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Installation of a RNA-Seq Analysis platform on Linux

The following installation was based on Ubuntu 23.04 distribution.

Basic and common procedures


























































































# Directory for Bioinformatic tools
sudo mkdir -p /usr/local/bioinfo

# APT UPDATE
sudo apt-get -y update
sudo apt-get -y upgrade
sudo apt-get -y full-upgrade

# The following 4 (four) commands are usefull for Ubuntu 20.04.3
#The swap UUID needs to be added to the /etc/initramfs-tools/conf.d/resume file.
printf "RESUME=UUID=$(blkid | awk -F\" '/swap/ {print $2}')\n" | sudo tee /etc/initramfs-tools/conf.d/resume
sudo update-initramfs -u -k all
sudo nohup shutdown -r now &>/dev/null &
sudo apt autoremove

# updatedb
sudo apt-get -y install mlocate
# tree
sudo apt-get -y install tree
# build-essential package
sudo apt-get -y install build-essential
# python 2
sudo apt-get -y install python-is-python3
sudo apt-get -y install python2 python2-dev
# screen
sudo apt-get -y install screen
# vim
sudo apt-get -y install vim
# curl
sudo apt-get -y install curl
# nsort
cd /usr/local/bioinfo
wget http://www.ordinal.com/try.cgi/nsort-x86_64-3.4.61.rpm
sudo apt-get -y install alien
sudo alien nsort-x86_64-3.4.61.rpm
sudo dpkg -i nsort_3.4.61-1_amd64.deb
echo "-license=\"nsort gratis license agreement in /usr/lib/nsort/gratislicense has been read by me, and I accept and agree to be bound by its terms\"" | sudo tee /usr/lib/nsort/license > /dev/null
# introntab.pl
cd /usr/local/bioinfo
wget http://wfleabase.org/genome-summaries/gene-structure/introntab.pl
chmod a+x introntab.pl
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/introntab.pl
# cpanm
cd /usr/local/bin
sudo curl -L https://cpanmin.us/ -o cpanm
sudo chmod a+x cpanm
# apt-file
sudo apt-get -y install apt-file
sudo apt-file update

# Java
cd /usr/local/bioinfo
wget https://download.oracle.com/java/18/latest/jdk-18_linux-x64_bin.deb
sudo apt-get -y install libc6-i386 libc6-x32
sudo dpkg -i jdk-18_linux-x64_bin.deb
sudo update-alternatives --install /usr/bin/javac javac /usr/lib/jvm/jdk-18/bin/javac 1
sudo update-alternatives --install /usr/bin/java java /usr/lib/jvm/jdk-18/bin/java 1
sudo update-alternatives --install /usr/bin/jar jar /usr/lib/jvm/jdk-18/bin/jar 1

# choose in each command the Oracle JDK
sudo update-alternatives --config java
sudo update-alternatives --config javac
sudo update-alternatives --config jar

# Multiple libraries and tools
sudo apt-get -y install gdebi-core \
 gfortran gfortran-multilib \
 libreadline-dev \
 xorg-dev \
 libjson-perl \
 libterm-readline-perl-perl \
 libbz2-dev \
 liblzma-dev \
 libpcre2-dev \
 libcurl4-openssl-dev \
 texlive-fonts-extra \
 texinfo \
 libtool \
 libpcre3-dev \
 cmake \
 git \
 libssl-dev \
 libxml2-dev \
 ruby-bundler \
 ruby-dev \
 htop

Fail2Ban





sudo apt-get -y install fail2ban
sudo service fail2ban restart
sudo service fail2ban status
sudo fail2ban-client status sshd

Anaconda

First, here are some recommended packages to install:

sudo apt-get -y install libgl1-mesa-glx libegl1-mesa libxrandr2 libxrandr2 libxss1 libxcursor1 libxcomposite1 libasound2 libxi6 libxtst6

So you need to download and install Anaconda
(https://www.anaconda.com/products/individual#linux). Please, see https://docs.anaconda.com/anaconda/install/linux/ .

# PREFIX=/usr/local/bioinfo/anaconda3

After root installation you need to run one time with each user:

/usr/local/bioinfo/anaconda3/bin/conda init

Then you need to reconnect to have effect.

