From dfa7b8c8db1ed80605bb4a0db3d7ecfb43c72eff Mon Sep 17 00:00:00 2001 From: Shifu Chen Date: Sun, 22 Sep 2024 08:07:48 +0800 Subject: [PATCH] update README for isa-l and libdeflate --- README.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/README.md b/README.md index 4ecca53..fd0142a 100644 --- a/README.md +++ b/README.md @@ -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) @@ -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 @@ -143,7 +143,7 @@ git clone https://github.com/OpenGene/fastp.git # build cd fastp -make +make -j # Install sudo make install