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update README for isa-l and libdeflate
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Shifu Chen authored and Shifu Chen committed Sep 22, 2024
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Expand Up @@ -19,8 +19,8 @@ Citation: Shifu Chen. 2023. Ultrafast one-pass FASTQ data preprocessing, quality
- [install with Bioconda](#install-with-bioconda)
- [or download the latest prebuilt binary for Linux users](#or-download-the-latest-prebuilt-binary-for-linux-users)
- [or compile from source](#or-compile-from-source)
- [Step 1: download and build libisal](#step-1-download-and-build-libisal)
- [step 2: download and build libdeflate](#step-2-download-and-build-libdeflate)
- [Step 1: install isa-l](#step-1-install-isa-l)
- [step 2: install libdeflate](#step-2-install-libdeflate)
- [Step 3: download and build fastp](#step-3-download-and-build-fastp)
- [input and output](#input-and-output)
- [output to STDOUT](#output-to-stdout)
Expand Down Expand Up @@ -114,20 +114,20 @@ chmod a+x ./fastp
## or compile from source
`fastp` depends on `libdeflate` and `libisal`, while `libisal` is not compatible with gcc 4.8. If you use gcc 4.8, your fastp will fail to run. Please upgrade your gcc before you build the libraries and fastp.

### Step 1: download and build libisal
See https://github.com/intel/isa-l
`autoconf`, `automake`, `libtools`, `nasm (>=v2.11.01)` and `yasm (>=1.2.0)` are required to build this isal
### Step 1: install isa-l
It's recommended that to install it using your package manager, for example `apt install isa-l` on ubuntu, or `brew install isa-l` on Mac. Otherwise you can compile isa-l from source. Please be noted that `isa-l` is not compatible with gcc 4.8 or older versions. See https://github.com/intel/isa-l
`autoconf`, `automake`, `libtools`, `nasm (>=v2.11.01)` and `yasm (>=1.2.0)` are required to build this isa-l
```shell
git clone https://github.com/intel/isa-l.git
cd isa-l
./autogen.sh
./configure --prefix=/usr --libdir=/usr/lib64
make
make -j
sudo make install
```

### step 2: download and build libdeflate
See https://github.com/ebiggers/libdeflate
### step 2: install libdeflate
It's recommended that to install it using your package manager, for example `apt install libdeflate` on ubuntu, or `brew install libdeflate` on Mac. Otherwise you can compile isa-l from source. See https://github.com/ebiggers/libdeflate
```shell
git clone https://github.com/ebiggers/libdeflate.git
cd libdeflate
Expand All @@ -143,7 +143,7 @@ git clone https://github.com/OpenGene/fastp.git

# build
cd fastp
make
make -j

# Install
sudo make install
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