【软件安装】interproscan-5.59-91.0

【1】conda 安装

conda create -n interpro -c bioconda interproscan

存在问题 share/InterProScan/bin/prosite/pfsearchV3 依赖GLIBC_2.27

GLIBC_2.27 not found会发生在ubuntu16.04系统上
有root权限可以参考
GLIBC_2.23 not found错误解决

   ``
     /lib64/libm.so.6: version `GLIBC_2.27' not found (required by bin/prosite/pfscanV3)
     strings  /lib64/libm.so.6|grep GLIBC 
    ``
   如果linux 版本高可以直接用下载的包，conda 主要解决其它软件依赖问题

【2】配置

cd /data/envs/interpro/share/InterProScan
配置 interproscan.properties 

data.directory
bin.directory
perl.command
python3.command

【3】如果是conda 安装,使用完整的data 替换
下载特定版本(与conda版本一致)：Index of /pub/software/unix/iprscan/5 (ebi.ac.uk)

     cd  /data/envs/interpro/share/InterProScan/
     rm -rf data
     move interproscan-5.59-91.0/data   /data/envs/interpro/share/InterProScan/ /data/envs/interpro/share/InterProScan/

【3.1】修复
SSI index construction failed: primary keys not unique: '7,8-didemethyl-8-hydroxy-5-de' occurs more than once

for f in data/sfld/*/sfld.hmm data/superfamily/*/hmmlib_*[0-9]; do
cp $f $f.bak;
perl -lne '$_=~s/[\s\n]+$//g;if(/^(NAME|ACC) +(.*)$/){if(exists $d{$2}){$d{$2}+=1;$_.="-$d{$2}"}else{$d{$2}=0;}}print "$_"' $f > $f.tmp; mv $f.tmp $f;
done
#https://github.com/ebi-pf-team/interproscan/issues/305

【4】初始化

/data/envs/interpro/bin/python3 setup.py interproscan.properties