2020.7.30丨Linux CentOS安装Abyss全流程（最新）

Abyss安装前需要安装依赖包

1.gcc(CentOS默认安装)：使用gcc -v查阅版本，有anaconda可以直接

conda install gcc

2.open MPI-4.0.4：https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.4.tar.bz2

open MPI-4.0.4：https://download.open-mpi.org/release/open-mpi/v4.0/openmpi-4.0.4.tar.bz2
tar xf openmpi-4.0.4.tar.bz2
cd openmpi-4.0.4.tar.bz2/
configure –prefix=/home/XXX/soft/openmpi-4.0.4
make all install

(其他软件类似)
3.boost
boost1.73.0:https://sourceforge.net/projects/boost/files/boost/1.73.0/boost_1_73_0.tar.bz2/download

直接解压安装：

tar jxf boost_1_73_0.tar.bz2

解压后如果是在指定安装目录下就不用再管了，

4.sparsehash-2.0.3:https://github.com/sparsehash/sparsehash/archive/sparsehash-2.0.3.tar.gz

cd sparsehash-2.0.3
./configure –prefix=home/XXX/soft/sparsehash-sparsehash-2.0.3
make
make install

5.sqlite3.32.3:https://www.sqlite.org/2020/sqlite-autoconf-3320300.tar.gz

tar -xvf sqlite-autoconf-3320300.tar.gz
cd sqlite-autoconf-3320300 
 ./configure -prefix=/home/XXX/soft/sqlite-autoconf-3320300
make
make install

最后安装abyss-2.2.4：https://github.com/bcgsc/abyss/archive/2.1.5.tar.gz

tar -zxvf abyss-2.2.4.tar.gz
./configure -prefix=/home/XXX/soft/abyss-2.2.4/ -with-boost=/home/XXX/soft/boost_1_73_0 -with-mpi=/home/XXX/soft/openmpi-4.0.4 CPPFLAGS=-I/home/XXX/soft/sparsehash-sparsehash-2.0.3/include/ -enable-maxk=96 -with-sqlite=/home/XXX/soft/sqlite-autoconf-3320300
make
make install

设置环境变量（因为我好像没有设置好，所以每次重启使用都需要重新设置，求大佬指教）

export abyss_home=/home/XXX/soft/abyss-2.2.4/
(base) [XXX@localhost ~]$ export 
PATH=$abyss_home/ABYSS:$PATH

验证安装是否成功：
ABYSS --help （注意此处是大写）

以下显示为成功安装

Usage: ABYSS -k<kmer> -o<output.fa> [OPTION]... FILE...
Assemble the input files, FILE, which may be in FASTA, FASTQ,
qseq, export, SAM or BAM format and compressed with gz, bz2 or xz.

 Options:

      --chastity        discard unchaste reads [default]
      --no-chastity     do not discard unchaste reads
      --trim-masked     trim masked bases from the ends of reads
                        [default]
      --no-trim-masked  do not trim masked bases from the ends of
                        reads
  -q, --trim-quality=N  trim bases from the ends of reads whose
                        quality is less than the threshold
  -Q, --mask-quality=N  mask all low quality bases as `N'
  --standard-quality    zero quality is `!' (33)
                        default for FASTQ and SAM files
  --illumina-quality    zero quality is `@' (64)
                        default for qseq and export files
      --SS              assemble in strand-specific mode
      --no-SS           do not assemble in strand-specific mode
  -o, --out=FILE        write the contigs to FILE
  -k, --kmer=N          the length of a k-mer (when -K is not set) [<=96]
                        or the span of a k-mer pair (when -K is set)
  -K, --single-kmer=N   the length of a single k-mer in a k-mer pair
  -t, --trim-length=N   maximum length of blunt contigs to trim [k]
  -c, --coverage=FLOAT  remove contigs with mean k-mer coverage
                        less than this threshold
      --kc=N            remove all k-mers with multiplicity < N [0]
  -b, --bubbles=N       pop bubbles shorter than N bp [3*k]
  -b0, --no-bubbles     do not pop bubbles
  -e, --erode=N         erode bases at the ends of blunt contigs with coverage
                        less than this threshold [round(sqrt(median))]
  -E, --erode-strand=N  erode bases at the ends of blunt contigs
                        with coverage less than this threshold on
                        either strand [1 if sqrt(median) > 2 else 0]
  --coverage-hist=FILE  write the k-mer coverage histogram to FILE
  -m, --mask-cov        do not include kmers containing masked bases in
                        coverage calculations [experimental]
  -s, --snp=FILE        record popped bubbles in FILE
  -v, --verbose         display verbose output
      --help            display this help and exit
      --version         output version information and exit
      --db=FILE         specify path of database repository in FILE
      --library=NAME    specify library NAME for database
      --strain=NAME     specify strain NAME for database
      --species=NAME    specify species NAME for database

 ABYSS Options: (won't work with ABYSS-P)

  -g, --graph=FILE      generate a graph in dot format