USEARCH not found

[carlo pacioni]

Hi all,
I recently downloaded the virtual box (version 1.5) and installed on
W7 pro. I received an error message when running the script
pick_otus.py –m usearch, saying that usearch was not found.

Following instructions found in other posts, I verified that usearch
was not installed (using print_qiime_config.py), downloaded the 5.2.32
version for linux into the directory home/qiime_software/usearch,
changed its name to ‘usearch’ made it executable with chmod 755
usearch from the directory where the file is, added the path with
export PATH=$PATH:/home/qiime_software/usearch but I still get
‘command not found’ when I type usearch --version. This is the print
out I get with
qiime@qiime-VirtualBox:~/qiime_software/usearch$ ls -l
total 1516
-rwxr-xr-x 1 qiime qiime 1551097 May 22 01:59 usearch
And I get the correct version when, from the directory where usearch
is, I type
./usearch --version

PATH seems to be correctly set:
qiime@qiime-VirtualBox:~$ echo $PATH

/home/qiime/qiime_software/qiime-1.5.0-release/bin:/home/qiime/
qiime_software/pprospector-1.0.1-release/bin:/home/qiime/
qiime_software/pynast-1.1-release/bin:/home/qiime/qiime_software/biom-
format-0.9.3-release/scripts/:/home/qiime/qiime_software/r-2.12.0-
release/bin:/home/qiime/qiime_software/pyzmq-2.1.9-release/bin:/home/
qiime/qiime_software/ipython-0.12-release/bin:/home/qiime/
qiime_software/tornado-2.2.1-release/bin:/home/qiime/qiime_software/
python-2.7.1-release/bin:/home/qiime/qiime_software/vienna-1.8.4-
release/.:/home/qiime/qiime_software/infernal-1.0.2-release/bin:/home/
qiime/qiime_software/cdhit-3.1-release/.:/home/qiime/qiime_software/
uclust-1.2.22-release/.:/home/qiime/qiime_software/cytoscape-2.7.0-
release/.:/home/qiime/qiime_software/rdpclassifier-2.2-release/.:/home/
qiime/qiime_software/muscle-3.8.31-release/.:/home/qiime/
qiime_software/parsinsert-1.0.4-release/.:/home/qiime/qiime_software/
blast-2.2.22-release/bin:/home/qiime/qiime_software/pplacer-1.1-
release/.:/home/qiime/qiime_software/fasttree-2.1.3-release/.:/home/
qiime/qiime_software/chimeraslayer-4.29.2010-release/ChimeraSlayer:/
home/qiime/qiime_software/chimeraslayer-4.29.2010-release/NAST-iEr:/
home/qiime/qiime_software/mothur-1.25.0-release/.:/home/qiime/
qiime_software/cdbtools-10.11.2010-release/.:/home/qiime/
qiime_software/ampliconnoise-1.25-release/Scripts:/home/qiime/
qiime_software/ampliconnoise-1.25-release/bin:/home/qiime/
qiime_software/raxml-7.3.0-release/.:/home/qiime/qiime_software/
drisee-1.2-release/.:/home/qiime/qiime_software/clearcut-1.0.9-
release/.:/home/qiime/qiime_software/rtax-0.981-release/.:/usr/lib/
lightdm/lightdm:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/
sbin:/bin:/usr/games:/home/qiime_software/usearch
However, the path :/home/qiime_software/usearch is not there anymore
when I reboot the virtual machine.

I think I’m setting the path incorrectly, and I know this is probably
something elementary, but I couldn’t figure out how to fix this
problem…

Any suggestions???

Thank you in advance,
Carlo

[Jose Navas]

Hi Carlo,

You should edit the file $HOME/.bashrc and add the export command at the end:

export PATH=$PATH:/home/qiime_software/usearch

This automatically add the usearvh directory to the path every time you open a terminal.

Let me know if it works!!

Cheers,

Jose

2012/5/27 carlo pacioni <carlo....@gmail.com>

[carlo pacioni]

Thanks Jose,
it seems fine now.
For some reasons it didn't work when I typed

qiime@qiime-VirtualBox:~$ echo "export PATH=/home/qiime_software/
usearch/:$PATH" >> /home/.bashrc
bash: /home/.bashrc: Permission denied

But it seems to have worked with

qiime@qiime-VirtualBox:~$ echo "export PATH=./qiime_software/usearch/:
$PATH" >> ./.bashrc
qiime@qiime-VirtualBox:~$ source ./.bashrc
qiime@qiime-VirtualBox:~$ export PATH=$PATH:/home/qiime_software/
usearch
qiime@qiime-VirtualBox:~$ usearch --version
usearch v5.2.32

I will now try to run pick_otus.py -m usearch

Thnak you very much!

carlo

On May 28, 11:52 am, Jose Navas <josenavasmol...@gmail.com> wrote:
> Hi Carlo,
>
> You should edit the file $HOME/.bashrc and add the export command at the
> end:
>
> export PATH=$PATH:/home/qiime_software/usearch
>
> This automatically add the usearvh directory to the path every time you
> open a terminal.
>
> Let me know if it works!!
>
> Cheers,
> Jose
>

> 2012/5/27 carlo pacioni <carlo.paci...@gmail.com>

[Antonio González Peña]

Hi Carlo,

Notice that the user's home ($HOME) in the virtual machine is
/home/qiime and you are trying to modify files in /home.

Cheers.

--
Antonio González Peña
Research Assistant, Knight Lab
University of Colorado at Boulder
https://chem.colorado.edu/knightgroup/

[carlo pacioni]

Thank you very much Antonio for pointing that out.
still getting my head around the unix environment.... In fact, I had
trouble to run the pick_otus.py script, but then repeated the sequence
of commands with /home/qiime and everything is working.

cheers,
carlo

> >> > wasnotinstalled (using print_qiime_config.py), downloaded the 5.2.32

> >> > version for linux into the directory home/qiime_software/usearch,
> >> > changed its name to ‘usearch’ made it executable with chmod 755

> >> >usearchfrom the directory where the file is, added the path with

> >> > export PATH=$PATH:/home/qiime_software/usearchbut I still get

> >> > ‘commandnotfound’ when I typeusearch--version. This is the print

> >> > However, the path :/home/qiime_software/usearchisnotthere anymore