From 02696ee7c7676a708e98765a9f10b3a33c528f91 Mon Sep 17 00:00:00 2001 From: Kai Zhang Date: Fri, 19 Aug 2022 23:30:16 -0700 Subject: [PATCH] upgrade to ghc 9.0 --- Taiji.cabal | 4 ++-- src/Taiji/Core.hs | 6 ++--- src/Taiji/Core/Network/DeNovo.hs | 2 +- src/Taiji/SingleCell.hs | 2 +- stack.yaml | 38 +++++++++++++++++--------------- 5 files changed, 27 insertions(+), 25 deletions(-) diff --git a/Taiji.cabal b/Taiji.cabal index 2ad13e7..61fe67f 100644 --- a/Taiji.cabal +++ b/Taiji.cabal @@ -1,5 +1,5 @@ name: Taiji -version: 1.3.1 +version: 1.3.1.2 synopsis: Multi-omics bioinformatics analysis pipeline description: Taiji is an integrated multi-omics bioinformatics analysis pipeline. It can analyze ATAC-seq, RNA-seq, single cell @@ -10,7 +10,7 @@ license: BSD3 license-file: LICENSE author: Kai Zhang maintainer: kai@kzhang.org -copyright: (c) 2017-2021 Kai Zhang +copyright: (c) 2017-2022 Kai Zhang category: Bio build-type: Simple extra-source-files: diff --git a/src/Taiji/Core.hs b/src/Taiji/Core.hs index 9146d5c..f11ce9e 100644 --- a/src/Taiji/Core.hs +++ b/src/Taiji/Core.hs @@ -53,12 +53,12 @@ builder = do return $ getHiCLoops hic |] $ doc .= "Read HiC loops from input file." - node "Create_Linkage_Prep" 'aggregate $ return () - nodePar "Create_Linkage" 'saveAssociations $ memory .= 20 + node "Create_Linkage_Prep" [| aggregate |] $ return () + nodePar "Create_Linkage" [| saveAssociations |] $ memory .= 20 path ["Create_Linkage_Prep", "Create_Linkage"] uNode "Compute_Ranks_Prep" [| \(x, expr) -> return $ zip x $ repeat expr |] - nodePar "Compute_Ranks" 'computeRanks $ do + nodePar "Compute_Ranks" [| computeRanks |] $ do doc .= "Perform personalized Pagerank." memory .= 20 node "Output_Ranks" [| \input -> do diff --git a/src/Taiji/Core/Network/DeNovo.hs b/src/Taiji/Core/Network/DeNovo.hs index b69e5ef..9347b38 100644 --- a/src/Taiji/Core/Network/DeNovo.hs +++ b/src/Taiji/Core/Network/DeNovo.hs @@ -84,7 +84,7 @@ getTFBS :: Monad m getTFBS peaks = concatMapC f .| sinkList >>= return . (fmap . fmap) nub' . bedToTree (++) where - f site = case IM.elems (intersecting peaks site) of + f site = case IM.elems (within peaks site) of [] -> Nothing xs -> Just $ (bed, [SiteInfo (getTFName site) siteSc (maximum xs)]) where diff --git a/src/Taiji/SingleCell.hs b/src/Taiji/SingleCell.hs index 4547c30..bb3d64c 100644 --- a/src/Taiji/SingleCell.hs +++ b/src/Taiji/SingleCell.hs @@ -80,6 +80,6 @@ mkTFBSMap = mapC (\x -> (x^._bed, [x^._data])) .| sinkList >>= builder :: Builder () builder = do uNode "Compute_Ranks_SC_Prep" [| return . prepareData |] - nodePar "Compute_Ranks_SC" 'computeRanksCluster $ return () + nodePar "Compute_Ranks_SC" [| computeRanksCluster |] $ return () node "Output_Ranks_SC" [| outputRanksCluster "/Rank/Cluster/" |] $ return () path ["Compute_Ranks_SC_Prep", "Compute_Ranks_SC", "Output_Ranks_SC"] \ No newline at end of file diff --git a/stack.yaml