Why does samtools need to be in /usr/bin
when it is in a directory (samtools-1.2) downloaded from github, unzipped, and make was run?
samtools view \
-H /media/cmccabe/C2F8EFBFF8EFAFB9/LCH pool I 090215/IonXpress_008_150902.bam | \
sed '/^@PG/d' | \
samtools reheader - \
/media/cmccabe/C2F8EFBFF8EFAFB9/LCH pool I 090215/IonXpress_008_150902.bam > /home/cmccabe/Desktop/ngs_analysis/pool1/IonXpress_008_150902_newheader.bam
I added the below to path:
echo 'export PATH=$PATH:/home/cmccabe/Desktop/ngs_analysis/samtools-1.2' >> ~/.bashrc
Thank you :)
you set, the PATH, now bash can find samtools. So, what is the question ?
With that PATH bash can not find samtools but I am not sure why. I have also tried changing the path as listed below. Thank you :).