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Software installed for Abdulfatai on Monster server in Addis in 2020-08

Software Installation Notes

A list of software installed on the Monster server in Addis in 2020-08:

  • AdapterRemoval/2.3.1
  • AdmixTools/7.0.1
  • bamstats/1.25
  • bcftools/1.10.2
  • bowtie2/2.4.1
  • fastq_screen/0.14.1
  • fastqc/0.11.9
  • dedup/0.12.6
  • gatk/4.1.8.0
  • iqtree/1.6.12
  • samtools/1.10
  • xpclr/1.1.2
  • bite/1.20008

Installation Notes

AdapterRemoval/2.3.1

$ cd /tmp
$ wget https://github.com/MikkelSchubert/adapterremoval/archive/v2.3.1.tar.gz
$ tar xf v2.3.1.tar.gz
$ cd adapterremoval-2.3.1
$ make
$ sudo mkdir -p /home/apps/AdapterRemoval/2.3.1
$ sudo chown aorth /home/apps/AdapterRemoval/2.3.1
$ make PREFIX=/home/apps/AdapterRemoval/2.3.1 install
$ sudo chown -R root:root /home/apps/AdapterRemoval/2.3.1

AdmixTools/7.0.1

$ cd /tmp
$ wget https://github.com/DReichLab/AdmixTools/archive/v7.0.1.tar.gz
$ tar xf v7.0.1.tar.gz
$ cd AdmixTools-7.0.1/src
$ sudo dnf install openblas-devel.x86_64
$ make
$ make install
$ cd /tmp
$ sudo mkdir -p /home/apps/AdmixTools
$ sudo cp -r AdmixTools-7.0.1 /home/apps/AdmixTools/7.0.1

bamstats/1.25

$ cd /tmp
$ wget https://downloads.sourceforge.net/project/bamstats/BAMStats-1.25.zip?r=https%3A%2F%2Fsourceforge.net%2Fprojects%2Fbamstats%2Ffiles%2FBAMStats-1.25.zip%2Fdownload&ts=1598110314 -O BAMStats-1.25.zip
$ unzip BAMStats-1.25.zip
$ sudo mkdir -p /home/apps/bamstats
$ sudo cp -r BAMStats-1.25 /home/apps/bamstats/1.25

bcftools/1.10.2

First install its htslib/1.10.2 dependency:

$ cd /tmp
$ wget https://github.com/samtools/htslib/releases/download/1.10.2/htslib-1.10.2.tar.bz2
$ cd htslib-1.10.2
$ ./configure --enable-plugins --enable-libcurl --prefix=/home/apps/htslib/1.10.2
$ make
$ sudo mkdir -p /home/apps/htslib/1.10.2
$ sudo chown aorth /home/apps/htslib/1.10.2
$ make install
$ sudo chown -R root:root /home/apps/htslib/1.10.2

Then install bcftools/1.10.2:

$ cd /tmp
$ wget https://github.com/samtools/bcftools/releases/download/1.10.2/bcftools-1.10.2.tar.bz2
$ tar xf bcftools-1.10.2.tar.bz2
$ cd bcftools-1.10.2
$ ./configure --prefix=/home/apps/bcftools/1.10.2 --with-htslib=/home/apps/htslib/1.10.2
$ make
$ sudo mkdir -p /home/apps/bcftools/1.10.2
$ sudo chown aorth /home/apps/bcftools/1.10.2
$ make install
$ sudo chown -R root:root /home/apps/bcftools/1.10.2

bowtie2/2.4.1

$ cd /tmp
$ wget https://sourceforge.net/projects/bowtie-bio/files/bowtie2/2.4.1/bowtie2-2.4.1-linux-x86_64.zip/download -O bowtie2-2.4.1-linux-x86_64.zip
$ unzip bowtie2-2.4.1-linux-x86_64.zip
$ sudo mkdir -p /home/apps/bowtie2/2.4.1
$ sudo cp -r bowtie2-2.4.1-linux-x86_64/* /home/apps/bowtie2/2.4.1

fastq_scree/0.14.1

$ cd /tmp
$ wget https://github.com/StevenWingett/FastQ-Screen/archive/v0.14.1.tar.gz
$ tar xf v0.14.1.tar.gz
$ cd FastQ-Screen-0.14.1
$ sudo dnf install perl-GD
$ mv fastq_screen.conf.example fastq_screen.conf

Problems with data files. FTP locations have changed and FastQ Screen's own tools for downloading don't work anymore.

