Merge pull request #1 from jakobilab/devel

Merging devel branch into main

.github/workflows/build_docker.yml

@@ -0,0 +1,53 @@
+name: Build and Publish Docker Container
+
+on:
+  # run it on push to the default repository branch
+  push:
+    branches: [devel]
+  # run it during pull request
+  pull_request:
+
+jobs:
+  # define job to build and publish docker image
+  build-and-push-docker-image:
+    name: Build Docker image and push to repositories
+    # run only when code is compiling and tests are passing
+    runs-on: ubuntu-latest
+
+    # steps to perform in job
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v3
+
+      # setup Docker buld action
+      - name: Set up Docker Buildx
+        id: buildx
+        uses: docker/setup-buildx-action@v2
+
+      - name: Login to DockerHub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKERHUB_TOKEN }}
+
+      - name: Login to Github Packages
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Build image and push to Docker Hub and GitHub Container Registry
+        uses: docker/build-push-action@v2
+        with:
+          # relative path to the place where source code with Dockerfile is located
+          context: ./docker/
+          # Note: tags has to be all lower-case
+          tags: |
+            jakobilab/circtools:devel
+            ghcr.io/jakobilab/circtools/circtools:devel
+          # build on feature branches, push only on main branch
+          push: ${{ github.ref == 'refs/heads/devel' }}
+
+      - name: Image digest
+        run: echo ${{ steps.docker_build.outputs.digest }}

.github/workflows/run_circtools_detect.yml

@@ -0,0 +1,81 @@
+name: Circtools CI
+
+on:
+  push:
+  pull_request:
+#  schedule:
+#    - cron: '0 7 * * *'
+
+concurrency:
+  group: ci-tests-${{ github.ref }}-1
+  cancel-in-progress: true
+
+jobs:
+  Main:
+    strategy:
+      matrix:
+        os: [ubuntu-18.04, ubuntu-20.04, ubuntu-22.04, macos-11, macos-12]
+        R: ['4.1.0' , '4.2.0' ]
+        python-version: ["3.7", "3.8", "3.9", "3.10"]
+#        os: [ubuntu-22.04]
+#        R: ['4.2.0' ]
+#        python-version: ["3.7"]
+    name: R ${{ matrix.R }} | Python ${{ matrix.python-version }} | ${{ matrix.os }}
+    steps:
+    - name: Create files
+      uses: actions/checkout@v3
+      with:
+       ref: devel
+    - name: Set up R
+      uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: ${{ matrix.R }}
+    - name: Set up R dependencies
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        cache-version: 1
+        extra-packages: |
+          local::contrib/circtest
+          local::contrib/primex
+    - name: Checking library loading
+      run: Rscript -e 'library(primex)'
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        architecture: 'x64'
+    - name: Updating setuptools
+      run: |
+         python3 -m pip install -U pip setuptools
+    - name: Updating pip
+      run: |
+         python3 -m pip install --upgrade pip
+    - name: Installing circtools & Python dependencies
+      run: |
+         python3 -m pip install ./
+    - name: Check if circtools starts
+      run: |
+         circtools --version
+         which circtools
+    - name: Downloading circtools detect test data
+      run: |
+         wget https://arizona.box.com/shared/static/3xr9wmu2rq2i240leh5rothntgkmgzq3.bz2 -O circtools_detect_ci_input_data.tar.bz2
+         tar xvf circtools_detect_ci_input_data.tar.bz2
+    - name: Running circtools detect with minimal data set
+      run: |
+         cd circtools_detect_ci_input_data
+         circtools detect @samplesheet -ss -T 2 -D -an chr1.gtf -A chr1.fa -B @bam_files.txt -M -Nr 2 2 -fg -G -F -L 20 -O circtools_ci -k
+    - name: Checking generated output against master output
+      run: |
+         cd circtools_detect_ci_input_data
+         cd circtools_ci
+         ls -la
+         wc -l *
+         diff ../circtools_master/LinearCount LinearCount
+         if [ "$RUNNER_OS" == "Linux" ]; then
+           sha1sum -c ../circtools_master/sha1sums.txt
+         elif [ "$RUNNER_OS" == "macOS" ]; then
+           shasum -c ../circtools_master/sha1sums.txt
+         fi
+
+    runs-on: ${{ matrix.os }}

DESCRIPTION

@@ -0,0 +1,14 @@
+Package: ciRctools
+Title: Meta package to install R dependencies of circtools
+Version: 1.0.0
+Authors@R:
+    c(person(given = "Tobias",
+             family = "Jakobi",
+             role = c("aut", "cre"),
+             email = "tjakobi@arizona.edu"))
+Description: This is a simple package used to test the installation of all R dependencies of circtools.
+Depends:
+Imports: aod, ballgown, biomaRt, data.table, GenomicFeatures, GenomicRanges, ggbio, ggfortify, ggplot2, ggrepel, gridExtra, openxlsx, plyr, reshape2, devtools, kableExtra, formattable, dplyr, RColorBrewer, EnsDb.Rnorvegicus.v79, EnsDb.Mmusculus.v79, EnsDb.Hsapiens.v86
+Suggests:
+License: GPL (>= 2)
+VignetteBuilder:

README.rst

@@ -140,10 +140,10 @@ for follow up wet lab experiments to verify circRNA candidates.
     :scale: 100%
     :target: https://circtools.readthedocs.io/en/latest/?badge=latest
 
-.. |build| image:: https://travis-ci.org/dieterich-lab/circtools.svg?branch=master
+.. |build| image:: https://github.com/jakobilab/circtools/actions/workflows/run_circtools_detect.yml/badge.svg?branch=devel
     :alt: Build Status
     :scale: 100%
-    :target: https://travis-ci.org/dieterich-lab/circtools
+    :target: https://github.com/jakobilab/circtools/actions
 
 .. |zenodo| image:: https://zenodo.org/badge/83248654.svg
     :alt: Zenodo DOI link

circtools/circtest/circtest.py

@@ -50,17 +50,17 @@ def run_module(self):
             exit(-1)
 
         # check DCC directory
-        if not (os.path.exists(self.cli_params.DCC_dir)):
+        if not (os.path.exists(self.cli_params.detect_dir)):
             self.log_entry("DCC/detect data directory %s does not exist (or is not accessible)."
-                           % self.cli_params.DCC_dir)
+                           % self.cli_params.detect_dir)
             # exit with -1 error if we can't use it
             exit(-1)
 
         # check DCC files (only existence, not the content)
         self.check_input_files([
-            self.cli_params.DCC_dir + "CircRNACount",
-            self.cli_params.DCC_dir + "LinearCount",
-            self.cli_params.DCC_dir + "CircCoordinates"
+            self.cli_params.detect_dir + "CircRNACount",
+            self.cli_params.detect_dir + "LinearCount",
+            self.cli_params.detect_dir + "CircCoordinates"
         ])
 
         # check sample names
@@ -136,7 +136,7 @@ def run_module(self):
 
         # Variable number of args in a list
         args = [
-            self.cli_params.DCC_dir,
+            self.cli_params.detect_dir,
             self.cli_params.num_replicates,
             self.cli_params.condition_list,
             self.cli_params.condition_columns,