files.txt

/media/VD_Research/NGSData/RawData/Roche454/2009_05_19
/media/VD_Research/NGSData/RawData/Roche454/2010_03_19
/media/VD_Research/NGSData/RawData/Roche454/2010_05_11
/media/VD_Research/NGSData/RawData/Roche454/2010_06_09
/media/VD_Research/NGSData/RawData/Roche454/2010_09_23
/media/VD_Research/NGSData/RawData/Roche454/2011_06_15
/media/VD_Research/NGSData/RawData/Roche454/2011_08_11
/media/VD_Research/NGSData/RawData/Roche454/2011_08_31
/media/VD_Research/NGSData/RawData/Roche454/2011_10_19
/media/VD_Research/NGSData/RawData/Roche454/2011_12_23
/media/VD_Research/NGSData/RawData/Roche454/2012_01_25
/media/VD_Research/NGSData/RawData/Roche454/2012_02_15
/media/VD_Research/NGSData/RawData/Roche454/2012_03_09
/media/VD_Research/NGSData/RawData/Roche454/2012_03_15
/media/VD_Research/NGSData/RawData/Roche454/2012_04_04
/media/VD_Research/NGSData/RawData/Roche454/2012_05_07
/media/VD_Research/NGSData/RawData/Roche454/2012_05_11
/media/VD_Research/NGSData/RawData/Roche454/2012_06_22
/media/VD_Research/NGSData/RawData/Roche454/2012_07_19
/media/VD_Research/NGSData/RawData/Roche454/2012_08_06
/media/VD_Research/NGSData/RawData/Roche454/2012_08_07
/media/VD_Research/NGSData/RawData/Roche454/2012_08_31
/media/VD_Research/NGSData/RawData/Roche454/2013_02_01
/media/VD_Research/NGSData/RawData/Roche454/2013_03_12
/media/VD_Research/NGSData/RawData/Roche454/2013_05_01
/media/VD_Research/NGSData/RawData/Roche454/2013_05_03
/media/VD_Research/NGSData/RawData/Roche454/2013_05_10
/media/VD_Research/NGSData/RawData/Roche454/2013_05_22
/media/VD_Research/NGSData/RawData/Roche454/2013_06_15
/media/VD_Research/NGSData/RawData/Roche454/2013_07_03
/media/VD_Research/NGSData/RawData/Roche454/R_2011_10_19_13_13_50_FLX12070283_Administrator_101911_pathogenDiscovery
/media/VD_Research/NGSData/RawData/Roche454/R_2011_12_23_11_20_18_FLX12070283_Administrator_12232011_AFRIMS_Den2AndPathogenDiscovery
/media/VD_Research/NGSData/RawData/Roche454/R_2012_03_15_10_09_58_FLX12070283_Administrator_03152012_Pathogen_Adv_Phage
/media/VD_Research/NGSData/RawData/Roche454/R_2012_05_07_10_47_49_FLX12070283_Administrator_05072012_phagebac_pathogen
/media/VD_Research/NGSData/RawData/Roche454/R_2012_06_22_07_51_49_FLX12070283_Administrator_062212_FluBAndAH3
/media/VD_Research/NGSData/RawData/Roche454/R_2013_02_01_16_31_49_FLX12070283_Administrator_20130201_16s_phage
/media/VD_Research/NGSData/RawData/Roche454/R_2013_05_01_13_27_15_FLX12070283_Administrator_20130501_pH1N1DenAndDen4
/media/VD_Research/NGSData/RawData/Roche454/R_2013_05_03_16_14_38_FLX12070283_Administrator_30130503_16s_EoE_Buny_Phage_Leish
/media/VD_Research/NGSData/RawData/Roche454/R_2013_05_22_13_52_58_FLX12070283_Administrator_05222013_Den2AndDen3
/media/VD_Research/NGSData/RawData/Roche454/2009_05_19
/media/VD_Research/NGSData/RawData/Roche454/2010_03_19
/media/VD_Research/NGSData/RawData/Roche454/2010_05_11
/media/VD_Research/NGSData/RawData/Roche454/2010_06_09
/media/VD_Research/NGSData/RawData/Roche454/2010_09_23
/media/VD_Research/NGSData/RawData/Roche454/2011_06_15
/media/VD_Research/NGSData/RawData/Roche454/2011_08_11
/media/VD_Research/NGSData/RawData/Roche454/2011_08_31
/media/VD_Research/NGSData/RawData/Roche454/2011_10_19
/media/VD_Research/NGSData/RawData/Roche454/2011_12_23
/media/VD_Research/NGSData/RawData/Roche454/2012_01_25
/media/VD_Research/NGSData/RawData/Roche454/2012_02_15
/media/VD_Research/NGSData/RawData/Roche454/2012_03_09
/media/VD_Research/NGSData/RawData/Roche454/2012_03_15
/media/VD_Research/NGSData/RawData/Roche454/2012_04_04
/media/VD_Research/NGSData/RawData/Roche454/2012_05_07
/media/VD_Research/NGSData/RawData/Roche454/2012_05_11
/media/VD_Research/NGSData/RawData/Roche454/2012_06_22
/media/VD_Research/NGSData/RawData/Roche454/2012_07_19
/media/VD_Research/NGSData/RawData/Roche454/2012_08_06
/media/VD_Research/NGSData/RawData/Roche454/2012_08_07
/media/VD_Research/NGSData/RawData/Roche454/2012_08_31
/media/VD_Research/NGSData/RawData/Roche454/2013_02_01
/media/VD_Research/NGSData/RawData/Roche454/2013_03_12
/media/VD_Research/NGSData/RawData/Roche454/2013_05_01
/media/VD_Research/NGSData/RawData/Roche454/2013_05_03
/media/VD_Research/NGSData/RawData/Roche454/2013_05_10
/media/VD_Research/NGSData/RawData/Roche454/2013_05_22
/media/VD_Research/NGSData/RawData/Roche454/2013_06_15
/media/VD_Research/NGSData/RawData/Roche454/2013_07_03
/media/VD_Research/NGSData/RawData/Roche454/R_2011_10_19_13_13_50_FLX12070283_Administrator_101911_pathogenDiscovery
/media/VD_Research/NGSData/RawData/Roche454/R_2011_12_23_11_20_18_FLX12070283_Administrator_12232011_AFRIMS_Den2AndPathogenDiscovery
/media/VD_Research/NGSData/RawData/Roche454/R_2012_03_15_10_09_58_FLX12070283_Administrator_03152012_Pathogen_Adv_Phage
/media/VD_Research/NGSData/RawData/Roche454/R_2012_05_07_10_47_49_FLX12070283_Administrator_05072012_phagebac_pathogen
/media/VD_Research/NGSData/RawData/Roche454/R_2012_06_22_07_51_49_FLX12070283_Administrator_062212_FluBAndAH3
/media/VD_Research/NGSData/RawData/Roche454/R_2013_02_01_16_31_49_FLX12070283_Administrator_20130201_16s_phage
/media/VD_Research/NGSData/RawData/Roche454/R_2013_05_01_13_27_15_FLX12070283_Administrator_20130501_pH1N1DenAndDen4
/media/VD_Research/NGSData/RawData/Roche454/R_2013_05_03_16_14_38_FLX12070283_Administrator_30130503_16s_EoE_Buny_Phage_Leish
/media/VD_Research/NGSData/RawData/Roche454/R_2013_05_22_13_52_58_FLX12070283_Administrator_05222013_Den2AndDen3

