Problem with print_qiime_config.py

[MikeGJohnson]

Hey Andy!

This is probably just because I don't understand enough to know where I'm screwing up, but...

I am trying to run your tutorial so that I can be prepared for data (hopefully getting it on Monday). I can't get past the installation though. Everything seems to work fine, and I get to the part that says "Installations Complete (hopefully)" but the test that it says to do just gets me "command not found". When I scroll up it looks like there were some errors installing vsearch and bamtools: Installing vsearch.

cp: cannot stat '/home/mike//vsearch/bin/vsearch': No such file or directory Installing bamtools.

cp: cannot stat '/home/mike//bamtools/bin/bamtools': No such file or directory

and then a bit latter here:

Executing QIIME deploy script.

chown: cannot access '/home/mike//qiime_1.9.1/': No such file or directory analyze_primers.py not where expected. Python library not corrected.

/bin/bash: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 430: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 431: print_qiime_config.py: command not found

Any ideas?

Thanks! Mike

[alk224]

Hi Mike,

Sounds like you still need to source your .bashrc file because the commands are not yet in your system path.

Type this and try again:

source ~/.bashrc

Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen

On Fri, May 6, 2016 at 12:08 PM, MikeGJohnson notifications@github.com wrote:

Hey Andy!

This is probably just because I don't understand enough to know where I'm screwing up, but...

I am trying to run your tutorial so that I can be prepared for data (hopefully getting it on Monday). I can't get past the installation though. Everything seems to work fine, and I get to the part that says "Installations Complete (hopefully)" but the test that it says to do just gets me "command not found". When I scroll up it looks like there were some errors installing vsearch and bamtools: Installing vsearch.

cp: cannot stat '/home/mike//vsearch/bin/vsearch': No such file or directory Installing bamtools.

cp: cannot stat '/home/mike//bamtools/bin/bamtools': No such file or directory

and then a bit latter here:

Executing QIIME deploy script.

chown: cannot access '/home/mike//qiime_1.9.1/': No such file or directory analyze_primers.py not where expected. Python library not corrected.

/bin/bash: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 430: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 431: print_qiime_config.py: command not found

Any ideas?

Thanks! Mike

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[MikeGJohnson]

That didn't seem to work, for some reason it wasn't installing bamtools, vsearch, or qiime. I mannually installed them and I think it is working ow.

Thanks! Mike

On Fri, May 6, 2016 at 12:22 PM, alk224 notifications@github.com wrote:

Hi Mike,

Sounds like you still need to source your .bashrc file because the commands are not yet in your system path.

Type this and try again:

source ~/.bashrc

Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen

On Fri, May 6, 2016 at 12:08 PM, MikeGJohnson notifications@github.com wrote:

Hey Andy!

This is probably just because I don't understand enough to know where I'm screwing up, but...

I am trying to run your tutorial so that I can be prepared for data (hopefully getting it on Monday). I can't get past the installation though. Everything seems to work fine, and I get to the part that says "Installations Complete (hopefully)" but the test that it says to do just gets me "command not found". When I scroll up it looks like there were some errors installing vsearch and bamtools: Installing vsearch.

cp: cannot stat '/home/mike//vsearch/bin/vsearch': No such file or directory Installing bamtools.

cp: cannot stat '/home/mike//bamtools/bin/bamtools': No such file or directory

and then a bit latter here:

Executing QIIME deploy script.

chown: cannot access '/home/mike//qiime_1.9.1/': No such file or directory analyze_primers.py not where expected. Python library not corrected.

/bin/bash: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 430: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 431: print_qiime_config.py: command not found

Any ideas?

Thanks! Mike

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217535739

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

[alk224]

Sometimes the path variable isn't successfully changed during the install process. Logging out and logging in and rerunning the installer up to 3 times can solve issues like this. Since the install functions are all behind conditional statements, it shouldn't rerun any commands except qiime-deploy, so the really painful steps like the R updates won't happen over again.

Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen

On Fri, May 6, 2016 at 1:03 PM, MikeGJohnson notifications@github.com wrote:

That didn't seem to work, for some reason it wasn't installing bamtools, vsearch, or qiime. I mannually installed them and I think it is working ow.

Thanks! Mike

On Fri, May 6, 2016 at 12:22 PM, alk224 notifications@github.com wrote:

Hi Mike,

Sounds like you still need to source your .bashrc file because the commands are not yet in your system path.

Type this and try again:

source ~/.bashrc

Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen

On Fri, May 6, 2016 at 12:08 PM, MikeGJohnson notifications@github.com wrote:

Hey Andy!

