[GenoMax]

I am going to re-install. Did you have to do anything besides download, extract, and add to path? Was chmod or make necessary? Thank you

Since it is source code you have to compile it by "make". Did you not do that?

[cmccabe]

Here are the steps:

wget https://github.com/BenLangmead/bowtie2/archive/master.zip
unzip master.zip
cd /home/dnascopev/Desktop/master
make

after that I renamed the folder to bowtie2-2.2.6 and added that to path using:

 echo 'export PATH=$PATH:/home/dnascopev/Desktop/bowtie2-2.6.0' >> ~/.bashrc

Thank you .

[cmccabe]

the build indexs is running:

Are these normal?

Warning: Encountered empty reference sequence
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered empty reference sequence
Warning: Encountered empty reference sequence
Warning: Encountered reference sequence with only gaps
Warning: Encountered empty reference sequence

 bowtie2-build -f /home/dnascopev/Desktop/hg19_fasta/hg19.fa /home/dnascopev/Desktop/hg19_fasta/my_hg19

was used to build the index

 cat *.fa > hg19.fa

was used to concatenate the fa from chromFa.tar.gz

Thank you .

[sahil.jain]

bowtie2-build: command not found

I downloaded the bowtie 2-2.3.5.1 for mac using the link:https://sourceforge.net/projects/bowtie-bio/

It was a zipped file so I unzipped it.

I opened the unzipped folder on the terminal and then typed the command:

(base) linglabs-ipro:bowtie2-2.3.5.1-macos-x86_64 linglab$ bowtie2-build
-bash: bowtie2-build: command not found
(base) linglabs-ipro:bowtie2-2.3.5.1-macos-x86_64 linglab$

Please Help!

[GenoMax]

@sahil: Please go through this UNIX basics tutorial, if you are unfamiliar with the command line.