Give ownership "users" group and write permission for that group:




sudo chgrp -R users /usr/local/bioinfo/anaconda3/
sudo chgrp users /usr/local/bioinfo/

Instructions after installation

conda install scikit-learn-intelex

Bioinformatics

SRA Toolkit

apt-get install sra-toolkit

Other














































#FastQC
cd /usr/local/bioinfo
sudo wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.12.1.zip
sudo unzip fastqc_v0.12.1.zip
cd FastQC
chmod a+x fastqc
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/FastQC/fastqc

#RSeQC
sudo apt-get -y install python3-pip
pip install blosc2~=2.0.0
pip install RSeQC

#deepTools
sudo apt-get -y install python3-deeptools

#Atropos
sudo apt-get -y install atropos

#PrinSeq
cd /usr/local/bioinfo
wget "https://sourceforge.net/projects/prinseq/files/standalone/prinseq-lite-0.20.4.tar.gz/download" -O prinseq-lite-0.20.4.tar.gz
tar -zxvf prinseq-lite-0.20.4.tar.gz
cd prinseq-lite-0.20.4
sudo cpanm Statistics::PCA
chmod a+x prinseq-lite.pl prinseq-graphs-noPCA.pl prinseq-graphs.pl
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/prinseq-lite-0.20.4/prinseq-lite.pl

#bedtools
sudo apt-get -y install bedtools

#bedops
sudo apt-get -y install bedops

#pullseq
cd /usr/local/bioinfo
wget https://github.com/bcthomas/pullseq/archive/refs/tags/1.0.2.tar.gz -O pullseq-1.0.2.tar.gz
tar -zxvf pullseq-1.0.2.tar.gz
cd pullseq-1.0.2
./bootstrap
./configure --prefix=/usr/local
make
sudo make install

For Ubuntu after 22.04 (gcc v.11.2.0) please follow this instructions before the build (make):

  • Copy the following three variable's declaration to the src/pullseq.c and src/seqdiff.c, before the line with #include "global.h", so remove those (QUALITY_SCORE and verbose_flag) after that line.

char const *progname;
int QUALITY_SCORE;
int verbose_flag;

  • Change the following three variable's declaration in src/global.h. Adding the extern modifier:

extern char const *progname;
extern int QUALITY_SCORE;
extern int verbose_flag;































#Bowtie2
sudo apt-get -y install bowtie2

#Bowtie
sudo apt-get -y install bowtie

# Create python2 environment within conda
conda create --name python2 python=2.7

# TopHat2
cd /usr/local/bioinfo
wget http://ccb.jhu.edu/software/tophat/downloads/tophat-2.1.1.Linux_x86_64.tar.gz
tar -zxvf tophat-2.1.1.Linux_x86_64.tar.gz 
cd tophat-2.1.1.Linux_x86_64/
conda activate python2
python --version
#for i in `grep -R -H -P '\/bin\/env python$' * | cut -d ':' -f 1`; do sed 's/\/bin\/env python/\/bin\/env python2/' ${i} > ${i}.new; mv ${i}.new ${i}; chmod a+x ${i}; done
#cd /usr/local/bin
cd /usr/local/bioinfo/anaconda3/envs/python2/bin/

sudo ln -s /usr/local/bioinfo/tophat-2.1.1.Linux_x86_64/tophat2
sudo ln -s /usr/local/bioinfo/tophat-2.1.1.Linux_x86_64/gtf_to_fasta

conda deactivate

# STAR
sudo apt-get -y install rna-star

The Cufflinks package installation requires some manual procedures in Ubuntu 22.04 and also in 23.04.

The Cufflinks package has a problem in cuffmerge that needs to be patched:

https://github.com/cole-trapnell-lab/cufflinks/issues/130



































#Cufflinks
sudo apt-get -y install cufflinks
sudo apt-get -y install libboost-all-dev
sudo apt-get -y install libeigen3-dev