This is probably just because I don't understand enough to know where I'm screwing up, but...

I am trying to run your tutorial so that I can be prepared for data (hopefully getting it on Monday). I can't get past the installation though. Everything seems to work fine, and I get to the part that says "Installations Complete (hopefully)" but the test that it says to do just gets me "command not found". When I scroll up it looks like there were some errors installing vsearch and bamtools: Installing vsearch.

cp: cannot stat '/home/mike//vsearch/bin/vsearch': No such file or directory Installing bamtools.

cp: cannot stat '/home/mike//bamtools/bin/bamtools': No such file or directory

and then a bit latter here:

Executing QIIME deploy script.

chown: cannot access '/home/mike//qiime_1.9.1/': No such file or directory analyze_primers.py not where expected. Python library not corrected.

/bin/bash: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 430: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 431: print_qiime_config.py: command not found

Any ideas?

Thanks! Mike

— You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub < https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217535739

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217544740

[alk224]

You probably need to rerun the installer anyway because the analyze_primers issue is important for the format_database step (if following the full tutorial). Again, just log out and log back in and rerun the installer a couple of times.

[MikeGJohnson]

Yeah, it looks like I am missing some things. Do you mean to rerun every step of the installation or just the last one?

Mike

On Fri, May 6, 2016 at 3:00 PM, alk224 notifications@github.com wrote:

You probably need to rerun the installer anyway because the analyze_primers issue is important for the format_database step (if following the full tutorial). Again, just log out and log back in and rerun the installer a couple of times.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217570759

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

[alk224]

Just issue the same command you did the first time:

sudo bash akutils_ubuntu_installer/akutils_ubuntu_installation.sh install

It should skip over most parts (the ones already completed).

[MikeGJohnson]

Gotcha...I am working from a full ubuntu download, not a VM...what do I log in and out of? The whole Ubuntu OS?

On Fri, May 6, 2016 at 3:42 PM, alk224 notifications@github.com wrote:

Just issue the same command you did the first time:

sudo bash akutils_ubuntu_installer/akutils_ubuntu_installation.sh install

It should skip over most parts (the ones already completed).

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217580944

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

[alk224]

Any time you start a fresh terminal instance, it should source your .bashrc file. Type "exit" to close the terminal, and then open a new one (ctrl-alt-t).

[alk224]

It is possible that some programs won't fully work until your log in and out of your user account or reboot, but simply closing the terminal and opening a new one should suffice.

[MikeGJohnson]

Great thanks! Give Bo and Derek high-fives for me if you see them tonight!

Mike

On Fri, May 6, 2016 at 3:46 PM, alk224 notifications@github.com wrote:

Any time you start a fresh terminal instance, it should source your .bashrc file. Type "exit" to close the terminal, and then open a new one (ctrl-alt-t).

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217581499

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

[alk224]

Will do. Saw Dereks defense this morning, but missed Bo's. Will meet him at the watering hole instead.

[MikeGJohnson]

Nice! Wish we could be there!

On Fri, May 6, 2016 at 4:00 PM, alk224 notifications@github.com wrote:

Will do. Saw Dereks defense this morning, but missed Bo's. Will meet him at the watering hole instead.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217583414

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

[MikeGJohnson]

Well, I've re-installed a number of times and still hitting a dead end here:

analyze_primers.py not where expected. Python library not corrected.

/bin/bash: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 430: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 431: print_qiime_config.py: command not found

It was giving this error riight before those: chown: cannot access '/home/mike//qiime_1.9.1/': No such file or directory ...but I added a directory with that name and the error went away..still getting the rest though.

Any ideas? No rush :-) Mike

On Fri, May 6, 2016 at 4:03 PM, Michael G Johnson <mike.johnson@berkeley.edu

wrote:

Nice! Wish we could be there!

On Fri, May 6, 2016 at 4:00 PM, alk224 notifications@github.com wrote:

Will do. Saw Dereks defense this morning, but missed Bo's. Will meet him at the watering hole instead.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217583414

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

[alk224]

Try a reboot and rerun the installer and let me know if its any different.

Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen

On Fri, May 6, 2016 at 4:32 PM, MikeGJohnson notifications@github.com wrote:

Well, I've re-installed a number of times and still hitting a dead end here:

analyze_primers.py not where expected. Python library not corrected.

/bin/bash: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 430: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 431: print_qiime_config.py: command not found

It was giving this error riight before those: chown: cannot access '/home/mike//qiime_1.9.1/': No such file or directory ...but I added a directory with that name and the error went away..still getting the rest though.