b/stack.yaml index b80326f..ed76588 100644 --- a/stack.yaml +++ b/stack.yaml @@ -1,4 +1,4 @@ -resolver: lts-18.12 +resolver: lts-19.19 packages: - '.' @@ -12,25 +12,25 @@ flags: extra-deps: - git: https://github.com/Taiji-pipeline/Taiji-utils.git - commit: f5e009cf7a9a683f7e43bf97fb33c758ba13d97b + commit: 7dbe3dfdcdfc0a5f28bfe3c6162cf9f9a56bda91 - git: https://github.com/Taiji-pipeline/bio-pipelines.git - commit: 90f242992001be3672ddc2c1749beff432bbc5f3 + commit: 453223010d0f3b94d43fecc65e1e105fbb7e6354 - git: https://github.com/Taiji-pipeline/bio-experiments.git - commit: 12d62074c50f746482c3c2db4e5b47bc43803a60 + commit: ffea141128e7b63a21162c76358194ad433a19a9 - git: https://github.com/Taiji-pipeline/Taiji-RNA-seq.git - commit: a567e632e1167d7105974e1acf87be9f356fc494 + commit: 747625a6a6eec34af5d948ed99791998bbb07936 - git: https://github.com/Taiji-pipeline/Taiji-ATAC-seq.git - commit: ba7a073b56bf4ca60a227d70b4508f2f83a57d16 + commit: e1aef69746ca52f07dc5ba3bbe6b72e75b1f271a - git: https://github.com/Taiji-pipeline/Taiji-scRNA-seq.git - commit: 0362dc0fc0024ff474f4d582d048852444eac5b9 + commit: 989a71d593806b8726c37b61f79b132b4c9a6a8d - git: https://github.com/Taiji-pipeline/Taiji-scATAC-seq.git - commit: 6e912364ddce0f7ddcaae7938cd9696aac4937ca + commit: 86559067dd3dd374bdfda93c1f1aaf2fc30de4f3 - git: https://github.com/Taiji-pipeline/Taiji-fusion.git commit: a2ef0b3c162028ba1bd89c7f151b3e703f4cde8d @@ -38,32 +38,34 @@ extra-deps: - git: https://github.com/kaizhang/HsHTSLib.git commit: a2fcc435fc752152f06f14e0cfa56153fa0b7d02 -- git: https://github.com/kaizhang/ChromVAR.git - commit: d64dd55579c8db9625028065b4cb3314e8f0c4a9 - - git: https://github.com/kaizhang/matrix-sized.git - commit: aed69651b2da5ca4c9076c8c4d981b876932e5b8 + commit: 2c26f974936b20bdae3e17c92d8ff43c83587348 - git: https://github.com/kaizhang/haskell-igraph.git - commit: d790e030e6e08b04dc0971221b6054d6700d82e7 + commit: de809a8ff9486c8bdce9a620ca7357a61bc64abb - git: https://github.com/kaizhang/bioinformatics-toolkit.git - commit: 463cb8d16230a0777072e8793338b89a7c420487 + commit: b8949495069a61e56ae125ee5e4f87b9a423868f subdirs: - bioinformatics-toolkit +- git: https://github.com/Taiji-pipeline/ftp-client.git + commit: 9c4c577ea39c85e5da28b7fd76c54b31743fc9df + subdirs: + - ftp-client-conduit + - bbi-0.1.1 - clustering-0.4.1 -- jmacro-0.6.17 +- jmacro-0.6.17.1 -- git: https://github.com/Taiji-pipeline/distributed-process.git - commit: e143f6bce9d7f1e13b0d12f11763f6f24d2da4df +- git: https://github.com/haskell-distributed/distributed-process.git + commit: 8de080874b7671186af8dc04deb471e909b10719 - distributed-process-monad-control-0.5.1.3 - network-transport-tcp-0.8.0 - distributed-static-0.3.9 - git: https://github.com/kaizhang/SciFlow.git - commit: ee510340b54f4e2c416cc6e121c767885abce374 + commit: 6c617a15a99596c9fb50ef1034e9da33c1111f7e subdirs: - SciFlow - SciFlow-app