cd /usr/local/bioinfo/
wget http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.tar.gz
tar -zxvf cufflinks-2.2.1.tar.gz
cd cufflinks-2.2.1/
wget "https://sourceforge.net/projects/samtools/files/samtools/1.2/samtools-1.2.tar.bz2/download" -O samtools-1.2.tar.bz2
tar -jxvf samtools-1.2.tar.bz2
cd samtools-1.2
make
cd ./htslib-1.2.1/
ln -s version.h version.hpp
make
cd ../../
mkdir lib/ include/
wget "https://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1.18.tar.bz2/download" -O samtools-0.1.18.tar.bz2
tar -jxvf samtools-0.1.18.tar.bz2
cd samtools-0.1.18
make
cd ../
cd include/
ln -s /usr/local/bioinfo/cufflinks-2.2.1/samtools-0.1.18/ bam
ln -s /usr/local/bioinfo/cufflinks-2.2.1/samtools-1.2/htslib-1.2.1/htslib
ln -s /usr/include/eigen3/Eigen
cd ../lib
ln -s /usr/local/bioinfo/cufflinks-2.2.1/samtools-0.1.18/libbam.a
cd ../
wget "https://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz/download" -O boost_1_55_0.tar.gz
tar -zxvf boost_1_55_0.tar.gz
cd boost_1_55_0

To enable MPI in boost, add "using mpi ;" to your ./tools/build/v2/user-config.jam in boost directory before installation.




































conda activate python2

./bootstrap.sh --prefix=/usr/local/bioinfo/cufflinks-2.2.1 --with-python-root=/usr/lib/python2.7 --with-python=/usr/bin/python2 --with-python-version=2.7
./b2
./b2 install

cd /usr/local/bioinfo/anaconda3/envs/python2
mkdir -p ./etc/conda/activate.d
mkdir -p ./etc/conda/deactivate.d
touch ./etc/conda/activate.d/env_vars.sh
touch ./etc/conda/deactivate.d/env_vars.sh

echo "export BACKUP_PATH=\"\${PATH}\"" > ./etc/conda/activate.d/env_vars.sh
echo "export BACKUP_CPLUS_INCLUDE_PATH=\"\${CPLUS_INCLUDE_PATH}\"" >> ./etc/conda/activate.d/env_vars.sh
echo "export BACKUP_LD_LIBRARY_PATH=\"\${LD_LIBRARY_PATH}\"" >> ./etc/conda/activate.d/env_vars.sh

echo "export CPLUS_INCLUDE_PATH=\"/usr/local/bioinfo/cufflinks-2.2.1/boost_1_55_0:\${CPLUS_INCLUDE_PATH}\"" >> ./etc/conda/activate.d/env_vars.sh
echo "export LD_LIBRARY_PATH=\"/usr/local/bioinfo/cufflinks-2.2.1/boost_1_55_0/stage/lib:\${LD_LIBRARY_PATH}\"" >> ./etc/conda/activate.d/env_vars.sh


echo "export CPLUS_INCLUDE_PATH=\"\${BACKUP_CPLUS_INCLUDE_PATH}\"" > ./etc/conda/deactivate.d/env_vars.sh
echo "export LD_LIBRARY_PATH=\"\${BACKUP_LD_LIBRARY_PATH}\"" >> ./etc/conda/deactivate.d/env_vars.sh


conda deactivate


cd /usr/local/bioinfo/cufflinks-2.2.1

wget "https://gitweb.gentoo.org/repo/gentoo.git/plain/sci-biology/cufflinks/files/cufflinks-2.2.1-gcc7.patch?id=ccbd59a1a246014bf441e44a9f2bd8632a70c20e" -O cufflinks-2.2.1-gcc7.patch

patch src/GHash.hh < cufflinks-2.2.1-gcc7.patch

Edit "src/lemon/error.h" using the patch information below.















--- a/src/lemon/error.h 2021-11-23 14:23:50.527680311 -0300
+++ b/src/lemon/error.h 2012-03-12 10:29:49.000000000 -0300
@@ -67,9 +67,9 @@
    }
 
     ExceptionMember& operator=(const ExceptionMember& copy) {
-      if (ptr.get() == 0) return copy;
+      if (ptr.get() == 0) return;
       try {
-       if (!copy.valid()) return copy;
+       if (!copy.valid()) return;
        *ptr = copy.get();
       } catch (...) {}
     }

For Ubuntu 22.04 (gcc v.11.2.0) please follow this instructions before the build (make):

Replace byte for cfbyte to avoid ambiguity in files on src/ directory (src/*.h and src/*.cpp).

