esohkevin / scripts

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Random scripts

• Python
• Shell
• R
• etc

For generating ssh keys, click here

Conda pkgs

• conda build: Build pkgs

Terms

Conda channels: Source repositories for conda pkgs. Conda-forge is one such channel. Also bioconda

Specifying a channel

conda install scipy --channel conda-forge

More than one channels

conda install numpy --channel conda-forge --channel bioconda

Suppress all default channels and only look from specified channel

conda install pandas --channel file:///home/user/path --overide-channels

Add alias to local channels

conda config --set channel_alias file:///home/esoh/bioTools

Install pkgs from local channel using alias name

conda install -c bioTools <pkg>

Make a copy of all installed packages in current env and use to create a new identical env

conda list --explicit > spec-file.txt
conda create --name newenv --file spec-file.txt

Create identical env from an env.yml file

conda env create [-f|--file] environment.yml 

Bioinfo pkgs

Install all packages without comment on availability by running the command-line below

conda search <pkg>
conda install <pkg>=version [--channel | -c] <channel>  

Example

conda search eigensoft
conda install eigensoft=6.0.1 -c bioconda
conda install eigensoft=6.0.1 --channel bioconda

• Picard
• bcftools
• vcftools
• samtools
• bwa
• hisat2
• bowtie2
• plink1.9 (plink2 absent. Use linux-installed)
• emmax (Absent. Use linux-installed)
• bolt-lmm (Absent. Use linux-installed)
• eagle (v0.9.4.6 available. Use linux-installed v2.4)
• beagle (v4.1 available. Use)
• bedtools
• eigensoft
• fastqc
• multiqc
• tophat
• trimmomatic
• gatk3 (gatk4 not available. Use linux-installed)

Download and unzip GATK4. Copy the gatk executable into home bin. Then run the line below to set gatk global environ variable Preferably, place the line in ~/.bashrc file

export GATK_LOCAL_JAR=~/bioTools/gatk-4.1.3.0/gatk-package-4.1.3.0-local.jar

• shapeit2
• qqman
• admixture
• finestructure
• hierfstat (R)
• pegas (read VCF in R)
• adegenet (R)
• gcta (NA)
• snptest
• hapFlk (selection scan)
• phangorn (genetic trees)
• vtools (bioconda) NGS, Exome Seq Analysis
• modeller

conda config --add channels salilab
KEY_MODELLER='XXX'
conda install modeller

• Pymol

conda config --prepend channels schrodinger
conda install -c schrodinger pymol

• Geoplotting (python)

conda create --yes --name geo python=3.7 geopandas geoplot jupyterlab -c conda-forge