Closed ndreey closed 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 installedcd ../NGSNGS; make HTSSRC=../htslib
ran without issues!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:
/mnt/c/Users/andbo/thesis_andbo/NGSNGS/ngsngs
.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.
CLOSING ISSUE as
Set up conda environment for the mock data simulation to meet the req from NGSNGS