vsearch-1.1.3-osx-x86_64: command not found after installation

[veronic...@gmail.com]

Hello,

We are trying to install search on a Mac Yosemite following the instructions of the README. We tried both:

    cd ~

    mkdir -p bin

    cd ./bin/

    wget  https://github.com/torognes/vsearch/releases/download/v1.1.3/vsearch-1.1.3-osx-x86_64

    ln -s vsearch-1.1.3-osx-x86_64 vsearch

and

    git clone https://github.com/torognes/vsearch.git

    cd ./vsearch/src/

    make -f Makefile

    cd ../bin/

and also tried installing elsewhere. We can see 'vsearch-1.1.3-osx-x86_64' and 'vsearch' are sitting down there, however after trying 

    vsearch

or 

    vsearch-1.1.3-osx-x86_64

or 

    ./vsearch-1.1.3-osx-x86_64

and even sudoing, but the result is always the same:

    -bash: vsearch-1.1.3-osx-x86_64: command not found

    -bash: /bin/vsearch: No such file or director

We are sure we are missing something obvious, but we just can't figure it out. Could you please give us a clue?

Many thanks,

Vero

[Jimmy O'Donnell]

Hi Vero,

I'm not a vsearch developer, but pasted below are some notes I kept on installing vsearch. I'm assuming you've checked that the file is executable, but I didn't note this and so assume it already was when I downloaded it.

Hope this helps,

Jimmy

1. Download the vsearch folder from [vsearch GitHub page](https://github.com/torognes/vsearch) as a .zip file and unzip.

2. Rename it if you want (e.g. vsearch-master -> vsearch)

3. Move it wherever you want it to live (I moved it to `/Applications/vsearch`).

4. Make a link to the binary executable vsearch file from inside of a directory that is in your bash PATH variable. You can see which folders these are by typing `echo $PATH`. I like `/usr/bin`. Give the link a name that's easier to type than the full executable name:

`sudo ln -s '/Applications/vsearch/bin/vsearch-1.1.3-osx-x86_64' '/usr/bin/vsearch'`

5. make a symbolic link to the manual

`sudo ln -s '/Applications/vsearch/doc/vsearch.1' '/usr/share/man/man1/vsearch.1'`

6. Now you can run the program in terminal by simply typing `vsearch` and view the manual by simply typing `man vsearch` -- no need to change directories.

[Torbjørn Rognes]

Hi Vero,

Sorry for your trouble.

Please make sure that the file is executable, i.e. "chmod o+x vsearch-1.1.3-osx-x86_64".

If the executable is in the current directory try putting "./" in front of the command, i.e. "./vsearch" or "./vsearch-1.1.3-osx-x86_64".

I hope this helps.

- Torbjørn

[tic...@gmail.com]

Hi guys,

I'm was helping Vero to sort this out. Just to let you know that indeed it was an issue with the file not being executable by default.

Torbjorn's suggestion ('chmod o+x vsearch-1.1.3-osx-x86_64') worked fine, but only with sudo, so we also used 'chmod u+x vsearch-1.1.3-osx-x86_64'. Hope this helps others. 

Thank you,

Alicia

[Elianne Sirnæs Egge]

Hi,
I am sorry to be bothering you with a really basic question, but if you have the time I would greatly appreciate your help. I followed your tips on how to install vsearch (Thanks!), but I actually get lost at the "Make a link to the binary executable vsearch file from inside of a directory that is in your bash PATH variable" step. After googling I tried the following
PATH=~/IlluminaMP/vsearch-1.9.0-linux-x86_64/bin/vsearch:$PATH (I should say that I have very little understanding of what I am doing here)
(I also did chmod u+x vsearch)

but when I try to run the executable vsearch when I am in the ~/IlluminaMP/ -directory, it does not work (./vsearch: No such file or directory).

So I am assuming that I failed to make the link to the binary executable vsearch.

Any advice on how to do this would be much appreciated.

Best regards,
Elianne Egge

[Frédéric Mahé]

Hi Elianne,

once the folder containing the vsearch binary is in your path, you don't need to indicate the current folder anymore (replace ./vsearch with vsearch).

If you cannot put the folder containing the vsearch binary in your path, simply add a variable in your scripts:

VSEARCH=~/IlluminaMP/vsearch-1.9.0-linux-x86_64/bin/vsearch

"${VSEARCH}" --threads 8 (+ more options)

Best,

PS: your should add a folder to your path, not a binary

PATH=~/IlluminaMP/vsearch-1.9.0-linux-x86_64/bin/:$PATH

instead of

PATH=~/IlluminaMP/vsearch-1.9.0-linux-x86_64/bin/vsearch:$PATH