualAuthClient socketfile" >> exitSuccess
+
+getSocketFile :: IO String
+getSocketFile = do 
+  args <- getArgs
+  case args of
+    [] -> help
+    [x] -> return x
+    _ -> help
+
+main :: IO b
+main = do
+  socketName <- getSocketFile
+  s <- socket AF_UNIX Stream 0
+  connect s (SockAddrUnix socketName)
+  h <- socketToHandle s ReadWriteMode
+  hSetBuffering h LineBuffering
+  forever $ interactOnHandle h
+
+whileM :: IO Bool -> IO () -> IO ()
+whileM p v = p >>= \b -> if b then v >> whileM p v else return ()
+
+interactOnHandle :: Handle -> IO ()    
+interactOnHandle h = putStrLn "Listening." >> transput stdin h >> putStrLn "Receiving." >> transput h stdout >> interactOnHandle h
+
+transput :: Handle -> Handle -> IO ()
+transput from to = do l <- hGetLine from
+                      hPutStrLn to l
+                      if l == "." then hFlush to else transput from to
+
diff --git a/Bein/BeinCtl.hs b/Bein/BeinCtl.hs
new file mode 100644
--- /dev/null
+++ b/Bein/BeinCtl.hs
@@ -0,0 +1,165 @@
+-- This file is part of Bein.
+--
+-- Bein is free software: you can redistribute it and/or modify
+-- it under the terms of the GNU General Public License as published by
+-- the Free Software Foundation, either version 3 of the License, or
+-- (at your option) any later version.
+--    
+-- Bein is distributed in the hope that it will be useful,
+-- but WITHOUT ANY WARRANTY; without even the implied warranty of
+-- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+-- GNU General Public License for more details.
+--
+-- You should have received a copy of the GNU General Public License
+-- along with Bein.  If not, see <http://www.gnu.org/licenses/>.
+
+
+module Main where
+
+import Data.Maybe (fromJust)
+import System.FilePath
+import System.Exit ( exitSuccess, exitFailure )
+import System.IO ( hPutStrLn, stderr )
+import System.Directory
+import System.Console.GetOpt
+import Database.HDBC
+import Database.HDBC.PostgreSQL
+import System.Environment (getArgs, getProgName)
+import Bein.ShellScripting
+import System.Posix.Files
+import Bein.Configuration
+
+data State = State { sqlDir :: Maybe FilePath,
+                     outputFile :: Maybe FilePath,
+                     verbose :: Bool } deriving (Eq,Show,Read)
+
+defaultState :: State
+defaultState = State { sqlDir = Nothing,
+                       outputFile = Nothing,
+                       verbose = False }
+
+main :: IO ()
+main = do (cmd,st) <- getState
+          cmd st
+            
+getState :: IO (State -> IO (), State)
+getState = do
+  args <- getArgs
+  case getOpt RequireOrder options args of
+    (actions, [commandTxt], []) -> do opts <- foldl (>>=) (return defaultState) actions
+                                      let command = parseCmd commandTxt
+                                      case () of
+                                        _ | (commandTxt `elem` ["init","cold-init","reload","deep-reload"]) && sqlDir opts == Nothing ->
+                                          printHelpAndDie (Just "Must give an SQL source directory to init database.")
+                                        _ | (commandTxt == "dump" && outputFile opts == Nothing) ->
+                                          printHelpAndDie (Just "Must give a file to dump database to with -o option.")
+                                        _ -> return (command,opts)
+    (_, _, []) -> printHelpAndDie (Just "beinctl takes exactly one command.")
+    (_, _, errs) -> printHelpAndDie (Just $ concat errs)
+
+options :: [OptDescr (State -> IO State)]
+options = [
+  Option "h" ["help"]
+         (NoArg (\_ -> printHelpAndDie Nothing))
+         "Show help",
+  Option "v" ["verbose"]
+         (NoArg (\opt -> return opt { verbose = True }))
+         "Be verbose.",
+  Option "o" ["output"]
+         (ReqArg (\arg opt -> return opt { outputFile = Just arg }) "OUTPUTFILE")
+         "File to dump database to.",
+  Option "d" ["sqldir"]
+         (ReqArg (\arg opt -> do b <- doesDirectoryExist arg
+                                 if b then return opt { sqlDir = Just arg }
+                                   else printHelpAndDie (Just $ "Invalid directory: " ++ arg)) "SQLDIRECTORY")
+         "Directory containing SQL source."
