VM_tool_install_error_fixes.md

Summary of fixes used for the NGSBioAfrica2022 VM so far

To fix lumpyexpress error:

conda create --name thelumpyenv python=2.7

conda activate thelumpyenv

conda install pysam

conda install numpy

cd /home/manager/course_data/structural_variation/data/exercise3/

samtools view -bh -F 1294 ERR1015069.bam | samtools sort -O bam -T ERR1015069.temp -o ERR1015069.discordants.bam

samtools index ERR1015069.discordants.bam 

samtools view -h ERR1015069.bam | extractSplitReads_BwaMem -i stdin | samtools view -b - | samtools sort -O bam -T ERR1015069.temp -o ERR1015069.splitters.bam

samtools index ERR1015069.splitters.bam

lumpyexpress -B ERR1015069.bam -S ERR1015069.splitters.bam -D ERR1015069.discordants.bam -o ERR1015069.vcf

ls
# deactivate the environment when done
conda deactivate

To install snpdists

conda install snp-dists

To resolve an iqtree error - big thanks to Gebremeskel Mamu Werid for posting this on Vula

#1. To uninstall the iqtree package, you can use:  
sudo apt remove iqtree 
# or 
pip uninstall iqtree

#2. update your system: 
sudo apt-get update

#3. install a specific version of iqtree package: 
conda install -c bioconda -c defaults iqtree=1.6.12

#4.  update your system: 
sudo apt-get update

#5. check if you installed the right version of iqtree 
iqtree --version

To install figtree

sudo apt install figtree
# the password is manager

To install sleuth for module 7:

# Begin by running R

R

BiocManager::install()

install.packages(“devtools”)

BiocManager::install(“pachterlab/sleuth”)

# continue with the practical from here

to install tximportData in R

# Begin by running R

R

BiocManager::install("tximportData")

# continue with the practical from here

To install salmon for mod 8:

conda create -n salmon salmon
conda activate salmon

# run your salmon commands

# deactivate the environment when done

conda deactivate