DSOSU-Dev https://dsosu-dev.datasci.oregonstate.edu/ 2026-04-07T23:01:07+00:00 DSOSU-Dev https://dsosu-dev.datasci.oregonstate.edu/ https://dsosu-dev.datasci.oregonstate.edu/lib/exe/fetch.php?media=wiki:dokuwiki.svg text/html 2024-04-16T21:10:48+00:00 keistc (keistc@undisclosed.example.com) bandage - created https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:bandage&rev=1713301848&do=diff 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 . text/html 2024-04-16T21:05:16+00:00 keistc (keistc@undisclosed.example.com) fastqc https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:fastqc&rev=1713301516&do=diff 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 . text/html 2024-03-28T15:42:01+00:00 keistc (keistc@undisclosed.example.com) rclone - created https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:rclone&rev=1711640521&do=diff Before tearing down any JH cluster at the end of term, need to make sure and make a backup copy of all the course JH home folders to Box. Below is how to use rclone to copy the data to Box. First will need to download the Linux binary of rclone from text/html 2024-03-26T17:08:07+00:00 keistc (keistc@undisclosed.example.com) alen - created https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:alen&rev=1711472887&do=diff 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. text/html 2024-03-26T16:55:07+00:00 keistc (keistc@undisclosed.example.com) iqtree - created https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:iqtree&rev=1711472107&do=diff 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/. text/html 2024-03-26T16:51:22+00:00 keistc (keistc@undisclosed.example.com) mafft - created https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:mafft&rev=1711471882&do=diff 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/. text/html 2024-03-25T22:24:22+00:00 keistc (keistc@undisclosed.example.com) bakta - created https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:bakta&rev=1711405462&do=diff To install bakta run: hubpip install bakta text/html 2024-03-25T22:21:49+00:00 keistc (keistc@undisclosed.example.com) bbtools - created https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:bbtools&rev=1711405309&do=diff Installing bbtools Download scripts here Untar the file and then move all contents in the bbmap folder to the /home/.hub_local/bin folder. text/html 2024-03-22T23:20:01+00:00 keistc (keistc@undisclosed.example.com) fastp https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:fastp&rev=1711149601&do=diff 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 text/html 2024-03-22T22:22:46+00:00 keistc (keistc@undisclosed.example.com) spades - created https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:spades&rev=1711146166&do=diff 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/. text/html 2024-03-20T22:20:39+00:00 keistc (keistc@undisclosed.example.com) mb668 https://dsosu-dev.datasci.oregonstate.edu/doku.php?id=wiki:software:mb668&rev=1710973239&do=diff 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.