+  ]
+
+printHelpAndDie :: Maybe String -> IO a
+printHelpAndDie msg = do
+    case msg of
+      Nothing -> help >> exitSuccess
+      Just m -> hPutStrLn stderr m >> help >> exitFailure
+    where help = do 
+            programName <- getProgName
+            hPutStrLn stderr (usageInfo (programName ++ " [-hvd] command") options)
+            printCommands
+
+parseCmd :: String -> (State -> IO ())
+parseCmd "cold-init" = coldInitialize
+parseCmd "init" = initialize
+parseCmd "teardown" = teardown
+parseCmd "full-teardown" = fullTeardown
+parseCmd "dump" = dump
+parseCmd "reload" = reload
+parseCmd "deep-reload" = deepReload
+parseCmd "show-config" = showConfig
+parseCmd cmd = \_ -> printHelpAndDie (Just ("Unknown command: " ++ cmd))
+
+printCommands :: IO ()
+printCommands = do
+  mapM_ putStrLn 
+    ["  where command is one of:",
+     "    init            - create Bein database ready for loading",
+     "    cold-init       - create Bein database from scratch, including users",
+     "    teardown        - delete the Bein database",
+     "    full-teardown   - delete the Bein database and all users, leaving system pristine",
+     "    dump            - dump data in the database to tar archive file", 
+     "    reload          - same as teardown followed by init",
+     "    deep-reload     - same as full-teardown followed by cold-init",
+     "    show-config     - print the system configuration from the database"]
+    
+coldInitialize :: State -> IO ()
+coldInitialize st = do
+  nologin <- takeFirstM fileExist ["/sbin/nologin", "/usr/sbin/nologin"]
+  systemM_ $ "useradd --system -M --user-group --shell " ++ nologin ++ " bein"
+  systemM_ $ "sudo -u postgres createuser --no-superuser --login bein --no-createdb --no-createrole --no-superuser"
+  initialize st
+  
+initialize :: State -> IO ()
+initialize State { sqlDir = Nothing } = 
+  printHelpAndDie (Just "Cannot initialize database without SQL directory.  Set -d option.")
+initialize State { sqlDir = Just d, verbose = v } = do
+  let inPath p = joinPath [d,p]
+      unlessVerbose p = if v then "" else p
+  systemM $ "sudo -u postgres createdb --owner bein bein"
+  systemM $ "sudo -u postgres createlang plpgsql bein"
+  systemM $ "sudo -u postgres createlang plpythonu bein"
+  systemM $ "sudo -u bein psql " ++ unlessVerbose "--quiet" ++ " --dbname bein --file " ++ inPath "core_tables.sql"
+  systemM $ "sudo -u postgres psql " ++ unlessVerbose "--quiet" ++ " --dbname bein --file "++ inPath "untrusted_functions.sql"
+  systemM $ "sudo -u bein psql " ++ unlessVerbose "--quiet" ++ " --dbname bein --file " ++ inPath "triggers.sql"
+  systemM $ "sudo -u bein psql " ++ unlessVerbose "--quiet" ++ " --dbname bein --file " ++ inPath "utility_functions.sql"
+
+fullTeardown :: State -> IO ()
+fullTeardown st = do
+  teardown st
+  systemM_ $ "userdel bein"
+  systemM_ $ "groupdel bein"
+  systemM_ $ "sudo -u postgres dropuser bein"
+
+teardown :: State -> IO ()
+teardown _ = do
+  systemM_ $ "sudo -u postgres dropdb bein"
+
+dump :: State -> IO ()
+dump st = do
+  systemM_ $ "sudo -u bein pg_dump --format=t -f " ++ fromJust (outputFile st) ++ " bein"
+
+reload :: State -> IO ()
+reload st = teardown st >> initialize st
+
+deepReload :: State -> IO ()
+deepReload st = fullTeardown st >> coldInitialize st
+
+dbCommand :: (Connection -> IO a) -> IO ()
+dbCommand cmd = do conn <- connectPostgreSQL "dbname=bein"
+                   _ <- cmd conn
+                   commit conn
+
+showConfig :: State -> IO ()
+showConfig _ = dbCommand (\conn -> readConfiguration conn >>= putStrLn . show)
+
+takeFirstM :: Monad m => (a -> m Bool) -> [a] -> m a
+takeFirstM _ [] = fail $ "Nothing in list succeeds."
