以前有的是非完整时间写的博客,抽时间需要统一整理一下。
今天在重新装repeatmasker。
整个过程是这样的,有关联的事情有两个。
1. 装repeatmasker需要各种Prerequisites,其中就可能用到了blast,而之前一直找这个版本的blast,在ncbi硬是没有找到:
- For RMBlast ( NCBI Blast modified for use with RepeatMasker/RepeatModeler ) please go to our download page: http://www.repeatmasker.org/RMBlast.htm
blastdb_aliastool blastn deltablast makeblastdb rmblastn tblastn
blastdbcheck blastp dustmasker makembindex rpsblast tblastx
blastdbcmd blastx get_species_taxids.sh makeprofiledb rpstblastn update_blastdb.pl
blast_formatter convert2blastmask legacy_blast.pl psiblast segmasker windowmasker
2. 我有一些基因,需要找一下这些基因在各个物种的基因组上的位置,并注释出来。
然后我用了ncbi的版本:好吧,区别不到,少了 rmblastn
3. 安装repeatmasker
按照路径指示没有问题
4.安装repeatmodeler
perl ./configure
#
The following perl modules required by RepeatModeler are missing from
your system. Please install these first:
JSON
没看懂,去找,没找到怎么下的
$ wget https://centos.pkgs.org/7/centos-x86_64/perl-JSON-2.59-2.el7.noarch.rpm.html
$ rpm2cpio perl-JSON-2.90-1.of.el7.src.rpm |cpio -div
$ tar zxvf JSON-2.90.tar.gz
$ perl Makefile.PL
make
make install
完事
4.继续装repeatmodeler,
**REPEATMASKER INSTALLATION PATH** 将repeatmasker的路径喂给它
**RECON INSTALLATION PATH** 找找这个是啥
RECON - De Novo Repeat Finder, Bao Z. and Eddy S.R. Developed and tested with our patched version of RECON ( 1.08 ). The 1.08 version fixes problems with running RECON on 64 bit machines and supplies a workaround to a division by zero bug along with some buffer overrun fixes. The program is available at: http://www.repeatmasker.org/RECON-1.08.tar.gz. The original version is available at http://eddylab.org/software/recon/.
**RepeatScout INSTALLATION PATH**
RepeatScout - De Novo Repeat Finder, Price A.L., Jones N.C. and Pevzner P.A. Developed and tested with our multiple sequence version of RepeatScout ( 1.0.6 ). This version is available at http://www.repeatmasker.org/RepeatScout-1.0.6.tar.gz
http://bix.ucsd.edu/repeatscout/
**NSEG INSTALLATION PATH**
http://www.pdas.com/packages/nseg.zip
不对
ftp://ftp.ncbi.nih.gov/pub/seg/nseg/.
然后就可以了。
继续报错:
exist! RepeatModeler will not run correctly without these
然后去看贴吧
'm only guessing, but [n??] sounds like the extensions of files generated by formatdb when creating nucleotide database. Given that RepeatMasker.lib is a FASTA file, maybe you need to run formatdb on it.
./makeblastdb: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./makeblastdb)
所以可能存在的问题有两个,一个是没有建库,一个是建库软件错误,无法建库。
不行!!!继续找别人的经验
不想折腾了,下载RepeatModeler-2.0.tar.gz
注意,如果不想折腾的话,不要选yes,我去下载LTR_Retriever,MAFFT
说实话,我想回滚了。
wget http://mafft.cbrc.jp/alignment/software/mafft-7.158-without-extensions-src.tgz (备份一个wget http://mafft.cbrc.jp/alignment/software/mafft-7.158-gcc_fc6.x86_64.rpm)
按照说明安装和编译,repeatmodeler说不想玩,下另一个,OK
https://github.com/traviswheelerlab/ninja/releases/tag/0.95-cluster_only
make all
应该通关了吧。
Congratulations! RepeatModeler is now ready to use.
今天准备将所有的常用软件备份到自己的网站undef.cn里面,但是这个网站还没有备案,所以可以先在cospure.cn上看到。
以上,repeatmodeler安装通关记录
abyss king