Problem installing biobakery tool suite on Mac

[ETaSky]

Hello, I got following output while installing biobakery tool: ==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/strainphlan/2.6.0/libexec/vendor --single-version-exte Last 15 lines from /Users/wangj50/Library/Logs/Homebrew/strainphlan/09.python2: 2017-06-13 10:07:06 -0400

python2 -c import setuptools, tokenize file = 'setup.py' exec(compile(getattr(tokenize, 'open', open)(file).read() .replace('\r\n', '\n'), file, 'exec')) --no-user-cfg install --prefix=/usr/local/Cellar/strainphlan/2.6.0/libexec/vendor --single-version-externally-managed --record=installed.txt

I don't know if this is an error or not, but it seems the tools were not successfully installed. I followed all instructions and tried on both installing the whole suite, or individual tool (e.g. lefse). Please help and thank you very much!

Jincheng

[ljmciver]

Hi Jincheng - That does not look like an error message. Maybe there is one in the log file? Can you let me know the command you ran and possibly provide the full output running with --verbose? Also let me know which tools you tried to install and those that do/don't work. Then I can help debug.

Thanks! Lauren

[ETaSky]

@ljmciver Hi Lauren, thank you for your reply. I am just trying to install lefse. I have installed homebrew, and then brew tap biobakery/biobakery, and then brew install lefse. Then the output is:

wangj50@DOMINM05-I27-01:~$ brew install lefse ==> Installing lefse from biobakery/biobakery ==> Downloading https://bitbucket.org/nsegata/lefse/get/e3cabe93a0d1.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse-1.0.0-dev-e3cabe9.tar.gz ==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse--numpy-1.11.0.tar.gz ==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec --single-version-externally-managed --record=installed.txt Last 15 lines from /Users/wangj50/Library/Logs/Homebrew/lefse/01.python2: 2017-06-14 10:56:57 -0400

python2 -c import setuptools, tokenize file = 'setup.py' exec(compile(getattr(tokenize, 'open', open)(file).read() .replace('\r\n', '\n'), file, 'exec')) --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec --single-version-externally-managed --record=installed.txt

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core): https://github.com/biobakery/homebrew-biobakery/issues

Given this output, I don't think it has been installed. I was wondering if this helps. Thanks! Jincheng

[ljmciver]

Thank you for the additional information. Can you run again with the "--verbose" flag? $ brew install leftse --verbose This output will help identify the error. Also can you check you have python2 installed? $ python2 --version

Thank you, Lauren

[ETaSky]

@ljmciver Thanks! I am using Mac which has python 2.7.10 pre-installed. And since you were specifically asking about python2, I guess if that is the problem. Because python2 is not a command on my machine. Should I create an alias to python or anything else should I do?

The --verbose output: ==> Installing lefse from biobakery/biobakery ==> Downloading https://bitbucket.org/nsegata/lefse/get/e3cabe93a0d1.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse-1.0.0-dev-e3cabe9.tar.gz ==> Verifying lefse-1.0.0-dev-e3cabe9.tar.gz checksum tar xzf /Users/wangj50/Library/Caches/Homebrew/lefse-1.0.0-dev-e3cabe9.tar.gz ==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse--numpy-1.11.0.tar.gz ==> Verifying lefse--numpy-1.11.0.tar.gz checksum tar xzf /Users/wangj50/Library/Caches/Homebrew/lefse--numpy-1.11.0.tar.gz ==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec --single-version-externally-managed --record=installed.txt Failed to execute: python2