In vim interface (vim src/*.h src/*.cpp)
":bufdo %s/byte/cfbyte/ge | update"

Edit "src/gff.cpp" change cfbyte to byte in "_crc_result.process_cfbytes", because the right one is "_crc_result.process_bytes"

Replace on src/locfit/c_plot.c file (line 12):

INT curwin;

for

extern int curwin;

And then finish the build and installation procedures.
























conda activate python2

./configure --prefix=/usr/local/bioinfo/cufflinks-2.2.1  --with-bam=/usr/local/bioinfo/cufflinks-2.2.1  --with-eigen=/usr/local/bioinfo/cufflinks-2.2.1 --with-boost=/usr/local/bioinfo/cufflinks-2.2.1/

make
make install
#find ./lib -type l -name '*.so' -exec rm -f {} \;
#echo 'export LD_LIBRARY_PATH="/usr/local/bioinfo/cufflinks-2.2.1/lib:${LD_LIBRARY_PATH}"' | sudo tee -a /etc/profile.d/bioinfo.sh > /dev/null
#sudo apt-get -y remove cufflinks
#cd /usr/local/bin
#find /usr/local/bioinfo/cufflinks-2.2.1/bin/ -type f -executable -exec sudo ln -s {} \;
#sudo sed -i 's/#!\/usr\/bin\/env python/#!\/usr\/bin\/env python2/' /usr/local/bin/cuffmerge
#rm -f /usr/local/bin/gffread

cd /usr/local/bioinfo/anaconda3/envs/python2

echo "export PATH=\"/usr/local/bioinfo/cufflinks-2.2.1/bin:\${PATH}\"" >> ./etc/conda/activate.d/env_vars.sh

echo "export PATH=\"/usr/local/bioinfo/cufflinks-2.2.1/bin:\${BACKUP_PATH}\"" >>  ./etc/conda/deactivate.d/env_vars.sh

conda deactivate
conda activate python2































#Stringtie
sudo apt-get -y install stringtie

#Samtools
sudo apt-get -y install samtools

# Jellyfish
cd /usr/local/bioinfo
wget "https://github.com/gmarcais/Jellyfish/releases/download/v2.3.0/jellyfish-linux"
cd /usr/local/bin
sudo chmod a+x /usr/local/bioinfo/jellyfish-linux
sudo ln -s /usr/local/bioinfo/jellyfish-linux jellyfish

#Trinity
cd /usr/local/bioinfo
wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/Trinity-v2.15.1/trinityrnaseq-v2.15.1.FULL.tar.gz
tar -zxvf trinityrnaseq-v2.15.1.FULL.tar.gz
cd trinityrnaseq-v2.15.1

# First edit the "trinity-plugins/bamsifter/sift_bam_max_cov.cpp"
# - Add the following line in the code header: #include <string>

make
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/trinityrnaseq-v2.15.1/Trinity
sudo ln -s /usr/local/bioinfo/trinityrnaseq-v2.15.1/util/misc/SAM_nameSorted_to_uniq_count_stats.pl
echo 'export TRINITY_HOME="/usr/local/bioinfo/trinityrnaseq-v2.15.1"' | sudo tee /etc/profile.d/bioinfo.sh > /dev/null
echo 'export EUK_MODULES="/usr/local/bioinfo/trinityrnaseq-v2.15.1/PerlLib/"' | sudo tee -a /etc/profile.d/bioinfo.sh > /dev/null

For Ubuntu 22.04 (gcc v.11.2.0) please follow this instructions before the build (make):

sudo apt-get -y autoconf2.69
cd /usr/bin
mv autoconf autoconf2.71
ln -s autoconf2.69 autoconf
































































































































#salmon for an old Trinity version
cd /usr/local/bioinfo
wget https://github.com/COMBINE-lab/salmon/releases/download/v1.0.0/salmon-1.0.0_linux_x86_64.tar.gz
tar -zxvf salmon-1.0.0_linux_x86_64.tar.gz
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/salmon-latest_linux_x86_64/bin/salmon

#salmon for Trinity 2.15.1
sudo apt-get -y install salmon

#kallisto
sudo apt-get -y install kallisto

#BLAST
sudo apt-get -y install ncbi-blast+

#Legacy BLAST
cd /usr/local/bioinfo/
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/blast-2.2.26-x64-linux.tar.gz
tar -zxvf blast-2.2.26-x64-linux.tar.gz
cd /usr/local/bin
sudo find /usr/local/bioinfo/blast-2.2.26/bin -type f -executable -exec ln -s {} \;

