Another error in mini test

[jcthrash]

Hello, I've successfully installed anvio (no errors during installation), but running the mini test causes the following problem- it can't be run without sudo, even in my Downloads directory (which is weird), and then when I use sudo, it errors with command not found:

$ ./run_mini_test.sh

#
#
# Creating the output directory ...
#
#

mkdir: test-output: Permission denied
thrashc-1:tests JCThrash$ sudo ./run_mini_test.sh

#
#
# Creating the output directory ...
#
#

#
#
# Anvo'o version ...
#
#

./run_mini_test.sh: line 12: anvi-profile: command not found

Thanks in advance!

[meren]

Good to hear that it is installed!

You should never need to use sudo to run mini_test. Very interesting. Can you please tell me what is the output of this command:

anvi-refine -v

[jcthrash]

$ anvi-refine -v -bash: anvi-refine: command not found

[meren]

Can you please run this command and provide the output:

pip show -f anvio > /tmp/_output && head -n 100 /tmp/_output && rm /tmp/_output

[jcthrash]

thrashc-1:~ JCThrash$ pip show -f anvio > /tmp/_output && head -n 100 /tmp/_output && rm /tmp/_output
---
Metadata-Version: 1.1
Name: anvio
Version: 1.2.0
Summary: An interactive analysis and visualization platform for 'omics data. See https://merenlab.org/projects/anvio for more information
Home-page: https://meren.github.io/projects/anvio/
Author: anvi'o Authors
Author-email: a.murat.eren@gmail.com
License: GPLv3+
Location: /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages
Requires: bottle, pysam, hcluster, ete2, scipy, scikit-learn, django, cython, h5py
Files:
  ../../../bin/00_README.txt
  ../../../bin/anvi-cluster-with-concoct
  ../../../bin/anvi-compute-completeness
  ../../../bin/anvi-experimental-organization
  ../../../bin/anvi-export-genes-table
  ../../../bin/anvi-export-splits-and-coverages
  ../../../bin/anvi-gen-contigs-database
  ../../../bin/anvi-gen-network
  ../../../bin/anvi-gen-samples-info-database
  ../../../bin/anvi-gen-variability-matrix
  ../../../bin/anvi-gen-variability-profile
  ../../../bin/anvi-get-db-table-as-matrix
  ../../../bin/anvi-get-sequences-for-hmm-hits
  ../../../bin/anvi-get-short-reads-from-bam
  ../../../bin/anvi-import-collection
  ../../../bin/anvi-init-bam
  ../../../bin/anvi-interactive
  ../../../bin/anvi-matrix-to-newick
  ../../../bin/anvi-merge
  ../../../bin/anvi-populate-genes-table
  ../../../bin/anvi-populate-search-table
  ../../../bin/anvi-profile
  ../../../bin/anvi-refine
  ../../../bin/anvi-report-linkmers
  ../../../bin/anvi-script-convert-annotation-db-to-contigs-db
  ../../../bin/anvi-script-gen_stats_for_single_copy_genes.R
  ../../../bin/anvi-script-gen_stats_for_single_copy_genes.README
  ../../../bin/anvi-script-gen_stats_for_single_copy_genes.py
  ../../../bin/anvi-script-gen_stats_for_single_copy_genes.sh
  ../../../bin/anvi-script-generate-auxiliary-data-from-summary-cp
  ../../../bin/anvi-script-get-collections-as-tab-delimited-matrix.py
  ../../../bin/anvi-script-get-prot-sequences.py
  ../../../bin/anvi-script-remove-short-contigs-from-fasta
  ../../../bin/anvi-script-upgrade-contigs-db-v2-to-v3
  ../../../bin/anvi-script-upgrade-profile-db-v4-to-v5
  ../../../bin/anvi-script-upgrade-profile-db-v5-to-v6
  ../../../bin/anvi-summarize
  anvio-1.2.0-py2.7.egg-info
  anvio-1.2.0-py2.7.egg-info/PKG-INFO
  anvio-1.2.0-py2.7.egg-info/SOURCES.txt
  anvio-1.2.0-py2.7.egg-info/dependency_links.txt
  anvio-1.2.0-py2.7.egg-info/requires.txt
  anvio-1.2.0-py2.7.egg-info/top_level.txt
  anvio/__init__.py
  anvio/__init__.pyc
  anvio/auxiliarydataops.py
  anvio/auxiliarydataops.pyc
  anvio/bamops.py
  anvio/bamops.pyc
  anvio/ccollections.py
  anvio/ccollections.pyc
  anvio/clustering.py
  anvio/clustering.pyc
  anvio/clusteringconfuguration.py
  anvio/clusteringconfuguration.pyc
  anvio/columnprofile.so
  anvio/completeness.py
  anvio/completeness.pyc
  anvio/concoct.py
  anvio/concoct.pyc
  anvio/constants.py
  anvio/constants.pyc
  anvio/contigops.py
  anvio/contigops.pyc
  anvio/data/__init__.py
  anvio/data/__init__.pyc
  anvio/data/clusterconfigs/README.md
  anvio/data/clusterconfigs/merged/cov
  anvio/data/clusterconfigs/merged/tnf
  anvio/data/clusterconfigs/merged/tnf-cov
  anvio/data/clusterconfigs/single/tnf
  anvio/data/clusterconfigs/single/tnf-ab-cov
  anvio/data/hmm/Alneberg_et_al/genes.hmm.gz
  anvio/data/hmm/Alneberg_et_al/genes.txt
  anvio/data/hmm/Alneberg_et_al/kind.txt
  anvio/data/hmm/Alneberg_et_al/notes.txt
  anvio/data/hmm/Alneberg_et_al/reference.txt
  anvio/data/hmm/Campbell_et_al/genes.hmm.gz
  anvio/data/hmm/Campbell_et_al/genes.txt
  anvio/data/hmm/Campbell_et_al/kind.txt
  anvio/data/hmm/Campbell_et_al/reference.txt
  anvio/data/hmm/Creevey_et_al/genes.hmm.gz
  anvio/data/hmm/Creevey_et_al/genes.txt
  anvio/data/hmm/Creevey_et_al/kind.txt
  anvio/data/hmm/Creevey_et_al/reference.txt
  anvio/data/hmm/Dupont_et_al/genes.hmm.gz
  anvio/data/hmm/Dupont_et_al/genes.txt
  anvio/data/hmm/Dupont_et_al/kind.txt