==> Formula Tap: biobakery/biobakery Path: /usr/local/Homebrew/Library/Taps/biobakery/homebrew-biobakery/lefse.rb ==> Configuration HOMEBREW_VERSION: 1.2.3 ORIGIN: https://github.com/Homebrew/brew HEAD: ed9942fbd1ec4243f0a92ab8f9b2411c8b1fb091 Last commit: 2 days ago Core tap ORIGIN: https://github.com/Homebrew/homebrew-core Core tap HEAD: 4d4594cd517f56cfa30bc04aec1a2188223c0771 Core tap last commit: 64 minutes ago HOMEBREW_PREFIX: /usr/local HOMEBREW_REPOSITORY: /usr/local/Homebrew HOMEBREW_CELLAR: /usr/local/Cellar HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com CPU: quad-core 64-bit skylake Homebrew Ruby: 2.0.0-p648 Clang: 8.1 build 802 Git: 2.11.0 => /Library/Developer/CommandLineTools/usr/bin/git Perl: /usr/bin/perl Python: /usr/bin/python Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby Java: N/A macOS: 10.12.5-x86_64 Xcode: N/A CLT: 8.3.2.0.1.1492020469 X11: N/A ==> ENV HOMEBREW_CC: clang HOMEBREW_CXX: clang++ MAKEFLAGS: -j4 CMAKE_PREFIX_PATH: /usr/local/opt/readline:/usr/local CMAKE_INCLUDE_PATH: /usr/include/libxml2:/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers CMAKE_LIBRARY_PATH: /System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries PKG_CONFIG_PATH: /usr/local/opt/libpng/lib/pkgconfig:/usr/local/opt/freetype/lib/pkgconfig PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Homebrew/Library/Homebrew/os/mac/pkgconfig/10.12 ACLOCAL_PATH: /usr/local/share/aclocal PATH: /usr/local/Homebrew/Library/Homebrew/shims/super:/usr/local/opt/libpng/bin:/usr/local/opt/freetype/bin:/usr/bin:/bin:/usr/sbin:/sbin

Error: biobakery/biobakery/lefse 1.0.0-dev-e3cabe9 did not build Logs: /Users/wangj50/Library/Logs/Homebrew/lefse/00.options.out /Users/wangj50/Library/Logs/Homebrew/lefse/01.python2 If reporting this issue please do so at (not Homebrew/brew or Homebrew/core): https://github.com/biobakery/homebrew-biobakery/issues

[ljmciver]

Thank you for running with verbose and checking on python2. If you install python with homebrew, you should have python2 ("brew install python"). Alternatively you could create an alias as you suggested if your current install is python2 (from python to python2). Both options should resolve the error you are seeing when installing lefse.

Thank you, Lauren

[ETaSky]

@ljmciver Hello, thanks! I tried both methods (alias) and "brew install python". But still, the same error occurred. python2 apparently installed because python2 now open python 2.7.13, and my original python is 2.7.10. Is it possible that homebrew installed python doesn't have setuptools installed? If so, I was wondering how I should install python package for homebrew python. Thanks!

[ljmciver]

Hi Jincheng - I believe brew python should also install pip and setuptools. If you think setuptools is not installed, you could install it with pip. Are you still seeing the error "Failed to execute: python2" or do you see a different error? If it is a different error, can you provide the new error?

Thanks! Lauren

[ETaSky]

@ljmciver Hi Lauren, I am seeing the exact error as mentioned in previous posts. "Failed to execute: python 2". Thanks! Jincheng

[ljmciver]

Hi Jincheng, Do you see an error when running "python2 --version" from the command line?

Thanks! Lauren

[ETaSky]

@ljmciver No error. It works. python2 is correctly installed. Thanks! Jincheng

[ljmciver]

Hi Jincheng, I updated the lefse formula to use "python" if it can't find the "python2" install. If you update your brew formulas (with "brew update") you should have the latest lefse. I believe this modification should resolve the error you are seeing with Homebrew unable to see the python2 install.

Thanks! Lauren

[ETaSky]

@ljmciver Hi Lauren, Thanks! After this update, I got some progress but the installation is still failing. Now I got following error:

==> Installing lefse from biobakery/biobakery ==> Downloading https://bitbucket.org/nsegata/lefse/get/e3cabe93a0d1.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse-1.0.0-dev-e3cabe9.tar.gz ==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse--numpy-1.11.0.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.5.1.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse--matplotlib-1.5.1.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec --single-version-externally-managed --record=installed.txt Last 15 lines from /Users/wangj50/Library/Logs/Homebrew/lefse/02.python: cairo: no [cairocffi or pycairo not found] windowing: no [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES dvipng: no ghostscript: no latex: no pdftops: no

OPTIONAL PACKAGE DATA dlls: no [skipping due to configuration]

============================================================================

• The following required packages can not be built:
• freetype

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core): https://github.com/biobakery/homebrew-biobakery/issues

It seems it is because of freetype. But when I tried to do "brew install freetype", it said freetype 2.8 has already been installed. I don't know what I can do now.

