Where should I store velvet file

Question

[suhalsuhaimi]

Hi, I'm new here. I already download velvet 1.2.10. After I extract that file, where should I store it. it is in the desktop or else. I always can call my file.

One more thing, I always get error when I write a command like this:

aconty@aconty-VirtualBox:~$ >make
aconty@aconty-VirtualBox:~$ >make 'CATEGORIES=57'
CATEGORIES=57: command not found

Answer 1

[Ram]

You can store the extracted file anywhere, as long as you add the path of the directory in which the file exists to the PATH environment variable. Let's say you store the extracted files in ~/Desktop/BioTools/velvet, run this command from the terminal:

echo 'export PATH=$PATH:~/Desktop/BioTools/velvet'  >> ~/.bashrc

I'm assuming you're on an Ubuntu VM, by the way. Some distros of Linux (such as Mac's BSD) use ~/.bash_profile instead of ~/.bashrc, so you might wanna check on that as well.

And on issue #2, you might be using backquotes (this: `,the key near the 1 key, on the top left of the keyboard) instead of the single quote (this: ', the key near the Enter/Return key). Ensure you're using the right quotes and are actually typing the command and not copy pasting from anywhere.

[suhalsuhaimi]

Thank You. I already follow the command as what you told.

I try to follow all the command as what manual wrote. The manual wrote like this:

make
./velveth
./velvetg

./velveth sillyDirectory 21 -shortPaired data/test_reads.fa
./velvetg sillyDirectory

I wrote command like this:

aconty@aconty-VirtualBox:~$ echo `export PATH=$PATH:~/Desktop/BioTool/velvet` >> ~/.bashrc

aconty@aconty-VirtualBox:~$ > make
aconty@aconty-VirtualBox:~$ > ./velveth
aconty@aconty-VirtualBox:~$ > ./velvetg
aconty@aconty-VirtualBox:~$ > ./velveth velvet 21 -shortPaired data/J99.fa
No command 'velvet' found, did you mean:
 Command 'velveth' from package 'velvet' (universe)
 Command 'velvetg' from package 'velvet' (universe)
velvet: command not found

What name should I replace with sillyDirectory? I still blur on it.

Can you help me again. I really appreciate you help.

P/s: I'm really sorry. I'm new here and this my first post. Thank a lot, I appreciate your help. Thank again.

[Ram]

It's OK, we're here to help and it's not unusual for someone to make such minor errors in their first few weeks here :)

[Ram]

Once you add velveth/g to PATH, you should be able to run it from your project directory. I suggest you use something like 'my_velvet_output' for your output directory name (in place of sillyDirectory). velvet will create a directory with that name and write output into it.

[suhalsuhaimi]

And another thing. I store my fasta file on my velvet folder. Am I doing right thing?

[Ram]

You might wanna store it in your actual project directory and link to it here using ln -s /path/to/project/folder/fastafile.fasta

You can directly run velveth/velvetg from your project folder once you add do the add-to-path step.

[suhalsuhaimi]

Great. I make it to folder because I have two types of sequence. It is true?

aconty@aconty-VirtualBox:~$ ln -s /path/to/project/folder/HPAG1.fasta
aconty@aconty-VirtualBox:~$ ln -s /path/to/project/folder/J99.fasta

But when I try to do my output project directory, It come out like this:

aconty@aconty-VirtualBox:~$ > ./velveth my_velvet_output 21 -shortPaired data/J99.fa
my_velvet_output: command not found
aconty@aconty-VirtualBox:~$ > ./velveth my_velvet_output 21 -shortPaired data/J99.fasta
my_velvet_output: command not found

And I also try another option. But still error:

aconty@aconty-VirtualBox:~$ > ./velveth my_velvet_output 21 -shortPaired data/J99.fasta HPAG1.fasta
my_velvet_output: command not found
aconty@aconty-VirtualBox:~$ > ./velveth my_velvet_output/
bash: my_velvet_output/: No such file or directory
aconty@aconty-VirtualBox:~$ > ./velveth my_velvet_output
my_velvet_output: command not found
aconty@aconty-VirtualBox:~$ > ./velvetg my_velvet_output
my_velvet_output: command not found

[Ram]

You might wanna skip the ~/ and just use velveth and velvetg. Also, it is always good to work in a separate directory for the project as you will create a multitude of files as you proceed with your work.

[suhalsuhaimi]

Thank you.

Thank you very much

[Ram]

Glad to help. I take it that worked?