v1.2.0

Taiji-pipeline · May 3, 2020 · 1eda209 · 1eda209
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -4,24 +4,148 @@ on: [push]
 jobs:
   build_macos:
     name: Build macos
-    runs-on: macos-latest
+    runs-on: macos-10.15
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
+
+      - name: Cache haskell packages
+        uses: actions/cache@v1
+        env:
+          cache-name: cache-haskell-packages
+        with:
+          path: ~/.stack
+          key: ${{ runner.os }}-build-${{ env.cache-name }}
+          restore-keys: |
+            ${{ runner.os }}-build-${{ env.cache-name }}
+            ${{ runner.os }}-build-
+            ${{ runner.os }}-
 
       - name: Install dependency
         run: brew install haskell-stack
 
       - name: Build
-        run: stack install
+        run: |
+          stack build
+          mv $(stack path --local-install-root)/bin/taiji taiji
+
+      - name: Upload build result
+        uses: actions/upload-artifact@v1
+        with:
+          name: taiji-macOS-Catalina-10.15
+          path: ./taiji
 
   build_ubuntu:
     name: Build ubuntu
     runs-on: ubuntu-18.04
     steps:
-      - uses: actions/checkout@v1
+      - uses: actions/checkout@v2
+
+      - name: Cache haskell packages
+        uses: actions/cache@v1
+        env:
+          cache-name: cache-haskell-packages
+        with:
+          path: ~/.stack
+          key: ${{ runner.os }}-build-${{ env.cache-name }}
+          restore-keys: |
+            ${{ runner.os }}-build-${{ env.cache-name }}
+            ${{ runner.os }}-build-
+            ${{ runner.os }}-
 
       - name: Install dependency
         run: sudo apt-get install haskell-stack
 
       - name: Build
-        run: stack install
+        run: |
+          stack build
+          mv $(stack path --local-install-root)/bin/taiji taiji
+
+      - name: Upload build result
+        uses: actions/upload-artifact@v1
+        with:
+          name: taiji-Ubuntu-x86_64
+          path: ./taiji
+
+  build_centos:
+    name: Build CentOS
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Cache haskell packages
+        uses: actions/cache@v1
+        env:
+          cache-name: cache-haskell-packages
+        with:
+          path: ~/.stack
+          key: CentOS-build-${{ env.cache-name }}
+          restore-keys: CentOS-build-${{ env.cache-name }}
+
+      - name: Build
+        run: |
+          docker pull kaizhang/centos-haskell-stack
+          docker run -v ~/.stack:/root/.stack:rw \
+            -v `pwd`:/source:rw kaizhang/centos-haskell-stack \
+            /bin/bash -c \
+            'cd source && stack build --allow-different-user && mv $(stack path --local-install-root --allow-different-user)/bin/taiji /source/taiji'
+          sudo chmod -R 777 ~/.stack
+
+      - name: Upload build result
+        uses: actions/upload-artifact@v1
+        with:
+          name: taiji-CentOS-x86_64
+          path: ./taiji
+
+  publish:
+    if: startsWith(github.ref, 'refs/tags/v')
+    name: Publish
+    runs-on: ubuntu-latest
+    needs: [build_macos, build_ubuntu, build_centos]
+    steps:
+      - name: Download
+        uses: actions/download-artifact@v2
+      - name: Create Release
+        id: create_release
+        uses: actions/create-release@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          tag_name: ${{ github.ref }}
+          release_name: Taiji ${{ github.ref }}
+          body: |
+            Changes in this Release:
+          draft: false
+          prerelease: false
+
+      - name: Upload macOS
+        id: upload-macOS
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./taiji-macOS-Catalina-10.15/taiji
+          asset_name: taiji-macOS-Catalina-10.15
+          asset_content_type: application/octet-stream
+
+      - name: Upload Ubuntu
+        id: upload-ubuntu
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./taiji-Ubuntu-x86_64/taiji
+          asset_name: taiji-Ubuntu-x86_64
+          asset_content_type: application/octet-stream
+
+      - name: Upload Centos
+        id: upload-centos
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }}
+          asset_path: ./taiji-CentOS-x86_64/taiji
+          asset_name: taiji-CentOS-x86_64
+          asset_content_type: application/octet-stream
diff --git a/.travis.yml b/.travis.yml
diff --git a/ChangeLog.md b/ChangeLog.md
@@ -1,10 +1,10 @@
-Latest
-======
+v1.2.0 (2020-05-03)
+===================
 
 Breaking changes:
 -----------------
 
-- BWA index 
+- Need to include the index prefix when specifying the location of the BWA or RSEM index in config.yml. For example: `(old) path-to-index/bwa_index => (new) path-to-index/bwa_index/GRCh38.fa`.
 
 Other changes:
 --------------
@@ -17,6 +17,8 @@ Other changes:
 
 - Implement the chromVAR algorithm in single cell ATAC analysis.
 
