chore: update.

fiberseq · Oct 20, 2023 · 1e08da2 · 1e08da2
1 parent e6e45a3
commit 1e08da2
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Showing 2 changed files with 24 additions and 54 deletions.
diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -2,9 +2,9 @@ name: CI
 
 on:
   push:
-    branches: [ main, master, dev, development ]
+    branches: [main, master, dev, development]
   pull_request:
-    branches: [ main, master ]
+    branches: [main, master]
 
 jobs:
   Formatting:
@@ -24,20 +24,20 @@ jobs:
         run: cargo fmt -- --check
 
   Linting:
-      runs-on: ubuntu-latest
-      steps:
-        - name: Checkout repository
-          uses: actions/checkout@v3
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
 
-        - name: Install stable toolchain
-          uses: actions-rs/toolchain@v1
-          with:
-            toolchain: stable
-            override: true
-            components: clippy
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          components: clippy
 
-        - name: Lint with clippy
-          run: docker run -i $(docker build --pull -q .) cargo clippy --release
+      - name: Lint with clippy
+        run: docker run -i $(docker build --pull -q .) cargo clippy --release
 
   Testing:
     needs: Formatting
@@ -55,4 +55,3 @@ jobs:
       - name: Run test
         run: |
           docker run -i $(docker build --pull -q .) cargo test  -p bio-io -p bamlift -p fibertools-rs --release -- --test-threads=1
- 
diff --git a/Dockerfile b/Dockerfile
@@ -1,24 +1,22 @@
-FROM ubuntu:20.04
-
-# Update default packages
-RUN apt-get update
+FROM pytorch/pytorch:2.1.0-cuda12.1-cudnn8-runtime
 
 # stop time prompt 
 ARG DEBIAN_FRONTEND=noninteractive
 
+# Update new packages
+RUN apt-get update
+
 # Get Ubuntu packages
 RUN apt-get install -y \
     build-essential \
     curl \
-    wget \
     zip \
     cmake \
     git \
     autoconf \
     automake \
     make \
     gcc \
-    perl \
     zlib1g-dev \
     libbz2-dev \
     liblzma-dev \
@@ -32,39 +30,12 @@ RUN apt-get update
 RUN curl https://sh.rustup.rs -sSf | bash -s -- -y
 ENV PATH="/root/.cargo/bin:${PATH}"
 
-
-# Install libtorch
-WORKDIR /src/fibertools-rs
-ENV TORCH_VERSION="2.1.0"
-# "cu117" or "cu118" or "cpu"
-ENV INSTALL_TYPE="cpu" 
-ENV PY_URL="https://download.pytorch.org/libtorch/${INSTALL_TYPE}/libtorch-shared-with-deps-${TORCH_VERSION}%2B${INSTALL_TYPE}.zip"
-#ENV PY_URL="https://download.pytorch.org/libtorch/${INSTALL_TYPE}/libtorch-cxx11-abi-shared-with-deps-${TORCH_VERSION}%2B${INSTALL_TYPE}.zip"
-RUN wget ${PY_URL}
-RUN unzip "libtorch-*${TORCH_VERSION}+${INSTALL_TYPE}.zip"
-ENV LIBTORCH=/src/fibertools-rs/libtorch
-ENV LD_LIBRARY_PATH=${LIBTORCH}/lib:$LD_LIBRARY_PATH
-#ENV LIBTORCH_CXX11_ABI=0
-RUN ls $LIBTORCH/lib
-
 COPY . .
 
-RUN cargo build --release && cp ./target/release/ft /usr/local/bin/ft
-
-RUN ft --help
-
-
-#RUN cargo install --path . --root /usr/local
+# use the install pytroch from docker image
+ENV LIBTORCH_USE_PYTORCH=1
+RUN python checkpy.py
+RUN ls "/opt/conda/lib/python3.10/site-packages/torch/lib/"
 
-# Install HTSlib
-# RUN wget https://github.com/samtools/htslib/releases/download/1.18/htslib-1.18.tar.bz2
-# RUN tar -xjvf htslib-1.18.tar.bz2
-# WORKDIR /htslib-1.18
-# RUN ./configure
-# RUN make
-# RUN make install
-
-
-#RUN wget "https://github.com/fiberseq/fibertools-rs/archive/refs/tags/v${FT_VERSION}.tar.gz"
-#RUN tar -xzf "v${FT_VERSION}.tar.gz"
-#RUN cd fibertools-rs-${FT_VERSION} && ls && 
+RUN cargo build --release && cp ./target/release/ft /usr/local/bin/ft
+RUN ft --help