# October 27, 2020 Julia Fitness Landscapes Julia compatability package: https://github.com/JuliaLang/Compat.jl https://github.com/glesica/NKLandscapes.jl ^old, broken package that we're going to try to use today Installation using package manager in julia fails (NKLandscapes not found) Installation through github - fails Information on paths in the cluster: http://www.hpc.caltech.edu/documentation/faq/how-do-i-modify-my-shell-environment - can edit path temporarily in command line - can edit path (more) permanantly using .bashrc file ```bash= cd bin #full path (for me) is /afs/crc.nd.edu/user/c/crivaldi/bin/ #add bin to path if not already added export PATH=/afs/crc.nd.edu/user/c/crivaldi/bin:$PATH wget https://julialang-s3.julialang.org/bin/linux/x64/0.6/julia-0.6.4-linux-x86_64.tar.gz tar -xvxf https://julialang-s3.julialang.org/bin/linux/x64/0.6/julia-0.6.4-linux-x86_64.tar.gz #clean up - remove zipped file rm julia-0.6.4-linux-x86_64.tar.gz #add softlink to older version of julia file in your bin ln -s /path/to/julia/bin ~/bin/julia0.6.4 #This command will look different for everyone, but for me it looks like this: #crcfe01$ln -s julia-9d11f62bcb/bin/julia julia-0.6.4 #exit and re-enter bash (may have to log out and log back in) #add bin to path if not already added export PATH=/afs/crc.nd.edu/user/c/crivaldi/bin:$PATH #test older version julia-0.6.4 #Should see julia screen come up with version 0.6.4 in info ``` continuing in julia verion 0.6.4 ```julia= julia> Pkg.add("NKLandscapes") julia> Pkg.test("NKLandscapes") #to try unit tests (not mandatory, but good practice for your own packages): #in runtests.sh, change julia variable to the version you just added using NKLandscapes #(in class, trying lines from source code - for me these are located here: #/afs/crc.nd.edu/user/c/crivaldi/.julia/v0.6/NKLandscapes/) ```
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chissa rivaldi
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Hack MD of Hack MDs

8/18/20-8/20/20 - CRC Scripts for genome assembly, including Fastqc, Trimmomatic, Velvet, and Glimmer thhbmnvk

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Last day of RNA seq in julia Practical Ten -use kmeans or hclust (however many clusters you want) -Distance matrix from practical 4, use MDS from Multivarate Stats on this matrix -Use same matrix with clustering, color according to cluster https://juliastats.org/Clustering.jl/stable/kmeans.html add Clustering package

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RNA Seq with Julia

Class 10/6/20 Goal: Build counts table and analyze expression data in Julia https://biojulia.net/GenomicFeatures.jl/v0.2/io/gff3/ log on to CRC Make new working directory for today and cd into it copy files for today cp /tmp/ND_ICG_OCT_6/* . module load julia

10/8/2020
RNA-seq count quantification with Salmon

The RNA-seq analysis we'll be doing today has a workflow like this: We're starting with the second to last step (Salmon), and then moving to R/Rstudio for the Differential Expression Analysis and Visualization. We definitely don't have the time in class to do everything you can do with RNASeq data, so there are some links at the bottom of this document that you can follow to tailor this workflow to your needs. To begin: Log on to the CRC Make a working directory for today and cd into it: mkdir SEP_29

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