How to fix broken links and dependencies - LRSDAY

[nicolo-tellini]

--- POST UPDATE---

Last update: 18/08/2022

--- END ---

The operations below are the results of hard debugging on the OS:

Linux Ubuntu 18.04.5 LTS 5.4.0-122-generic #138~18.04.1-Ubuntu SMP x86_64 GNU/Linux

I think that, as long as the OS is Debian/Linux distribution based on Debian (Ubuntu, Mint, Kali, Raspberry Pi OS, etc ...), the following points might be helpful to succeed with the installation and complete the tutorial of LRSDAY.

Please, note that the tutorial make use of PacBio reads. I did not test the software for analyzing nanopore reads, yet.

Please, install all the software with copy-paste from the installer as a new installer is not available yet.

You will need to make a few corrections along the way.

Note that the software may not occur in the same order of the installer so, before installing, check if they are on the list :

• cpanm needs libpq-dev (it is a Debian package see here. For SUSE the package should be this while I did not find the corresponding package for RedHat). If you install either in SUSE or RedHat consider to test if cpanm works properly without installing additional packages.

• nanopolish installation from ubuntu repo results in nanopolish v.0.9.0 (I need to check if it is compatible with LRSDAY script; this is true for all the software to analyze MinION data);

• CAP3 requires manual installation from Iowa State University;

• GATK3 moved to GATK4 so GATK3 needs manual installation from Google Cloud GATK. Please, note that GATK3 requires java 8 / openjdk v.1.8.0_302 find here how to install it and here how to set it as default;

• MAKER3.00.0 is outdated and not available anymore, a new version can be found at @Yandell-Lab (v3.01.04)

• pbalign v 0.3.0 was installed from ubuntu repos because of conda conflicts with other packages versions. As general rule, to find out if a package is available from Ubuntu repos :

nico@Thor: apt-cache policy pbalign
pbalign:
  Installed: 0.3.0-1
  Candidate: 0.3.0-1
  Version table:
 *** 0.3.0-1 500
        500 http://it.archive.ubuntu.com/ubuntu bionic/universe amd64 Packages
        500 http://it.archive.ubuntu.com/ubuntu bionic/universe i386 Packages
        100 /var/lib/dpkg/status

The command apt-cache policy runs also on software not installed yet.

• bax2bam v0.0.9 and 0.0.11 provided by conda do not run properly for a series of bugs never fixed by the developer. see bug v 0.0.11 issue 398, see bug v 0.0.9 issue 341.

The code below creates a fresh conda environment and fixes the problem.

pacbio_dir2=$build_dir/conda_pacbio_env2/bin
if [ -z $(check_installed $pacbio_dir2) ]; then
    
   cd $build_dir
    $miniconda3_dir/conda create -y -p $build_dir/conda_pacbio_env2 python=2.7
    source $miniconda3_dir/activate $build_dir/conda_pacbio_env2

    $miniconda3_dir/conda install -y -c bioconda pb-assembly=0.0.3
    $miniconda3_dir/conda install -y -c bioconda pbbam=0.18.0
    $miniconda3_dir/conda install -y -c bioconda bax2bam=0.0.9

    source $miniconda3_dir/deactivate
fi
note_installed $pacbio_dir2

note that, because a wonderful bug, conda install -y -c bioconda bax2bam=0.0.9 will end up installing the version 0.0.8 which works nicely !

• because of gnuplot error ( Inappropriate ioctl for device ) I installed mummer4.0.0beta5 and gnuplot 5.2 patchlevel 2 ( This second requires superuser privilege for running make install AND it will replace the gnuplot installed on your system so keep it in mind! ). With gnuplot 5.2 patchlevel 2 "Inappropriate ioctl for device" is a warning/not fatal error that allows the script to terminate correctly. If you cannot reach the end of the run please consider the solutions at the issue #36 proposed by the users asdcid and/or gonzalezibeas.

• before configuring RepeatMasker please check the package libtext-soundex-perl is installed (here HOWTO).

• variantCaller is not available in pb-assembly v.0.0.8, anymore. A solution is to install pb-assembly v.0.0.3, along with pb-assembly v.0.0.8. Please, note that v. 0.0.3 has several conflicts with python 3.7 packages thus it requires python 2.7. The path to variantCaller needs to be changed accordingly. variantCaller is a function installed with pb-assembly v.0.0.3 you will not find the installation commands on the installer.

• Bioperl functions for MFANNOT, ORGANELLAR GENOME ANNOTATION PROGRAM can be installed with:

apt-get install libbio-perl-perl

• modify the script REannotate_longname at line 1004; replace my($SEQ,$FASTAentries_, my $MESSAGES) = @_; with my($SEQ,$FASTAentries_,$MESSAGES) = @_; as suggested by @matdechiara ;

• IMPORTANT: Every new software version will probably come along with different PATH to the binary files. This NEW paths have to be correctly reported in env.sh and the scripts in Project_Example.

• PROTEINORTHO v.6.0.25 installs proteinortho6.pl ; the script LRSDAY.14.Gene_Orthology_Identification.sh has to be changed with a few replacements proposed in a new branch of LRSDAY.

best,

Nic