Jincheng

[ETaSky]

To followup, I think my system has messed up. I installed miniconda to install QIIME 2. And now python points to the python in miniconda folder. I was wondering if this might be the reason. Thanks!

Jincheng

[ljmciver]

Hi Jincheng, Yes, I think that might be it! I have found that conda and homebrew do not seem to be compatible. If you can change your paths so that the miniconda paths are not included, then install the lefse formula with homebrew, I think it should resolve your errors.

Thanks! Lauren

[ETaSky]

@ljmciver Hi Lauren, Thanks! I have changed the path but still not working. Right now, I am 80% sure what the problem is. It is most likely because the failsure of installing R dependencies in Mac. For example, I am trying to manually install rpy2, but I cannot build it or pip install it because it seems teh OSX build system "clang" doesn't support openmp right now. I am still trying to figure out a way to get it done. Do you have any suggestions? Perhaps you could share how you configure your system at the beginning if you are using a Mac. Thanks!

Jincheng

[ljmciver]

Hi Jincheng, I am sorry I use Linux so I can't help much with Mac configuration. Do you have other compilers installed? If not, I think you can install them by installing the command line tools for Xcode. Then you should have all of the basic compilers if you need them from openmp. Which tools do you need to install? Are you just trying to install lefse? If so, what errors do you get when you run the brew lefse install now?

Thanks, Lauren

[ETaSky]

Hi Lauren, Thanks! I already installed Xcode. Right now, brew install lefse still produce following error: ==> Installing lefse from biobakery/biobakery ==> Downloading https://bitbucket.org/nsegata/lefse/get/e3cabe93a0d1.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse-1.0.0-dev-e3cabe9.tar.gz ==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse--numpy-1.11.0.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec --single-version-externally-managed --record=installed.txt ==> Downloading https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.5.1.tar.gz Already downloaded: /Users/wangj50/Library/Caches/Homebrew/lefse--matplotlib-1.5.1.tar.gz ==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec --single-version-externally-managed --record=installed.txt Last 15 lines from /Users/wangj50/Library/Logs/Homebrew/lefse/02.python: cairo: no [cairocffi or pycairo not found] windowing: no [Microsoft Windows only]

OPTIONAL LATEX DEPENDENCIES dvipng: no ghostscript: no latex: no pdftops: no

OPTIONAL PACKAGE DATA dlls: no [skipping due to configuration]

============================================================================

• The following required packages can not be built:
• freetype

If reporting this issue please do so at (not Homebrew/brew or Homebrew/core): https://github.com/biobakery/homebrew-biobakery/issues

Even though I have added : depends_on "freetype" => :recommended in the lefse formulae.

I don't know what I can do right now.

Jincheng

[ljmciver]

Hi Jincheng - Can you run the following command to check that you have brew freetype installed "brew install freetype"? If it is not installed, that command should install it for you. Then can you run "locate freetype | grep ft2build.h"? This will find the freetype headers. Brew freetype should install the headers in a location that matplotlib can find but I have found on some systems this is not the case. Depending on where freetype is installed you might need a symbolic link so matplotlib can find it. Let me know the outputs of the commands and then I can help with the link if needed.

Thanks, Lauren

[ETaSky]

@ljmciver Hi Lauren, I have already have freetype installed. I forgot to mention in previous post. And I knew the header is not in the right place. I tried to ln -s the header from /usr/local/include/freetype2 to /usr/local. However, even I tried to use sudo, it still said Operation not permitted. In addition, I already have matplotlib installed separately on my system, and no errors. Besides, the command locate freetype just returns that the locate database does not exist. Should I create it? Thanks!

[ljmciver]

Hi Jincheng - For the symlink, I think it would be something like "ln -s /usr/include/freetype2/ft2build.h /usr/include/" . I think the final location should be /usr/include/ for matplotlib to find the libraries. Would you like to use lefse in biobakery instead of trying to install with brew? We have a VM with many tools installed (including lefse) that you can run with very few commands. If you would like to try this out, all documentation is located at http://huttenhower.sph.harvard.edu/biobakery .

Thanks! Lauren

[ETaSky]

@ljmciver Thanks! My symlink command is correct. I just don't know why it doesn't work. I used the VM machine before. But I just have too many bioinformatics tools using VM. I'll try around and if nothing works, I'll either use VM or the galaxy server. Thanks! Jincheng