#blastR
#BlastR is a new method for searching Non-Coding RNAs in databases. The strategy we adopted relies on the use of the mutual information embedded in di-nucleotides
cd /usr/local/bioinfo/
wget https://www.tcoffee.org/Projects/blastr/blastR_package_V2.2.tar.gz
tar -zxvf blastR_package_V2.2.tar.gz
cd blastR_package_V2.2/scripts
cd /usr/local/bin
find /usr/local/bioinfo/blastR_package_V2.2/scripts -name '*.pl' -exec perl -c {} \;
sudo find /usr/local/bioinfo/blastR_package_V2.2/scripts -name '*.pl' -exec ln -s {} \;

#silix
#ultra-efficient algorithm for the clustering of homologous sequences
cd /usr/local/bioinfo/
wget https://gitlab.com/vmiele/silix/-/archive/master/silix-master.tar.gz
tar -zxvf silix-master.tar.gz
cd silix-master/
libtoolize
aclocal
autoheader
automake -a
autoconf
# The following line is only necessary if you built the cufflinks
#LDFLAGS="-L/usr/local/bioinfo/cufflinks-2.2.1/lib/" CPPFLAGS="-I/usr/local/bioinfo/cufflinks-2.2.1/include/" ./configure --enable-mpi --enable-verbose
./configure --enable-mpi --enable-verbose
make
sudo make install

#diamond
cd /usr/local/bioinfo
wget https://github.com/bbuchfink/diamond/releases/download/v2.1.8/diamond-linux64.tar.gz
tar -zxvf diamond-linux64.tar.gz
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/diamond

#Transdecoder

cd /usr/local/bioinfo
wget https://github.com/TransDecoder/TransDecoder/archive/refs/tags/TransDecoder-v5.7.1.tar.gz
tar -zxvf TransDecoder-v5.7.1.tar.gz
cd TransDecoder-TransDecoder-v5.7.1/

cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/TransDecoder-TransDecoder-v5.7.1/TransDecoder.LongOrfs 
sudo ln -s /usr/local/bioinfo/TransDecoder-TransDecoder-v5.7.1/TransDecoder.Predict

#RSEM
#sudo apt-get -y install rsem

#RSEM-EVAL
cd /usr/local/bioinfo
git clone https://github.com/nfillmore/rsem-eval.git
cd rsem-eval
cd sam
make
cd ..
make CC='g++ -std=gnu++98'
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/rsem-eval/rsem-eval-calculate-score
sudo ln -s /usr/local/bioinfo/rsem-eval/rsem-eval-estimate-transcript-length-distribution

#Transrate
## instalado a partir de pacote obtido anteriormente 

cd /usr/local/bioinfo
wget https://bintray.com/artifact/download/blahah/generic/transrate-1.0.3-linux-x86_64.tar.gz
tar -zxvf transrate-1.0.3-linux-x86_64.tar.gz -C transrate-1.0.3/
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/transrate-1.0.3-linux-x86_64/transrate
cd /usr/local/bioinfo

#TableMaker
wget "https://figshare.com/ndownloader/files/3193031" -O tablemaker-2.1.1.tar.gz
tar -zxvf tablemaker-2.1.1.tar.gz
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/tablemaker-2.1.1.Linux_x86_64/tablemaker
cd /usr/local/bioinfo

# eggnog-mapper
#pip install pyqt5==5.12.3
#pip install pyqtwebengine==5.12.1
#pip install spyder
conda create --name eggnog-mapper python=3
conda activate eggnog-mapper
conda config --add channels bioconda
conda install eggnog-mapper
mkdir -p /usr/local/bioinfo/anaconda3/envs/eggnog-mapper/lib/python3.11/site-packages/data
download_eggnog_data.py


# Jim Kent tools used in UCSC
cd /usr/local/bioinfo
mkdir -p ucsc
rsync -azvP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./ucsc/
echo 'export PATH="/usr/local/bioinfo/ucsc:/usr/local/bioinfo/ucsc/blat:${PATH}"' | sudo tee -a /etc/profile.d/bioinfo.sh > /dev/null

