基因组注释——PASA

name: pasa
channels:
  - bioconda
  - conda-forge
  - defaults
dependencies:
  - _libgcc_mutex=0.1=conda_forge
  - _openmp_mutex=4.5=1_gnu
  - blat=36=0
  - bzip2=1.0.8=h7f98852_4
  - c-ares=1.18.1=h7f98852_0
  - ca-certificates=2021.10.26=h06a4308_2
  - curl=7.81.0=h2574ce0_0
  - fasta3=36.3.8=h779adbc_6
  - gmap=2018.03.25=pl526h2f06484_2
  - htslib=1.14=h9093b5e_0
  - k8=0.2.5=h9a82719_1
  - krb5=1.19.2=hac12032_0
  - libcurl=7.81.0=h2574ce0_0
  - libdb=6.2.32=h9c3ff4c_0
  - libdeflate=1.7=h7f98852_5
  - libedit=3.1.20210714=h7f8727e_0
  - libev=4.33=h516909a_1
  - libgcc=7.2.0=h69d50b8_2
  - libgcc-ng=11.2.0=h1d223b6_11
  - libgomp=11.2.0=h1d223b6_11
  - libnghttp2=1.46.0=hce63b2e_0
  - libpng=1.6.37=h21135ba_2
  - libssh2=1.10.0=ha56f1ee_2
  - libstdcxx-ng=11.2.0=he4da1e4_11
  - libzlib=1.2.11=h36c2ea0_1013
  - minimap2=2.24=h5bf99c6_0
  - mysql-connector-c=6.1.6=0
  - ncurses=6.2=h58526e2_4
  - openssl=1.1.1m=h7f8727e_0
  - pblat=2.5=he7163dc_1
  - perl=5.26.2=h36c2ea0_1008
  - perl-business-isbn=3.004=pl526_0
  - perl-business-isbn-data=20140910.003=pl526_0
  - perl-carp=1.38=pl526_3
  - perl-constant=1.33=pl526_1
  - perl-data-dumper=2.173=pl526_0
  - perl-db-file=1.852=pl526h516909a_1
  - perl-dbd-mysql=4.046=pl526h2d50403_0
  - perl-dbd-sqlite=1.64=pl526h516909a_0
  - perl-dbi=1.642=pl526_0
  - perl-encode=2.88=pl526_1
  - perl-exporter=5.72=pl526_1
  - perl-extutils-makemaker=7.36=pl526_1
  - perl-mime-base64=3.15=pl526_1
  - perl-parent=0.236=pl526_1
  - perl-uri=1.76=pl526_0
  - perl-xsloader=0.24=pl526_0
  - readline
  - samtools=1.7=1
  - sqlite=3.37.0=hc218d9a_0
  - transdecoder=5.5.0=pl526_1
  - xz=5.2.5=h516909a_1
  - zlib=1.2.11=h36c2ea0_1013
prefix: /home/user/miniconda3/envs/pasa

将以上保存为pasa.yml

# 安装pasa所需要的环境
mamba env create -f pasa.yml

# 切换到名为pasa的环境
conda activate pasa

# 下载pasa的源代码(服务器无法下载的，可以自行小飞机下载到本地然后传服务器)
git clone https://github.com/PASApipeline/PASApipeline.git
# 进入到pasa的目录
cd PASApipeline-master/
# 编译
make
# 如果没有error，应该就是成功了，正常都会成功

# 从pasa的目录里面复制出来配置文件
cp /path_of_pasa/pasa_conf/pasa.alignAssembly.Template.txt pasa_annotation/alignAssembly.config

# 修改配置文件中的这几项
DATABASE=（absolute_path/）database.sqlite #这里直接写database.sqlite就ok，括号里面的删掉如果安装了mysql，而且你熟悉mysql的配置，那就用相对路径，用绝对路径调用的是sqlite
validate_alignments_in_db.dbi:--MIN_PERCENT_ALIGNED=80
validate_alignments_in_db.dbi:--MIN_AVG_PER_ID=80

运行：
/absolute_path/PASApipeline-master/Launch_PASA_pipeline.pl  \
                                    -c alignAssembly.config \
                                     -C -R \
                                     -g ../genome/genome.fa \
                                     --ALIGNERS blat,gmap,minimap2 \
                                     -t transcript.fasta \
                                     --CPU 20
                                     -C # 报错让去除-C时候，就添加-C，我第一次运行没添加-C报错了，添加后解决

转自：https://zhuanlan.zhihu.com/p/638714558