From ff5759efc4a11580d585abe52f4fbe97b44f948e Mon Sep 17 00:00:00 2001
From: "Mitchell R. Vollger" <mrvollger@gmail.com>
Date: Fri, 20 Oct 2023 10:24:53 -0700
Subject: [PATCH] chore: update.

---
 Dockerfile | 29 ++++++++++++++++++++---------
 NOTES.md   | 13 +++++++++++--
 2 files changed, 31 insertions(+), 11 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index 23d653f0..50945f9c 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,7 @@
 FROM ubuntu:20.04
 
+ENV FT_VERSION="0.3.6"
+
 # Update default packages
 RUN apt-get update
 
@@ -29,9 +31,9 @@ RUN apt-get install -y \
 RUN apt-get update
 
 # Install HTSlib
-RUN wget https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2
-RUN tar -xjvf htslib-1.17.tar.bz2
-WORKDIR /htslib-1.17
+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
@@ -43,15 +45,24 @@ ENV PATH="/root/.cargo/bin:${PATH}"
 
 # Install libtorch
 WORKDIR /src/fibertools-rs
-RUN wget https://download.pytorch.org/libtorch/cpu/libtorch-shared-with-deps-2.0.1%2Bcpu.zip
-RUN unzip libtorch-shared-with-deps-2.0.1+cpu.zip
+ENV TORCH_VERSION="2.0.1"
+# "cu117" or "cu118" or "cpu"
+ENV INSTALL_TYPE="cu118" 
+ENV PY_URL="https://download.pytorch.org/libtorch/${INSTALL_TYPE}/libtorch-shared-with-deps-${TORCH_VERSION}%2B${INSTALL_TYPE}.zip"
+RUN wget ${PY_URL}
+RUN unzip "libtorch-shared-with-deps-${TORCH_VERSION}+${INSTALL_TYPE}.zip"
+#RUN unzip libtorch*.zip
 ENV LIBTORCH=/src/fibertools-rs/libtorch
 ENV LD_LIBRARY_PATH=/src/fibertools-rs/libtorch/lib:$LD_LIBRARY_PATH
 ENV LIBTORCH_CXX11_ABI=0
 
 COPY . .
 
-# RUN cargo install --path . --root /usr/local
-RUN cargo build --release  
-RUN cp ./target/release/ft /usr/local/bin/ft
-RUN ft --help
\ No newline at end of file
+#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
+
+#RUN cargo install --path . --root /usr/local
\ No newline at end of file
diff --git a/NOTES.md b/NOTES.md
index 87fb61a1..8797f60a 100644
--- a/NOTES.md
+++ b/NOTES.md
@@ -1,2 +1,11 @@
-how to install pytorch on conda with gpu
- mamba install pytorch=1.12 torchvision torchaudio pytorch-cuda=11.6 -c pytorch -c nvidia -c conda-forge
+# How to install pytorch on conda with gpu
+
+```
+mamba install pytorch=1.12 torchvision torchaudio pytorch-cuda=11.6 -c pytorch -c nvidia
+```
+
+# How to make the docker image using the Dockerfile
+
+```
+docker build --progress=plain -f Dockerfile .
+```