fixlinks.hs

import qualified Data.List.Utils as L
import System.Posix.Files as F
import System.Directory as D
import qualified System.IO
import Data.Foldable (for_)
import Control.Applicative (liftA2)
import Control.Monad (when)
import System.FilePath.Posix ((</>))

-- export LD_LIBRARY_PATH=/media/VD_Research/Admin/PBS/Software/miniconda/lib/:$LD_LIBRARY_PATH
-- stack install MissingH
-- stack runghc fixlinks.hs
-- OR
-- stack exec ghc fixlinks.hs
-- ./fixlinks (files.txt must be in same directory)

-- should check to make sure that this fixRoot actually did something, otherwise there is a broken link with something else causing it.
-- should also confirm that resulting path actually exists.
-- alternatively could make relative symlinks by Cd'ing first: http://superuser.com/questions/146231/how-do-i-create-a-relative-symbolic-link-in-linux

fixLink :: FilePath -> IO ()
fixLink f = tryReplaceLink f =<< fixRoot <$> F.readSymbolicLink f
 where 
  fixRoot = L.replace "/home/EIDRUdata/" "/media/VD_Research/" 
  tryReplaceLink src dest = do
    destExist <- fileExist dest
    if destExist then replaceLink src dest else putStrLn $ "Cannot rescue file " ++ src ++ " with link to " ++ dest
  replaceLink src dest = do
   F.removeLink src
   F.createSymbolicLink dest src 

main = do
  directories <- lines <$> System.IO.readFile "files.txt"
  for_ directories $ \dir -> do
    relFiles <- listDirectory dir
    for_ relFiles $ \relF -> do
      let absF = dir </> relF
      isBroken <- brokenLink absF
      when (isBroken && (relF /= "meta")) (fixLink absF)
  where
    brokenLink :: FilePath -> IO Bool
    brokenLink p = not <$> fileExist p
    listDirectory dir = filter (not . (`elem` [".", ".."])) <$> D.getDirectoryContents dir