+takeFirstM f (c:cs) = f c >>= \r ->
+  if r then return c else takeFirstM f cs
diff --git a/Bein/Daemon.hs b/Bein/Daemon.hs
new file mode 100644
--- /dev/null
+++ b/Bein/Daemon.hs
@@ -0,0 +1,30 @@
+{-# LANGUAGE ScopedTypeVariables #-}
+module Main where
+
+import Control.Concurrent.QSem
+import System.Posix.Daemonize (serviced,CreateDaemon(..), simpleDaemon)
+import Bein.Daemon.SignalHandlers (installSignalHandlers)
+import Bein.Daemon.Protocol
+import Bein.Daemon.Types 
+import Bein.SocketHandler (listenWith)
+import Control.Monad.Reader (ReaderT(..))
+import Control.Concurrent.STM
+import Database.HDBC.PostgreSQL
+import Bein.Configuration
+
+main :: IO ()
+main = serviced $ simpleDaemon { program = beind, user = Just "bein", group = Just "bein" }
+
+beind :: IO ()
+beind = getState >>= runReaderT beind'
+  where beind' = do installSignalHandlers
+                    socketFile <- configField daemon_port
+                    listenWith daemonProtocol socketFile
+
+getState :: IO DaemonState  
+getState = do
+  conn <- connectPostgreSQL "dbname=bein"
+  config <- readConfiguration conn
+  configTV <- newTVarIO config
+  sem <- newQSem 1
+  return $ State { stDb = conn, stConfigT = configTV, stSem = sem }
diff --git a/Bein/Minion.hs b/Bein/Minion.hs
new file mode 100644
--- /dev/null
+++ b/Bein/Minion.hs
@@ -0,0 +1,119 @@
+-- Add setting status to running in db, and checking state and finalizing status when doing cleanup
+module Main where
+
+import Database.HDBC
+import System.Posix.Syslog
+import System.Environment (getProgName)
+import Control.Monad.Reader
+import Database.HDBC.PostgreSQL
+import Control.Concurrent.STM
+import System.Exit (ExitCode(..))
+import System.Directory
+import System.Posix.Signals
+import System.Posix.Process
+import System.FilePath.Posix (joinPath)
+
+import Bein.Configuration
+import Bein.Minion.Types
+import Bein.Minion.Arguments
+import Bein.SocketHandler
+import Bein.Minion.Commands
+import Bein.Minion.Protocol
+
+main :: IO ()
+main = do
+  getSettings >>= getState >>= \st -> do
+    programName <- getProgName
+    withSyslog programName [PID,PERROR] DAEMON $ runReaderT main' st
+      
+getState :: Settings -> IO State
+getState opts = do
+  conn <- connectPostgreSQL "dbname=bein"
+  config <- readConfiguration conn
+  configTV <- newTVarIO config
+  minP <- newTVarIO Nothing
+  return $ State { stDb = conn, stConfigT = configTV, stSettings = opts, stMinionPid = minP }
+
+main' :: ReaderT State IO b
+main' = do 
+  execution >>= \e -> checkExecution e >>= \r -> case r of
+    Left errors -> dieWith errors
+    Right _ -> do installHandlers
+                  scratchDir >>= createScratchDirectory
+                  script <- execution >>= \_ -> scratchDir >>= \s -> writeScript e s
+                  forkR $ minionSocket >>= listenWith minionProtocol
+                  runScript script
+                  forever $ return () -- Doing this requires using exitImmediately to kill the program when we're done.
+
+checkExecution :: ExecutionID -> BeinM State (Either String ())
+checkExecution ex = do
+  [notFuture, isWaiting, nonemptyScript, noNullInputs] <- 
+    liftM (map fromSql) $ receiveOneRow $ query queryString [toSql ex]
+  let errors = concat $ map snd $ filter (not.fst) $
+               [(notFuture, "Execution " ++ show ex ++ " is not a future.\n"),
+                (isWaiting, "Execution " ++ show ex ++ " is not waiting.\n"),
+                (nonemptyScript, "Execution " ++ show ex ++ 
+                                 " refers to a program with an empty script.\n"),
+                (noNullInputs, "Execution " ++ show ex ++ " has null inputs.\n")]
+    in if (notFuture && isWaiting && nonemptyScript && noNullInputs) 
+         then do verboseMsgLn "Setting status to running."
+                 update "update executions set status = 'running' where id=?" [toSql ex]
+                 return (Right ())
+         else return (Left errors)
+    where queryString = "select not_future, is_waiting, nonempty_script, " ++ 
+                        "no_null_inputs from runnable where id = ?"
+
+installHandlers :: BeinM State ()
+installHandlers = ask >>= \s -> do 
+  verboseMsg "Installing handlers..."
