Set up conda environment

ndreey / ghost-magnet

Molecular Bioinformatics BSc thesis project at University of Skövde

MIT License

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Set up conda environment #8

Closed ndreey closed 1 year ago

ndreey commented 1 year ago

Set up conda environment for the mock data simulation to meet the req from NGSNGS

ndreey commented 1 year ago

git clone https://github.com/RAHenriksen/NGSNGS.git

git clone https://github.com/samtools/htslib.git

Error fixes for: cd htslib; make

sudo apt-get install libbz2-dev
git submodule update --init --recursive
sudo apt-get install libcurl4-openssl-dev
- sudo hwclock --hctosys My wsl differed in time which made it so I could not run sudo apt-get update which is needed to install libcurl4 (StackOverflow)
- sudo apt update
- sudo apt-get update
- libcurl successfully installed
cd ../NGSNGS; make HTSSRC=../htslib ran without issues!

ndreey commented 1 year ago

NGSNGS has been successfully run on the test data provided from NGSNGS.

./ngsngs -i Test_Examples/hg19MSub.fa -r 1000 -f fq -l 400 -seq PE -q1 Test_Examples/AccFreqL150R1.txt -q2 Test_Examples/AccFreqL150R1.txt -a1 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGATTCGATCTCGTATGCCGTCTTCTGCTTG -a2 AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATTT -o HgSim1337

I however could not get it to work for the practice data.

To do:

Add path/NGSNGS/ngsngs to PATH or create a variable for ngsngs so i don't need to write /mnt/c/Users/andbo/thesis_andbo/NGSNGS/ngsngs.
Read through parameters again and see where i go wrong. It firstly complained about reference being zipped with gzip when it wants bgzip.

ndreey commented 1 year ago

Global variable was set with export ngsngs=path/ngsngs/

The issues was because of the lack of -q1 and -q2 arguments regarding the quality profile.

ndreey commented 1 year ago

CLOSING ISSUE as

A: No need for conda atm
B: Runing CAMISIM instead of manually coding the abundances.