Python Virtual Environments#

We recommend you use virtual enviornments packages inside the standard library to manage your dependencies. This can be done using the following commands :
1. module load compiler/anaconda3
2. python -m venv <ENV_NAME>
3. source <ENV_NAME>/bin/activate
4. pip install <PACKAGENAME>

This allows you to efficiently manage, and version control the python based packages you are using inside your user space.

Currently, we provide a script to set-up your python environment for BIC(Indel-classification tasks related to Biology).

The BIC script allows you to setup a python environment with all the required packages for your BIC workflow.

In order to set-up the environment, run the bash script from your terminal using command .\storage\bic.sh; you'll have to stay at your system in order to provide permissions
for every package being installed.

In rare cases, some packages might fail to install due to change in conda repositories. You can either try manually installing these packages via conda or pip via the commands below
or get in touch with us. Currently the script installs following packages:

1. Snakemake: conda install -c bioconda snakemake
   2.
   

   #Nextflow:
   wget https://github.com/nextflow-io/nextflow/releases/download/v22.04.4/nextflow
   chmod +x nextflow
   

2. Bamtools: conda install -c bioconda bamtools

3. Bcftools: conda install -c bioconda bcftools
4. Barrnap: conda install -c barrnap
5. Bedtools: conda install -c bioconda bedtools
6. Bowtie2: conda install -c bioconda bowtie2
7. Bwa: conda install -c bioconda bwa
8. Cap3: conda install -c bioconda cap3
9. Cd-hit: conda install -c bioconda cd-hit
10. Circus: conda install -c conda-forge circus
11. Clustalw: conda install -c bioconda clustalw
12. Cufflinks: pip install cufflinks
13. Fasta3: conda install -c bioconda fasta3
14. Blast: conda install -c bioconda blast
15. Orfipy: conda install -c bioconda orfipy
16. Perl: conda install -c conda-forge perl
17. Pfam_scan: conda install -c bioconda pfam_scan
18. Plink: conda install -c bioconda plink
19. Fastqc: conda install -c bioconda fastqc
20. HiSat2: conda install -c bioconda hisat2
21. Hmmer: conda install -c bioconda/label/cf201901 hmmer
22. Kmergenie: conda install -c bioconda kmergenie
23. Quast: conda install -c bioconda quast
24. R: conda install -c conda-forge r
25. Repeatmasker: conda install -c bioconda repeatmasker
26. Rmblast: conda install -c bioconda rmblast
27. Rsem: conda install -c bioconda rsem
28. Samtools: conda install -c bioconda samtools
29. SeqKit: conda install -c bioconda seqkit
30. Saopaligner: conda install -c bioconda soapaligner
31. Soapdenovo2: conda install -c bioconda soapdenovo2
32. Sortmerna: conda install -c bioconda sortmerna
33. Spades: conda install -c bioconda spades
34. Sra-tools: conda install -c bioconda sra-tools
35. StringTie: conda install -c bioconda stringtie
36. Structure: conda install -c bioconda structure
37. Jellyfish: conda install -c conda-forge jellyfish
38. Trimmomatic: conda install -c bioconda trimmomatic
39. Trinity: conda install -c bioconda trinity
40. Velvet: conda install -c bioconda velvet
41. VcfTools: conda install -c bioconda vcftools
42. Megahit: conda install -c bioconda megahit
43. Diamond: conda install -c bioconda diamond
44. QuickMerge: conda install -c conda-forge -c bioconda quickmerge
    OR:
    

    git clone https://github.com/mahulchak/quickmerge
    cd quickmerge
    bash make_merger.sh
    cd ..
    
    username=$(whoami)
    export PATH=/home/$username/quickmerge:/home/$username/quickmerge/MUMmer3.23:$PATH
    

    
    46.
    

    #VCF2CNA:
    git clone https://github.com/XCLab/VCF2CNA
    cd VCF2CNA
    bash extract.sh
    

Note : Remember to activate the virtual environment inside your job.sh file submitted to qsub.