# Intel Math Kernel Library (MKL)

# To have PNG and TIFF support 
sudo apt-get -y install libpng++-dev libcairo2-dev libgtk2.0-dev xvfb xauth xfonts-base libxt-dev libtiff6 libtiff-dev

Before the R compilation, please, download icu4c-58_2 from SourceForge (https://sourceforge.net/projects/icu/files/ICU4C/58.2/icu4c-58_2-src.tgz/download), uncompressing the file and specifying:
-L/path/to/icu/source/lib/ in LDFLAGS for R configure script. It's not necessary to install this ICU build.









cd /usr/local/bioinfo
tar -zxvf icu4c-58_2-src.tgz
cd icu/source
sed -i 's/xlocale/locale/'  i18n/digitlst.cpp
./configure
make












# R
cd /usr/local/bioinfo
wget https://cran.r-project.org/src/base/R-4/R-4.3.1.tar.gz
tar -zxvf R-4.3.1.tar.gz
cd ./R-4.3.1/
./configure --prefix=/usr/local --enable-static --enable-shared --enable-R-shlib --with-blas --with-lapack --with-tcltk --with-readline --with-cairo --with-libpng --with-libtiff --with-jpeglib --with-system-tre --with-x --enable-memory-profiling --with-libtiff --enable-threads=posix LDFLAGS="-L/usr/local/bioinfo/icu/source/lib"
make
sudo make install

Inside the R environment you will install the recommended packages.

Firstly, it's necessary to config Java environment for rJava installation

sudo R CMD javareconf

So, enter the R environment.

sudo R

And, install the Bioconductor packages and other useful packages.























if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install()
BiocManager::install("annotate")
BiocManager::install("genefilter")
BiocManager::install("geneplotter")
BiocManager::install("edgeR")
BiocManager::install("dplyr")
BiocManager::install("rJava")
BiocManager::install("xlsx")
BiocManager::install("XLConnect")
install.packages("stringi", configure.args="--with-extra-ldflags=-L/usr/local/bioinfo/icu/source/lib")
BiocManager::install("stringr")
BiocManager::install("latticeExtra")
BiocManager::install("htmlTable")
BiocManager::install("Hmisc")
BiocManager::install("openxlsx")
BiocManager::install("DESeq2")
BiocManager::install("tidyr")
BiocManager::install("devtools")
BiocManager::install("ballgown")

It's also important to install the RStudio IDE (server)




cd /usr/local/bioinfo
wget https://download2.rstudio.org/server/jammy/amd64/rstudio-server-2023.09.0-463-amd64.deb
sudo gdebi rstudio-server-2023.09.0-463-amd64.deb

Bioinfoutilities


























#bioinfoutilities
cd /usr/local/bioinfo
git clone https://github.com/dgpinheiro/bioinfoutilities.git

sudo apt-get -y install libreadonly-perl \
 liblog-log4perl-perl \
 bioperl \
 libarchive-extract-perl \
 libjson-parse-perl \
 libwww-curl-perl \
 libfile-chdir-perl \
 libmath-combinatorics-perl \
 libdigest-md5-file-perl \
 libhttp-tiny-multipart-perl \
 libperl-dev \
 libmath-combinatorics-perl \
 libarchive-extract-perl \
 libfile-chdir-perl \
 libjson-parse-perl \
 libwww-curl-perl \
 libhttp-tiny-multipart-perl \
 libdigest-md5-file-perl

sudo apt-get install -y octave-dev

RSPerl is not compatible with Ubuntu > 22.0404





















## RSPerl (for some bioinfoutities scripts) *Arquivo RSPerl_0.92-3.tar.gz enviado sob demanda * modificado por dgpinheiro para as distribuições Linux mais recentes
echo 'export LD_LIBRARY_PATH="/usr/local/lib/R/lib/:/usr/local/lib/R/site-library/RSPerl/libs/:/usr/local/lib/R/site-library/RSPerl/perl/x86_64-linux-gnu-thread-multi/auto/R/:${LD_LIBRARY_PATH}"' | sudo tee -a /etc/profile.d/bioinfo.sh > /dev/null

echo 'export PERL5LIB="/usr/local/lib/R/lib:/usr/local/lib/R/site-library/RSPerl/perl/x86_64-linux-gnu-thread-multi/:${PERL5LIB}"' | sudo tee -a /etc/profile.d/bioinfo.sh > /dev/null

