samtools-1.2 re-header command

[cmccabe]

I downloaded the samtools-1.2 zip, unzip, and did make: I tried using the reheader command that used to work but am getting the below error. Do I still need the sudo apt-get install of samtools, it would appear that I do. Thank you .

 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
The program 'samtools' is currently not installed. You can install it by typing:
sudo apt-get install samtools
samtools-1.2: command not found

added to path:

 echo 'export PATH=$PATH:/home/cmccabe/Desktop/ngs_analysis/samtools-1.2' >> ~/.bashrc

[GenoMax]

Just adding a directory to your PATH does not mean it has the program you will eventually want to run (or that it is set as an executable). Does home/cmccabe/Desktop/ngs_analysis/samtools-1.2 have the samtools program and is it executable is the first thing I would look at.

[cmccabe]

The samtools exe is in that directory and should be executable. Maybe

echo 'export PATH=PATH=/home/cmccabe/Desktop/ngs_analysis/samtools-1.2:$PATH >> ~/.bashrc

Would help to find and use that exe? Thank you .

[GenoMax]

Before you get into piping multiple set of commands together make sure that the individual commands are working properly. One piece of advice: get away from using spaces in file/directory names ASAP. That is just asking for trouble.

[cmccabe]

I know the pipes work as I have used them before. I must have the path wrong as it is not finding the exe in the samtools-1.2 directory, is the below not the correct way to add to path:

 echo 'export PATH=PATH=/home/cmccabe/Desktop/ngs_analysis/samtools-1.2:$PATH >> ~/.bashrc

Thank you .

[dpryan]

Try removing the second "PATH=". You're also missing a '.

[cmccabe]

Thank you very much, its working .