[meren]

All seems correct, but the Python binaries are not in your PATH environment variable.

Do you remember whether you run this after installing Python with macports?

sudo port select --set python python27

[jcthrash]

Hrm. Weird.

Yes, I did run that command:

thrashc-1:~ JCThrash$ sudo port select --set python python27 Password: Selecting 'python27' for 'python' succeeded. 'python27' is now active. thrashc-1:~ JCThrash$ which python /opt/local/bin/python

[meren]

Can you open a new terminal and see whether anvi-profile -v works there or not?

If it doesn't, can you please share this output:

echo $PATH

[jcthrash]

Doesn’t seem to. Here’s all the output:

thrashc-1:~ JCThrash$ anvi-profile -v -bash: anvi-profile: command not found thrashc-1:~ JCThrash$ echo $PATH /opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/Users/JCThrash/anaconda/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin

[meren]

Well. One quick solution is to add this line into your ~/.bash_profile or ~/.bashrc file:

export PATH=$PATH:/opt/local/Library/Frameworks/Python.framework/Versions/2.7/bin

On the other hand I've been researching about why your PATH variable is not properly set. I haven't seen this before.

Can you please share the output of this:

port notes python27

[jcthrash]

Ok, understood. Here is the output. Should I change the path now?

$ port notes python27 python27 has the following notes: To make this the default Python or Python 2 (i.e., the version run by the 'python' or 'python2' commands), run one or both of:

  sudo port select --set python python27
  sudo port select --set python2 python27

[jcthrash]

Ok, I changed the path and it seems to work fine, except for two things:

1. I still have to use sudo
2. Even though Chrome is my default browser, it tried to use Safari

[meren]

OK. You are using sudo, because the tests directory that installed on your computer is trying to write to a protected area. And probably when you use sudo, it doesn't use your user's' preferences (such as the default browser).

Instead, can you try this please:

cd /tmp
git clone -b v1.2.0  --depth=1 https://github.com/meren/anvio.git
cd anvio/tests
./run_mini_test

[jcthrash]

Ok, this worked all the way to the end, and opened the Chrome browser, which had the editing functions, but no image.

[meren]

Did you click "Draw"? :)

[jcthrash]

No. Ha! Sorry. I've been so concerned with getting everything running I've not read how to use the interface yet! Thanks!

[meren]

I've not read how to use the interface yet!

Although it would have been great, unfortunately there is no tutorial to introduce people to the interface. I hope you will be able to find your way intuitively, and we will manage to generate such documentation at some point :)

Thanks for your patience.

Best wishes,

[jcthrash]

Thanks for all your help!

-jct

On Oct 9, 2015, at 16:39, A. Murat Eren notifications@github.com wrote:

I've not read how to use the interface yet!

Although it would have been great, unfortunately there is no tutorial to introduce people to the interface. I hope you will be able to find your way intuitively, and we will manage to generate such documentation at some point :)

Thanks for your patience.

Best wishes,

— Reply to this email directly or view it on GitHub.