+- Bug fixes.
+
 
 v1.1.0 (2020-01-10)
 ===================

diff --git a/README.md b/README.md
@@ -1,6 +1,7 @@
 # Taiji
 
-[![Build Status](https://travis-ci.org/Taiji-pipeline/Taiji.svg?branch=master)](https://travis-ci.org/Taiji-pipeline/Taiji)
+![Continuous integration](https://github.com/Taiji-pipeline/Taiji/workflows/Continuous%20integration/badge.svg)
+![GitHub All Releases](https://img.shields.io/github/downloads/Taiji-pipeline/Taiji/total)
 
 Taiji is an integrated analysis pipeline for analyzing bulk/single-cell ATAC-seq and RNA-seq data.
 Please go to this [website](https://taiji-pipeline.github.io/) for documentation and tutorials. 

diff --git a/app/Main.hs b/app/Main.hs
@@ -22,13 +22,12 @@ import qualified Taiji.Pipeline.SC.ATACSeq as SCATACSeq
 import qualified Taiji.Pipeline.RNASeq as RNASeq
 import qualified Taiji.Pipeline.SC.RNASeq as SCRNASeq
 
+import           Taiji.Prelude
 import           Taiji.Pipeline.ATACSeq.Types (ATACSeqConfig (..))
 import           Taiji.Pipeline.SC.ATACSeq.Types (SCATACSeqConfig (..))
 import           Taiji.Pipeline.RNASeq.Types (RNASeqConfig (..))
 import           Taiji.Pipeline.SC.RNASeq.Types (SCRNASeqConfig (..))
 
-import           Taiji.Prelude
-
 instance ATACSeqConfig TaijiConfig where
     _atacseq_output_dir = (<> "/ATACSeq") . _taiji_output_dir
     _atacseq_input = _taiji_input
@@ -123,15 +122,15 @@ getCoordConfig ip port fl = do
     str (String x) = T.unpack x
     str _ = error "Expecting string"
 
-commands = [ runParser getCoordConfig
-           , deleteParser
-           , showParser
-           , viewParser
-           , remoteParser (Proxy :: Proxy Remote) ]
-
 main :: IO ()
 main = defaultMain header descr commands wf
   where
     header = printf "Taiji-v%s" $ showVersion version
     descr = "Multi-omics bioinformatics analysis pipline. " <>
         "For more details, see: https://taiji-pipeline.github.io/"
+    commands =
+        [ runParser getCoordConfig
+        , deleteParser
+        , showParser
+        , viewParser
+        , remoteParser (Proxy :: Proxy Remote) ]
diff --git a/stack.yaml b/stack.yaml
@@ -7,39 +7,41 @@ packages:
 extra-deps:
 
 - git:     https://github.com/Taiji-pipeline/Taiji-utils.git
-  commit:  ccb65aae38764cd176ae8f79a9869a1d1f117234
+  commit:  4811e87ff6ce22a3ca3b0c7a19547f18b976274d
 
 - git:     https://github.com/Taiji-pipeline/bio-pipelines.git
-  commit:  c1f83502718bb4dff028eaab9493e79ce6634f1b
+  commit:  7db3d5030f85944a1151cc9654676f2c8b151de7
 
 - git:     https://github.com/Taiji-pipeline/bio-experiments.git
-  commit:  e4dd0b2dba06015b960287e18a01072badbcbb0a
+  commit:  07e7828d5ab7b097087d60bc716729dc88741279
 
 - git:     https://github.com/Taiji-pipeline/Taiji-RNA-seq.git
   commit:  e92cb6ce074f612f6152f6970a20f0acebe9c326
 
 - git:     https://github.com/Taiji-pipeline/Taiji-ATAC-seq.git
-  commit:  3bd264eb1cd24ec114b7fa077914334349fe6be1
+  commit:  afd7b0d98a420afa14ee3fcdd103ca9b4f171f6a
 
 - git:     https://github.com/Taiji-pipeline/Taiji-scRNA-seq.git
-  commit:  60e02353a5667d2dde41de9cc34e2c655d135ac0
+  commit:  93f70a4d80c6e3b2878ff27be150648876d5ba9c
 
 - git:     https://github.com/Taiji-pipeline/Taiji-scATAC-seq.git
-  commit:  caca3d02d391382ef6a16e49b9bf088116bf40c0
+  commit:  6e7ad0d514324ccbe51ecf97164460d082ca803f
 
 - git:     https://github.com/kaizhang/HsHTSLib.git
   commit:  c116cfa29e33d3142a6cb502f1dc4c02066d0aa9
 
 - git:     https://github.com/kaizhang/ChromVAR.git
-  commit:  d65357474b714e1eed4867b528fbb6995b13b000
+  commit:  5c252643a180bafaf80410767b9afabe8d825104
+
+- git:     https://github.com/kaizhang/matrix-sized.git
+  commit:  b7d1a52a09138366d92fb7c778257baaac9c6cc8
 
 - bioinformatics-toolkit-0.9.3.1
 - haskell-igraph-0.8.0
 
 - bbi-0.1.1
 - clustering-0.4.1
 - jmacro-0.6.16
-- matrix-sized-0.0.3
 
 - git:     https://github.com/haskell-distributed/distributed-static.git
   commit:  d34b5139a0c349fbda6ffea5fbbe960c3c91aeb1