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=$PATH:"/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0"/" >> ~/.bashrc
and confirmed it using:
/media/C2F8EFBFF8EFAFB9/picard-tools-1.135/:/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/
it appears to be added but when I try to build and index using combined files from chromFA.tar.gz using:
bowtie2-build hg19.fa hg19
No command 'bowtie2-build' found, did you mean:
Command 'bowtie-build' from package 'bowtie' (universe)
bowtie2-build: command not found
What did I do wrong? Thank you.
Maybe you want:
echo 'export PATH=$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=$PATH:export PATH=/usr/local/bin:/usr/bin:/bin:/media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/
I edited .bashrc and used the command provided:
Here is the error I get (its different):
dnascopev@ubuntu:/media/C2F8EFBFF8EFAFB9$ bowtie2-build hg19.fa hg19
bash: /media/C2F8EFBFF8EFAFB9/bowtie2-2.6.0/bowtie2-build: Permission denied
Thank you :)
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.
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 :).
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