bowtie2 install on ubuntu

Question

[bioguy24]

I downloaded bowtie2-2.6.0 from github as I am blocked from sourceforge, extracted, and installed it. I added it to path using:

echo "export PATH=\$PATH:export PATH=$PATH:"/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0"/" >> ~/.bashrc

and confirmed it using:

/media/C2F8EFBFF8EFAFB9/picard-tools-1.135/:/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/

it appears to be added but when I try to build and index using combined files from chromFA.tar.gz using:

 bowtie2-build hg19.fa hg19
No command 'bowtie2-build' found, did you mean:
 Command 'bowtie-build' from package 'bowtie' (universe)
bowtie2-build: command not found

What did I do wrong? Thank you.

Answer 1

[h.mon]

Maybe you want:

echo 'export PATH=$PATH:/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0' >> ~/.bashrc

Or edit .bashrc with nano.

edit: here is what gets appended to .bashrc with your command:

export PATH=$PATH:export PATH=/usr/local/bin:/usr/bin:/bin:/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/

[bioguy24]

I edited .bashrc and used the command provided:

Here is the error I get (its different):

dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ bowtie2-build hg19.fa hg19
bash: /media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/bowtie2-build: Permission denied

Thank you :)

[h.mon]

The files probably are not set as executables, do:

chmod +x /media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/bowtie2*

Now, judging by its name (/media/) this is an external drive, depending how it is mounted and its file system, you may not be able to run programs from this drive.

[bioguy24]

Getting closer:

You were right that /media/ wasn't mounted so I moved bowtie2 and added it to path.

dnascopev@ubuntu:~/Desktop/hg19_fasta$ bowtie2-build hg19.fa hg19
Traceback (most recent call last):
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 95, in <module>
    main()
  File "/home/dnascopev/Desktop/hg19_fasta/bowtie2-2.6.0/bowtie2-build", line 92, in main
    os.execv(build_bin_spec, argv)
OSError: [Errno 2] No such file or directory

Thank you :).

[h.mon]

bowtie2-build doesn't know where is hg19.fa, it seems. Is the file hg19.fa on the same folder where you are calling bowtie2 (~/Desktop/hg19_fasta/)?

[bioguy24]

I will double check tomorrow, but I think it is. I may have a typo (I do that a lot). Why did bowtie2 need chmod and bedtools did not. Bedtools mounted to /media/ but bowtie2 did not. Just trying to learn and understand, thank you :).