#cd /usr/lib/x86_64-linux-gnu
#sudo ln -s libperl.so.5.30.0 libperl.so

sudo PERL=`which perl` R --vanilla CMD INSTALL --no-test-load -c --configure-args='--with-in-perl' RSPerl_0.92-3.tar.gz

# Verificar RSPerl * resultado é 6
perl -e 'use R; &R::initR("--silent","--no-save"); print &R::sum(1,2,3),"\n";'

# Verificar dependências dos scripts
find ./ -type f -executable -name '*.pl' -exec perl -c {} \;

# Acrescentar ao PATH
echo 'export PATH="/usr/local/bioinfo/bioinfoutilities:${PATH}"' | sudo tee -a /etc/profile.d/bioinfo.sh > /dev/null

BEAR








cd /usr/local/bioinfo
git clone https://github.com/sej917/BEAR.git
cd BEAR
find ./ -name '*.pl' -exec perl -c {} \;
conda activate python2
python -m pip install biopython==1.76
conda deactivate

Trinotate










# libghttpd
sudo apt-get -y install lighttpd

sudo cpanm Text::NSP::Measures::2D::Fisher::twotailed

cd /usr/local/bioinfo
wget https://github.com/Trinotate/Trinotate/archive/refs/tags/Trinotate-v4.0.2.tar.gz
tar -zxvf Trinotate-v4.0.2.tar.gz

Edit line 51 of the script "./util/prep_nuc_prot_set_for_trinotate_loading.pl":

vim /usr/local/bioinfo/Trinotate-Trinotate-v4.0.2/util/prep_nuc_prot_set_for_trinotate_loading.pl

foreach my $tool ("makeblastdb", "tblastn") {

Check auxiliary scripts:




sudo apt-get -y install sqlite3

find /usr/local/bioinfo/Trinotate-Trinotate-v4.0.2/ -name '*.pl' -exec perl -I./PerlLib -c {} \;

Multiple Sequence Alignment (T-Coffee)









































cd /usr/local/bioinfo
tar -zxvf hmmtop_2.1.tgz
cd ./hmmtop_2.1/
cc hmmtop.c -lm -o hmmtop
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/hmmtop_2.1/hmmtop

cd /usr/local/bioinfo/GOR/SOURCE
make
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/GOR/SOURCE/gorIV

cd /usr/local/bioinfo
#wget https://www.tbi.univie.ac.at/RNA/download/ubuntu/ubuntu_20_04/viennarna_2.5.1-1_amd64.deb
#sdo apt-get -y install libgsl23 libgslcblas0
#sudo gdebi viennarna_2.5.1-1_amd64.deb
sudo apt-get -y install vienna-rna

wget http://prodata.swmed.edu/download/pub/PCMA/pcma.tar.gz
tar -zxvf pcma.tar.gz
cd pcma
make
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/pcma/pcma

cd /usr/local/bioinfo
wget https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.12.0/ncbi-blast-2.12.0+-x64-linux.tar.gz
tar -zxvf ncbi-blast-2.12.0+-x64-linux.tar.gz
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/ncbi-blast-2.12.0+/bin/legacy_blast.pl

cd /usr/local/bioinfo
wget https://github.com/rcedgar/muscle/releases/download/5.1.0/muscle5.1.linux_intel64
chmod a+x muscle5.1.linux_intel64
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/muscle5.1.linux_intel64 mus4


sudo apt-get -y install t-coffee

Amplicon-Seq




















# FLASH
cd /usr/local/bioinfo
wget http://ccb.jhu.edu/software/FLASH/FLASH-1.2.11.tar.gz
tar -zxvf FLASH-1.2.11.tar.gz
cd FLASH-1.2.11/
make
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/FLASH-1.2.11/flash

# PEAR
# https://www.h-its.org/downloads/pear-academic/
cd /usr/local/bioinfo
tar -zxvf pear-0.9.11-linux-x86_64.tar.gz
cd /usr/local/bin
sudo ln -s /usr/local/bioinfo/pear-0.9.11-linux-x86_64/bin/pear
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