+  mapM_ ignoreSignal [sigALRM, sigPIPE, sigPOLL, sigPROF, sigUSR1, sigUSR2, sigVTALRM]
+  liftIO $ installHandler sigCHLD (Catch $ runReaderT sigCHLDHandler s) (Just fullSignalSet)
+  liftIO $ installHandler sigHUP (Catch $ runReaderT (cleanUp (ExitFailure 1)) s) (Just fullSignalSet)
+  liftIO $ installHandler sigTERM (Catch $ runReaderT (cleanUp (ExitFailure 1)) s) (Just fullSignalSet)
+  verboseMsgLn "ok"
+
+sigCHLDHandler :: BeinM State ()
+sigCHLDHandler = do
+  v <- liftIO $ getAnyProcessStatus False False
+  case v of
+    Just (pid,status) -> do 
+      minionPid >>= \p -> if p /= Just pid 
+        then verboseMsgLn "Received sigCHLD from something besides script." >> sigCHLDHandler
+        else (verboseMsgLn $ "Child exited with status " ++ show status) >> cleanUp ExitSuccess
+    Nothing -> return ()
+                                                  
+
+createScratchDirectory :: FilePath -> BeinM State ()
+createScratchDirectory dir = do
+  verboseMsg $ "Creating scratch directory " ++ dir ++ "..."
+  (liftIO $ createDirectory dir) `catchR` 
+    (\e -> dieWith $ "Could not create scratch directory.\n" ++ show e)
+  (liftIO $ setCurrentDirectory dir) `catchR` 
+    (\e -> dieWith $ "Could not set working directory.\n" ++ show e)
+  verboseMsgLn "ok"
+
+writeScript :: ExecutionID -> FilePath -> BeinM State FilePath
+writeScript ex dir = do 
+  verboseMsg $ "Writing script to " ++ dir ++ "..."
+  [lang,script] <- liftM (map fromSql) $ receiveOneRow $ query queryString [toSql ex]
+  let scriptName = case lang of
+        "perl" -> "script.pl"
+        "r" -> "script.R"
+        _ -> error "Invalid value for language."
+  scriptPath <- scratchDir >>= (\d -> return $ joinPath [d,scriptName])
+  liftIO $ writeFile scriptPath script
+  verboseMsgLn "ok"
+  return scriptPath
+    where queryString = "select p.language,p.script from programs " ++ 
+                        "as p join executions as e on e.program=p.id where e.id=?"
+                     
+runScript :: FilePath -> BeinM State ()
+runScript script = do
+  verboseMsg $ "Running script " ++ script ++ "..."
+  perlCmd <- configField perl_executable
+  minionPort <- configField minion_port
+  p <- liftIO $ forkProcess $ executeFile perlCmd False [script,minionPort] Nothing
+  writeMinionPid p
+  verboseMsgLn "ok"
+
+
diff --git a/Bein/Web.hs b/Bein/Web.hs
new file mode 100644
--- /dev/null
+++ b/Bein/Web.hs
@@ -0,0 +1,46 @@
+module Main where
+
+import Bein.Web.Types
+import Bein.Web.Commands
+import Bein.Web.Routing
+import qualified System.Posix.Daemonize as D
+import Happstack.Server
+import Control.Concurrent
+import Control.Monad.Trans
+import Control.Monad.Reader
+import Control.Concurrent.STM
+import Database.HDBC.PostgreSQL
+import Bein.Configuration
+import Network
+import System.IO
+
+main :: IO ()
+main = D.serviced $ D.simpleDaemon { D.program = httpd, D.user = Just "bein", D.group = Just "bein" }
+
+getPort :: WebState -> IO Int
+getPort st = (liftIO.atomically.readTVar.configT) st >>= return.http_port
+
+httpd :: IO ()
+httpd = getState >>= \s -> do 
+  p <- getPort s
+  runReaderT sessionExpirer s
+  simpleHTTP' (\a -> runReaderT a s) (Conf p Nothing) routing
+
+sessionExpirer :: BeinM WebState ThreadId
+sessionExpirer = forkR f
+  where f = do update "select remove_expired_sessions()" []
+               liftIO $ threadDelay (5*60*1000000)
+               f
+
+getState :: IO WebState
+getState = do
+  conn <- connectPostgreSQL "dbname=bein"
+  config <- readConfiguration conn
+  configTV <- newTVarIO config
+  sockMV <- (connectTo "" (UnixSocket (daemon_port config)) >>= \h -> do
+                hSetBuffering h LineBuffering                                       
+                newMVar h) `catch` (\_ -> newEmptyMVar)
+  return $ WebState { stDb = conn, stConfigT = configTV, stDaemonPort = sockMV, 
+                      stObject = undefined, stUser = Nothing }
+
+
diff --git a/LICENSE b/LICENSE
new file mode 100644
--- /dev/null
+++ b/LICENSE
@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+                            Preamble
+
+  The GNU General Public License is a free, copyleft license for
+software and other kinds of works.
