LRSDAY performes chromosome-level end-to-end genome assembly and comprehensive annotations for Saccharomyces yeasts.
The instructions that follow help to meet the dependencies on SUSE-based OS for LRSDAY v.1.6.
After the download of LRSDAY remove Project_Template and copy the content of LRSDAY-Patch inside LRSDAY folder.
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The following dependecies have been tested on a virgin virtual copy of OpenSUSE Leap 15.4. They represent the minimum indispensable dependecies to successfully install the pipeline. Please, consider if you want to change the repositories according with your Leap version. In order to complete the installation of LRSDAY install the following packages:
sudo zypper install cmake make gcc git zlib-devel libbz2-devel libz1
Bioperl:
zypper addrepo https://mirror-jp.firstyear.id.au/repositories/devel:/languages:/perl/openSUSE_Leap_15.2/devel:languages:perl.repo
zypper refresh
zypper install perl-BioPerl
Additional repos for BioPerl: https://download.opensuse.org/repositories/devel:/languages:/perl/ .
If the repo does not work you can try different mirrors.
Example (for Leap 15.0):
- click on https://download.opensuse.org/repositories/devel:/languages:/perl/;
- enter in
/openSUSE_Leap_15.0/and click onDetailsin the columnMetadata; - pick a different mirror.
General packages:
sudo zypper install perl-Text-Soundex liblzma5 pkg-config autoconf hdf5-devel postgresql-devel libpqxx
Python3:
sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/python/15.4/devel:languages:python.repo
zypper refresh
zypper install python3
Additional repos for Python3: https://download.opensuse.org/repositories/devel:/languages:/python/
The "build essential" for SUSE OS:
sudo zypper install -t pattern devel_basis
Additional general packages:
sudo zypper install curl libcurl-devel libcurl4 lzma-devel
Install java 8 for GATK3:
sudo zypper install java-1_8_0-openjdk
NOTE: starting from LRSDAY v.1.7.2 the path to java can be specified directly inside env.sh file.
In addition, you have to meet the dependecies indicated in prerequisites.
Sotware with [S] are already provided with the installation of OpenSUSE.
bash [S]
bzip2 [S] and libbz2-devel
cmake v3.2 or newer
gcc and g++ v4.9.1 or newer
ghostscript [S]
git
make
gzip [S]
java runtime environment (JRE) v1.8.0
perl v5.12 or newer [S]
python v2.7 [S] 3.6 [S] 3.8
python-devel
python3-devel
tar [S]
unzip [S]
wget [S]
zlib and zlib-devel
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Edit installer_patch.sh, set SUSE="yes" and run the command:
bash installer_patch.sh
By default, you are going to install all the software listed at the beginning of the installer (suggested if you are not familiar with the pipeline). This behavior can be modified based on errors that may occur along the process. Hence, if you need to repeat the installattion for a group of software, you can change the variable to all the others to "no". The installation time depends on the internet connection and varies between 30 and 50/55 min.
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Move in LRSDAY/soft/Err and run grep DBD *; if install_maker.err: * DBD::Pg is not installed install maker manually, find all the steps in LRSDAY/soft/install_maker.sh. Remind to run ./Build installdeps and follow the indications for a local installation of the dependecies before running ./Build install.
Move inside LRSDAY/soft/Err and run:
grep Exit *
If you see Exit status 0 you can move to the next step.
grep Error *
grep error *
grep ERROR *
If grep commands return empty, you are ready to run LRSDAY tutorial from the manual!
NOTE: some software may return compilation errors that are not fatal. Only running the pipeline we can understand if it is necessary to repeat/correct the installation of the software.
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If grep commands return non-empty results, you got an error and we have to fix it. Feel free to open an issue at https://github.com/nicolo-tellini/LRSDAY-UbuntuOS/issues with the content of the install_*_.err file in which the error occurred. I am going to help you to fix the error.