proovread installation and trial
2018.12.04 19:52:21 read 118 words 204
[TOC]
Installation Environment
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
installation
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.
try out
Test proovread -h
the beginning did not install the Log :: Log4perl, this error
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.
Use cpan Log::Log4perl
installed later, and tried proovread -h
not to install File :: Which this error
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.
Use cpan File::Whichinstallation
and then you can proovread -hsucceed.
Try to enter proovread folder make samplecan run a file folder in the sample and produces a result in the sample-results.