【1】conda 安裝
conda create -n interpro -c bioconda interproscan
存在問題 share/InterProScan/bin/prosite/pfsearchV3 依賴GLIBC_2.27
GLIBC_2.27 not found會(huì)發(fā)生在ubuntu16.04系統(tǒng)上
有root權(quán)限可以參考
GLIBC_2.23 not found錯(cuò)誤解決
``
/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載的包共屈，conda 主要解決其它軟件依賴問題
【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 安裝,使用完整的data 替換
下載特定版本(與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】修復(fù)
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