+
+  The licenses for most software and other practical works are designed
+to take away your freedom to share and change the works.  By contrast,
+the GNU General Public License is intended to guarantee your freedom to
+share and change all versions of a program--to make sure it remains free
+software for all its users.  We, the Free Software Foundation, use the
+GNU General Public License for most of our software; it applies also to
+any other work released this way by its authors.  You can apply it to
+your programs, too.
+
+  When we speak of free software, we are referring to freedom, not
+price.  Our General Public Licenses are designed to make sure that you
+have the freedom to distribute copies of free software (and charge for
+them if you wish), that you receive source code or can get it if you
+want it, that you can change the software or use pieces of it in new
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+
+  To protect your rights, we need to prevent others from denying you
+these rights or asking you to surrender the rights.  Therefore, you have
+certain responsibilities if you distribute copies of the software, or if
+you modify it: responsibilities to respect the freedom of others.
+
+  For example, if you distribute copies of such a program, whether
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+
+  Developers that use the GNU GPL protect your rights with two steps:
+(1) assert copyright on the software, and (2) offer you this License
+giving you legal permission to copy, distribute and/or modify it.
+
+  For the developers' and authors' protection, the GPL clearly explains
+that there is no warranty for this free software.  For both users' and
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+
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+
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diff --git a/Setup.lhs b/Setup.lhs
new file mode 100644
--- /dev/null
+++ b/Setup.lhs
@@ -0,0 +1,3 @@
+#!/usr/bin/env runhaskell
+> import Distribution.Simple
+> main = defaultMain
diff --git a/bein.cabal b/bein.cabal
new file mode 100644
--- /dev/null
+++ b/bein.cabal
@@ -0,0 +1,48 @@
+name:                bein
+version:             0.1
+synopsis:            Bein is a provenance and workflow management system for bioinformatics.
+description:         To avoid having thousands of files produced in a random way from a bunch of scripts, as is typically the case for a bioinformaticist, Bein keeps track of scripts, and their executions on various inputs.  It provides a web front end, and will integrate with LSF clusters.
+category:            Application
+license:             GPL-3
+license-file:        LICENSE
+author:              Fred Ross
+maintainer:          fred.ross@epfl.ch
+build-type:          Simple
+Cabal-Version:       >= 1.4
+
+Executable beinctl
+  Main-is:           Bein/BeinCtl.hs
+  Build-Depends:     base >= 3 && < 5, HDBC, HDBC-postgresql, process
+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread
+  Hs-Source-Dirs:    .
+  extra-libraries:   pgport xslt xml2 pam ssl crypto krb5 com_err gssapi_krb5 z readline crypt dl m
+
+Executable beind
+  Main-is:           Bein/Daemon.hs
+  Build-Depends:     base >= 3 && < 5, HDBC, HDBC-postgresql, process,
+                     hdaemonize >= 0.3, hsyslog, parsec, random, unix, network,
+                     convertible, stm, mtl, filepath
+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread
+  Hs-Source-Dirs:    .
+
+Executable beinclient
+  Main-is:           Bein/BeinClient.hs
+  Build-Depends:     base >= 3 && < 5, network
+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread
+  Hs-Source-Dirs:    .
+
+Executable beinminion
+  Main-is:           Bein/Minion.hs
+  Build-Depends:     base >= 3 && < 5, network, hsyslog, parsec, HDBC,
+                     HDBC-postgresql, process, unix, stm, mtl, filepath, directory
+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread
+  Hs-Source-Dirs:    .
+
+Executable beinhttpd
+  Main-is:           Bein/Web.hs
+  Build-Depends:     base >= 3 && < 5, HDBC, HDBC-postgresql, unix, stm, mtl, filepath,
+                     directory, hsyslog, hdaemonize, happstack-server, Crypto,
+                     happstack-util, containers, xhtml, time, old-locale, utf8-string,
+                     bytestring
+  Ghc-Options:       -Wall -threaded -fno-warn-unused-do-bind -optl-static -optl-pthread
+  Hs-Source-Dirs:    .