fastqc/0.11.9

$ cd /tmp
$ wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.9.zip
$ unzip fastqc_v0.11.9.zip
$ sudo mkdir -p /home/apps/fastqc/0.11.9
$ sudo cp -r FastQC/* /home/apps/fastqc/0.11.9
$ sudo chmod +x /home/apps/fastqc/0.11.9/fastqc

dedup/0.12.6

$ sudo mkdir -p /home/apps/dedup/0.12.6
$ sudo wget https://github.com/apeltzer/DeDup/releases/download/0.12.6/DeDup-0.12.6.jar -O /home/apps/dedup/0.12.6/DeDup-0.12.6.jar

Is a Java jar file so you need to run with java -jar DeDup-0.12.6.jar or create a wrapper DeDup shell script:

$ cat /home/apps/dedup/0.12.6/DeDup
#!/usr/bin/env bash

readonly PREFIX=$(dirname $0)

java -jar $PREFIX/DeDup-0.12.6.jar $*

gatk/4.1.8.0

Needs more time for installation. 4.1.8.0 requires Conda/Miniconda to be installed in order to create a virtual environment.

iqtree/1.6.12

$ wget https://github.com/Cibiv/IQ-TREE/releases/download/v1.6.12/iqtree-1.6.12-Linux.tar.gz
$ tar xf iqtree-1.6.12-Linux.tar.gz
$ sudo mkdir -p /home/apps/iqtree/1.6.12
$ sudo cp -r iqtree-1.6.12-Linux/* /home/apps/iqtree/1.6.12

samtools/1.10

Make sure to install the htslib/1.10.2 dependency (see above).

$ cd /tmp
$ wget https://github.com/samtools/samtools/releases/download/1.10/samtools-1.10.tar.bz2
$ tar xf samtools-1.10.tar.bz2
$ cd samtools-1.10
$ ./configure --enable-plugins --enable-libcurl --prefix=/home/apps/samtools/1.10 --with-htslib=/home/apps/htslib/1.10.2
$ make
$ sudo mkdir -p /home/apps/samtools/1.10
$ sudo chown -R aorth /home/apps/samtools/1.10
$ make install
$ sudo chown -R root:root /home/apps/samtools/1.10

xpclr/1.1.2

$ cd /tmp
$ git clone https://github.com/hardingnj/xpclr.git -b v1.1.2
$ cd xpclr
$ sudo mkdir -p /home/apps/xpclr/1.1.2
$ sudo chown aorth /home/apps/xpclr/1.1.2
$ python3 -m venv /home/apps/xpclr/1.1.2
$ source /home/apps/xpclr/1.1.2/bin/activate
$ pip install --upgrade pip setuptools
$ sed -i '/math/d' requirements.txt
$ pip install -r requirements.txt
$ python setup.py install
$ sudo chown -R root:root /home/apps/xpclr

bite/1.20008

$ cd /tmp
$ sudo dnf install libxml2-devel.x86_64
$ wget https://cran.r-project.org/src/contrib/Archive/GenABEL/GenABEL_1.8-0.tar.gz
$ wget https://cran.r-project.org/src/contrib/Archive/GenABEL.data/GenABEL.data_1.0.0.tar.gz
$ wget https://cran.r-project.org/src/contrib/Archive/RCircos/RCircos_1.1.3.tar.gz
$ wget https://github.com/marcomilanesi/BITE/blob/master/BITE_1.2.0008.tar.gz?raw=true -o BITE_1.2.0008.tar.gz
$ sudo mkdir -p /home/apps/bite/1.20008
$ sudo chown aorth /home/apps/bite/1.20008
$ module load R/3.6.1
$ mkdir -p /home/apps/bite/1.20008/extra-r-libs
$ R
> .libPaths(c('/home/apps/bite/1.20008/extra-r-libs',.libPaths()))
> install.packages(c("GenABEL.data_1.0.0.tar.gz", "GenABEL_1.8-0.tar.gz"), repos = NULL)
> install.packages(c("RCircos_1.1.3.tar.gz"), repos = NULL)
> install.packages('reshape2')
> install.packages('RColorBrewer')
> install.packages('lme4')
> install.packages('pbkrtest')
> install.packages('car')
> install.packages('rmarkdown')
> install.packages('knitr')
> install.packages('xml2')
> install.packages('kableExtra')
> install.packages('beanplot')
> install.packages(c("BITE_1.2.0008.tar.gz"), repos = NULL)
> quit()
$ sudo chown -R root:root /home/apps/bite/1.20008
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