DSOSU-Dev - wiki:software

alen

Anonymous (anonymous@undisclosed.example.com) — 2024-03-26T17:08:07+00:00

Installing alen. 1. Download binary package from here 2. Be sure to click on the release link on the page and go the the assets section. there you should find the pre-compiled binary package. Download that alen-v0.3.1-linux-amd64.zip 3. cd to the /home/.hub_local folder, do unpack.

bakta

Anonymous (anonymous@undisclosed.example.com) — 2024-03-25T22:24:22+00:00

To install bakta run: hubpip install bakta

bandage

Anonymous (anonymous@undisclosed.example.com) — 2024-04-16T21:10:48+00:00

Install Bandage package. Download package here. Download the Bandage_Ubuntu-x86-64_v0.9.0_AppDir.zip file. Unpack the and move the entire folder to /home/.hub_local mv Bandage_Ubuntu-x86-64_v0.9.0 /home/.hub_local/. cd /home/.hub_local/bin ln -s ../Bandage_Ubuntu-x86-64_v0.9.0/usr/bin/bandage .

bbtools

Anonymous (anonymous@undisclosed.example.com) — 2024-03-25T22:21:49+00:00

Installing bbtools Download scripts here Untar the file and then move all contents in the bbmap folder to the /home/.hub_local/bin folder.

cmake

Anonymous (anonymous@undisclosed.example.com) — 2023-01-18T21:09:45+00:00

Cmake install This is something should probably include in the docker image build. For now, will need to compile from the source. This is needed for some packages in R to compile. The source Unpack tar file and cd into the install folder. To build do the following:

fastp

Anonymous (anonymous@undisclosed.example.com) — 2024-03-22T23:20:01+00:00

Fastp Install Compiling from source requires three libraries: libdeflate, libisal and libtool. In addition, cmake is required as well. Source code for libtool here libisal requires nasm to compile here 1. For nasm cd to the source folder run configure --prefix=/home/.hub_local make make install

fastqc

Anonymous (anonymous@undisclosed.example.com) — 2024-04-16T21:05:16+00:00

Installing Fastqc Download here Unpack the zip file and move the folder to /home/.hub_local/. Then create a symlink to the fastqc binary. cd /home/.hub_local/bin ln -s ../FastQC/fastqc .

gnuplot

Anonymous (anonymous@undisclosed.example.com) — 2023-09-25T22:04:28+00:00

Install Gnuplot Installation to set up a new gnuplot icon on the Jupyter Notebook launch page. First, install the Python package hubpip install gnuplot_kernel Then each user will need to run the following command in the terminal app: python -m gnuplot_kernel install --user

iqtree

Anonymous (anonymous@undisclosed.example.com) — 2024-03-26T16:55:07+00:00

Installing iqtree 1. Download the binary package from here 2. Unpack and copy the binary from the source bin folder to the /home/.hub_local/bin/.

jbrowser

Anonymous (anonymous@undisclosed.example.com) — 2023-09-25T22:13:19+00:00

JBrowser in Jupyter Install the following Python packages: hubpip install jupyter-dash hubpip install jupyter-server-proxy hubpip install jbrowse-jupyter You can get the source here. However, trying out the example files in the source never worked.

julia

Anonymous (anonymous@undisclosed.example.com) — 2022-12-25T15:30:21+00:00

Julia Software Install For Julia software to run from the terminal app, the following environment variables must be set below ENV["LD_PRELOAD"]= ENV["LD_LIBRARY_PATH"]= ENV["JULIA_DEPOT_PATH"]="/home/USERNAME/.julia" This will allow students to install additional Julia packages in their home folder under the .julia folder. To set up a Julia kernel that allows central installation of packages do the following. Start terminal app, set enivronment vars as above. Start Julia.

mafft

Anonymous (anonymous@undisclosed.example.com) — 2024-03-26T16:51:22+00:00

To install mafft do the following. 1. download deb package from here 2. Create a folder to extra the package into. mkdir extracted 3. Then unpack dpkg-deb -x mafft_7.520-1_amd64.deb extracted/ 4. cd into the extracted/usr folder and copy everything to /home/.hub_local/.

mb668

Anonymous (anonymous@undisclosed.example.com) — 2024-03-20T22:20:39+00:00

MB 668 - Tom Sharpton/Maude David This class required numerous packages to download and compile. a list of software that we will need to run for the computing labs: * R and Rscript Already installed in the docker image. * Bowtie2 Click on tags and then download the latest version. Unzip the file and then cp the bowtie2* files into the hub bin folder.

perlmodules

Anonymous (anonymous@undisclosed.example.com) — 2023-03-10T23:01:40+00:00

Installing Perl Modules Centrally Looking for way to install Perl CPAN modules centrally on the JH hub. Found the following steps. * Make personal Perl configuration for use with CPAN * On the command line enter in: perl -MCPAN -e 'mkmyconfig'

ruby

Anonymous (anonymous@undisclosed.example.com) — 2023-03-17T19:49:47+00:00

Installing Ruby From Source To install Ruby you will first need to install the libyaml from source To install libyaml do the following: 1. change into the source directory cd libyaml-0.2.5 2. Run the bootstrap script ./bootstrap 3. Run configure script with prefix set to /home/.hub_local

rust

Anonymous (anonymous@undisclosed.example.com) — 2023-05-09T17:50:18+00:00

Installing Rust These are the steps to install Rust in the user's home folder. After you log in, start up a terminal app. In the terminal window run the following commands: curl --proto '=https' --tlsv1.3 https://sh.rustup.rs -sSf | sh Chose the first option to install (default) Then run:

spades

Anonymous (anonymous@undisclosed.example.com) — 2024-03-22T22:22:46+00:00

Installing Spades, a genome assembler package. Download source wget https://github.com/ablab/spades/releases/download/v3.15.5/SPAdes-3.15.5-Linux.tar.gz tar -xzf SPAdes-3.15.5-Linux.tar.gz cd SPAdes-3.15.5-Linux/bin/ cp -r * /home/.hub_local/.

sra-tools

Anonymous (anonymous@undisclosed.example.com) — 2024-02-13T18:35:17+00:00

Install SRA-Tools: First need to download prereq package . Unzip package and then run: configure --prefix=/home/.hub-local make make install Then Download the SRA-Tools: Unzip pacakge and then run: ./configure --prefix=/home/.hub_local --with-ncbi-vdb=/home/.hub_local make make install

st591

Anonymous (anonymous@undisclosed.example.com) — 2023-09-27T21:16:04+00:00

ST591 - Tom Sharpton This class required numerous packages to download and compile. This worked on the JH v1.0.5. a list of software that we will need to run our computing labs: NOTE: As of v1.1.3-dev, both cmake and cpio are now installed in the image.