Additional depedencies to be installed in the opt/ folder.
accessed 2019-04-11
mkdir -p kentutils
rsync -azvP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/ ./kentutils/
accessed 2019-04-26
git clone https://github.com/vezzi/FRC_align.git
wget http://ccb.jhu.edu/software/hisat2/downloads/hisat2-2.0.0-beta-source.zip
wget https://github.com/mummer4/mummer/releases/download/v4.0.0beta2/mummer-4.0.0beta2.tar.gz
Using statically linked version as there is some issue with Qt libraries
wget https://github.com/rrwick/Bandage/releases/download/v0.8.1/Bandage_Ubuntu_static_v0_8_1.zip
wget https://github.com/AdoptOpenJDK/openjdk11-binaries/releases/download/jdk-11.0.7%2B10/OpenJDK11U-jdk_x64_linux_hotspot_11.0.7_10.tar.gz
wget ftp://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/5.44-79.0/interproscan-5.44-79.0-64-bit.tar.gz
wget http://downloads.sourceforge.net/project/parafly/parafly-r2013-01-21.tgz
git clone git@github.com:Swart-lab/gbtquick.git
git clone https://github.com/marbl/Winnowmap.git
git checkout v2.0
git clone https://bitbucket.org/dkessner/harp.git
Original repository on Google Code, which has been deprecated. This is a mirror on Github. NB: superseded by pbsim2
git clone git@github.com:pfaucon/PBSIM-PacBio-Simulator.git
Updated version of pbsim from original authors. Latest commit e71f789 nominally v2.0.1
git clone git@github.com:yukiteruono/pbsim2.git
Masters project by David Vetter, git repo, latest commit 85731dc. Follow build instructions with maven
git clone git@github.com:Swart-lab/pogigwasc.git
Package build manager for Java, required to compile pogigwasc
wget https://ftp.fau.de/apache/maven/maven-3/3.6.3/binaries/apache-maven-3.6.3-bin.tar.gz
We want the get_asm_stats.py script to parse Falcon assembly
git clone https://github.com/PacificBiosciences/pb-assembly.git
Installed via Conda but we need the atMask.mat file from the test/ folder
git clone https://gitlab.com/mcfrith/tantan.git