Any ideas? No rush :-) Mike

On Fri, May 6, 2016 at 4:03 PM, Michael G Johnson < mike.johnson@berkeley.edu

wrote:

Nice! Wish we could be there!

On Fri, May 6, 2016 at 4:00 PM, alk224 notifications@github.com wrote:

Will do. Saw Dereks defense this morning, but missed Bo's. Will meet him at the watering hole instead.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub < https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217583414

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

— You are receiving this because you commented. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217587328

[MikeGJohnson]

Same problem, it happens right after "Executing QIIME deploy script."

On Fri, May 6, 2016 at 4:36 PM, alk224 notifications@github.com wrote:

Try a reboot and rerun the installer and let me know if its any different.

Andrew Krohn PhD Candidate, NAU Biological Sciences Research Technician, EnGGen

On Fri, May 6, 2016 at 4:32 PM, MikeGJohnson notifications@github.com wrote:

Well, I've re-installed a number of times and still hitting a dead end here:

analyze_primers.py not where expected. Python library not corrected.

/bin/bash: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 430: /home/mike//qiime_1.9.1/activate.sh: No such file or directory /home/mike/akutils_ubuntu_installer/akutils_ubuntu_installation.sh: line 431: print_qiime_config.py: command not found

It was giving this error riight before those: chown: cannot access '/home/mike//qiime_1.9.1/': No such file or directory ...but I added a directory with that name and the error went away..still getting the rest though.

Any ideas? No rush :-) Mike

On Fri, May 6, 2016 at 4:03 PM, Michael G Johnson < mike.johnson@berkeley.edu

wrote:

Nice! Wish we could be there!

On Fri, May 6, 2016 at 4:00 PM, alk224 notifications@github.com wrote:

Will do. Saw Dereks defense this morning, but missed Bo's. Will meet him at the watering hole instead.

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub <

https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217583414

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

— You are receiving this because you commented. Reply to this email directly or view it on GitHub < https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217587328

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217587740

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

[alk224]

OK, let's manually see if analyze_primers.py has been corrected. Issue the following command from your home directory:

md5sum akutils-v1.2/akutils_resources/analyze_primers.py

It should return this output:

f3c15b502fccb5d7eb8cf22e32d15090 akutils-v1.2/akutils_resources/analyze_primers.py

Then check where the file needs to go:

md5sum qiime_1.9.1/pprospector-1.0.1-release/lib/python2.7/site-packages/primerprospector/analyze_primers.py

If you get the same result, all is OK (the print_qiime_config at the end will always have a couple of errors). If not, you can manually correct the analyze_primers.py problem with:

sudo cp akutils-v1.2/akutils_resources/analyze_primers.py qiime_1.9.1/pprospector-1.0.1-release/lib/python2.7/site-packages/primerprospector/analyze_primers.py

[alk224]

Also, how did you install qiime manually? Did you use pip? If you used apt-get it will screw things up (files won't be where the installer expects). If you used apt-get, issue the following to remove the apt-get-based installs:

sudo apt-get --purge remove

where is qiime, bamtools or vsearch etc

[alk224]

Just a thought, because the packages you initially mentioned are all github repositories, you do have git installed, yes?

And you are using ubuntu 14.04.1, yes?

[MikeGJohnson]

1) When I try manually correcting the problem it results in: cp: cannot create regular file 'qiime_1.9.1/pprospector-1.0.1-release/lib/python2.7/site-packages/primerprospector/analyze_primers.py': No such file or directory

2) I did use apt-get, so I ran the purge and reran the installer. Go the same error as above again.

3) I am using ubuntu 16.04 ...is that the problem?

Mike

On Fri, May 6, 2016 at 5:02 PM, alk224 notifications@github.com wrote:

Just a thought, because the packages you initially mentioned are all github repositories, you do have git installed, yes?

And you are using ubuntu 14.04.1, yes?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/alk224/akutils_ubuntu_installer/issues/1#issuecomment-217590396

Mike Johnson, MSF PhD Student, Garbelotto Lab University of California at Berkeley Depart of Environmental Science, Policy, and Management

[alk224]

I tested it on 16.04 when the beta was made available a month or so ago, but it didn't work at all. I think some of the dependencies have changed names in the repositories and I haven't had time to make the necessary updates.

Use the 14.04.1 .iso here, reinstall your OS, and try again with the installer.

Follow the instructions here to get everything in place.

[alk224]

closing