proovread安装与试用

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[TOC]

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安装环境

Ubuntu18.10
Perl 5.10.1 or later
Log::Log4perl
File::Which (see #17)
NCBI Blast-2.2.24+ or later
samtools-1.1 or later

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安装

fresh install

git clone https://github.com/BioInf-Wuerzburg/proovread
(cd proovread && make && make install)

make install takes: PREFIX=/my/software/proovread

make a test run

(cd proovread && make sample)

update existing install to latest version

(cd proovread && make update)

NOTE: proovread comes with its own, modified version of bwa. Using it with a standard bwa built will fail.

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试用

试proovread -h
刚开始没安装Log::Log4perl，出现这个错误

Can't locate Log/Log4perl.pm in @INC (you may need to install the Log::Log4perl module) (@INC contains: /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.2 /usr/local/share/perl/5.26.2 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ./proovread line 11.
BEGIN failed--compilation aborted at ./proovread line 11.

使用cpan Log::Log4perl
安装了之后，又试proovread -h
出现没安装File::Which这个错误

Can't locate File/Which.pm in @INC (you may need to install the File::Which module) (@INC contains: /home/sjl/Downloads/proovread/bin/../lib/ /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.2 /usr/local/share/perl/5.26.2 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at ./proovread line 20.
BEGIN failed--compilation aborted at ./proovread line 20.

使用cpan File::Which安装
然后就可以proovread -h成功了。

试用可以进入proovread文件夹make sample就可以运行sample文件夹里的文件然后生成结果在sample-results里。