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Shifu ChenShifu Chen
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update README for isa-l and libdeflate
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README.md

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@@ -19,8 +19,8 @@ Citation: Shifu Chen. 2023. Ultrafast one-pass FASTQ data preprocessing, quality
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- [install with Bioconda](#install-with-bioconda)
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- [or download the latest prebuilt binary for Linux users](#or-download-the-latest-prebuilt-binary-for-linux-users)
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- [or compile from source](#or-compile-from-source)
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- [Step 1: download and build libisal](#step-1-download-and-build-libisal)
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- [step 2: download and build libdeflate](#step-2-download-and-build-libdeflate)
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- [Step 1: install isa-l](#step-1-install-isa-l)
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- [step 2: install libdeflate](#step-2-install-libdeflate)
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- [Step 3: download and build fastp](#step-3-download-and-build-fastp)
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- [input and output](#input-and-output)
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- [output to STDOUT](#output-to-stdout)
@@ -114,20 +114,20 @@ chmod a+x ./fastp
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## or compile from source
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`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.
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### Step 1: download and build libisal
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See https://github.com/intel/isa-l
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`autoconf`, `automake`, `libtools`, `nasm (>=v2.11.01)` and `yasm (>=1.2.0)` are required to build this isal
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### Step 1: install isa-l
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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
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`autoconf`, `automake`, `libtools`, `nasm (>=v2.11.01)` and `yasm (>=1.2.0)` are required to build this isa-l
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```shell
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git clone https://github.com/intel/isa-l.git
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cd isa-l
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./autogen.sh
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./configure --prefix=/usr --libdir=/usr/lib64
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make
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make -j
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sudo make install
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```
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### step 2: download and build libdeflate
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See https://github.com/ebiggers/libdeflate
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### step 2: install libdeflate
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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
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```shell
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git clone https://github.com/ebiggers/libdeflate.git
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cd libdeflate
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# build
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cd fastp
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make
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make -j
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# Install
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sudo make install

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