diff options
| author | Gabor Pali <pgj@FreeBSD.org> | 2013-06-04 18:53:40 +0000 |
|---|---|---|
| committer | Gabor Pali <pgj@FreeBSD.org> | 2013-06-04 18:53:40 +0000 |
| commit | 109269205e521bb1d2d87678a391e5adefff88d6 (patch) | |
| tree | 93f1f9278a9a48902904b7ff4a5ce711c10efe08 /science | |
| parent | ad7295cafd0e46ece6fcbf594ef39a767c296d0e (diff) | |
| download | ports-109269205e521bb1d2d87678a391e5adefff88d6.tar.gz ports-109269205e521bb1d2d87678a391e5adefff88d6.zip | |
Notes
Diffstat (limited to 'science')
| -rw-r--r-- | science/hs-bio/Makefile | 6 | ||||
| -rw-r--r-- | science/hs-bio/files/patch-Bio__GFF3__FeatureHierSequences.hs | 19 |
2 files changed, 21 insertions, 4 deletions
diff --git a/science/hs-bio/Makefile b/science/hs-bio/Makefile index 09b6caf80e80..2d685b87f086 100644 --- a/science/hs-bio/Makefile +++ b/science/hs-bio/Makefile @@ -3,16 +3,14 @@ PORTNAME= bio PORTVERSION= 0.5.2 -PORTREVISION= 3 +PORTREVISION= 4 CATEGORIES= science haskell MAINTAINER= haskell@FreeBSD.org -COMMENT= A bioinformatics library +COMMENT= Bioinformatics library LICENSE= LGPL21 -CABAL_SETUP= Setup.hs - USE_CABAL= mtl parallel parsec QuickCheck>=2 tagsoup>=0.8 EXECUTABLE= fastout flowclip flx frecover frename orf rselect-pe diff --git a/science/hs-bio/files/patch-Bio__GFF3__FeatureHierSequences.hs b/science/hs-bio/files/patch-Bio__GFF3__FeatureHierSequences.hs new file mode 100644 index 000000000000..6f83130df055 --- /dev/null +++ b/science/hs-bio/files/patch-Bio__GFF3__FeatureHierSequences.hs @@ -0,0 +1,19 @@ +--- ./Bio/GFF3/FeatureHierSequences.hs.orig 2012-02-23 14:45:38.000000000 +0100 ++++ ./Bio/GFF3/FeatureHierSequences.hs 2013-05-01 00:28:58.000000000 +0200 +@@ -15,6 +15,7 @@ + import qualified Data.Map as M + import Data.Maybe + import qualified Data.Set as S ++import System.IO.Error (catchIOError) + + import Bio.Sequence.SeqData + import Bio.Sequence.Fasta +@@ -72,7 +73,7 @@ + return $ Seq seqname sequ Nothing + + catchIOErrors :: IO a -> ErrorT String IO a +-catchIOErrors m = ErrorT { runErrorT = liftM Right m `catch` (return . Left . show) } ++catchIOErrors m = ErrorT { runErrorT = liftM Right m `catchIOError` (return . Left . show) } + + runGFF :: FilePath -> (ErrorT String (Reader FeatureHierSequences) a) -> ErrorT String IO a + runGFF gffname m = do gff <- catchIOErrors $ LBS.readFile gffname |