biobakery / homebrew-biobakery Goto Github PK

Biobakery formulae for the Homebrew package manager

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homebrew-biobakery's Introduction

homebrew-biobakery

The bioBakery Homebrew packages are no longer supported. We now provide Conda packages and Docker images. Please see the bioBakery documentation for information about how to install the tools with these two new methods.

Biobakery formulae for the Homebrew package manager.

To get started, install HomeBrew for MacOS or LinuxBrew for Linux platforms.

Install the full biobakery tool suite plus biobakery demos

Install dependencies Java Runtime Environment, USEARCH, and freetype/lapack/blas (required by matplotlib; available through brew depending on your operating system (ie "brew install freetype"))
Install the tool suite
- $ brew tap biobakery/biobakery
- $ brew install biobakery_tool_suite
Test the install
- $ biobakery_demos --tool all --mode test
- Testing all tools takes about 45 minutes.

If you have any issues installing dependencies of the tool suite and you have root permissions, install the bioBakery Docker images.

Install individual biobakery tools

If you do not want to install the full tool suite, you can select individual tools to install.

Tap the biobakery homebrew repository
- $ brew tap biobakery/biobakery
Install the individual tools needed
1. HUMAnN2
  - $ brew install humann2
  - Add the option --with-python3 to install with python3 (by default it is installed with python2).
  - Demo databases are included with the install. To install the full databases, see the humann2 documentation.
2. KneadData
  - Install Java Runtime Environment
  - $ brew install kneaddata
  - Add the option --with-python3 to install with python3 (by default it is installed with python2).
  - Demo databases are included with the install. To install the full databases, see the kneaddata documentation.
3. Picrust
  - $ brew install picrust
4. MaAsLin
  - $ brew install maaslin
5. MetaPhlAn2
  - $ brew install metaphlan2
  - Add the option --with-python3 to install with python3 (by default it is installed with python2).
6. ShortBRED
  - Install USEARCH
  - $ brew install shortbred
7. SparseDOSSA
  - $ brew install sparsedossa
8. PPANINI
  - Install USEARCH
  - $ brew install ppanini
9. LEfSe
  - $ brew install lefse
10. GraPhlAn
  - $ brew install graphlan
11. MicroPITA
  - $ brew install micropita
12. BreadCrumbs
  - $ brew install breadcrumbs
13. StrainPhlAn
  - $ brew install strainphlan
14. HAllA
  - $ brew install halla
  - Add the option --with-python3 to install with python3 (by default it is installed with python2).
15. Hclust2
  - $ brew install hclust2
16. PanPhlAn
  - $ brew install panphlan
  - Add the option --with-python3 to install with python3 (by default it is installed with python2).
17. bioBakery workflows
  - $ brew install workflows
  - Install Pandoc (only required for the visualization workflows)
  - Install LaTeX package with pdflatex, like TeXLive (only required for the visualization workflows)
  - Add the following to your PYTHONPATH to use this tool as a python library (export HOMBREW_PREFIX=$(brew --prefix))
    - $HOMEBREW_PREFIX/lib/python2.7/site-packages
    - $HOMEBREW_PREFIX/lib/python2.7/dist-packages
    - $HOMEBREW_PREFIX/lib64/python2.7/site-packages
  - Add the following to your R_LIBS to use this tool as a python library (if you require auto-doc features)
    - $HOMEBREW_PREFIX/R/library
Test the individual installs
1. Install biobakery_demos
  - $ brew install biobakery_demos
2. Test an individual tool install
  - $ biobakery_demos --tool humann2 --mode test
3. You can also view the commands for each demo run
  - $ biobakery_demos --tool humann2 --mode view
4. And you can run a demo and view the output files created
  - $ biobakery_demos --tool humann2 --mode run --output humann2_demo_output

FAQs

How do I get the latest formulas? To get the latest formulas run, $ brew update.
I have installed a lot of tools and my brew install folder takes up a lot of space. How can I free up space? Downloads for formulas are automatically installed in the brew cache. This way you only have to download something once but it also can use up disk space. To remove the cache run, $ rm -rf $(brew --cache).
How do I list the names of the brew tools and versions installed? Run the following command to list all of the tools and their versions, $ brew list --versions.
What should I do if I see an error during install that freetype is not installed but I have already installed freetype? Matplotlib is required by some of the tools and it depends on freetype. Matplotlib expects a specific freetype header to be installed in a specific folder and brew (and other package managers) don't always install the headers in this folder. If you are seeing this issue run the command $ locate freetype | grep ft2build.h to find where the header file is located. Then run the command $ ln -s /usr/include/freetype2/ft2build.h /usr/include/ (replacing the initial location with the one from the first command) to link this file to the location where matplotlib expects it. This should resolve the issue.
What should I do if I see errors about python2? The tools by default are installed with the python2 executable. For most environments on Linux and MacOS, you should have a python2 executable. If you run $ which python2 and python2 is not found you are likely in a python3 conda environment. If this is the case, then search for python3. If python3 is found add the option --with-python3 to install the tool with python3. The python3 install is available for all tools that are python2/3 compatible.
What should I do if I am seeing errors installing dependencies? The tools install some dependencies (like numpy/scipy/matplotlib) from source to get the exact version the tool has been developed and tested with. If you have issues, you can try installing the formula without the dependency. For example, tools with numpy as a dependency have the option --without-numpy which will allow you to bypass the numpy install step. Options exist to bypass installing may specific dependencies. For a complete list of options, run $ brew info FORMLUA, replacing FORMULA with that for which you would like to know the available options. Alternatively, you can choose to not install all of the python packages by using the flag --without-python-packages. If you do not install these dependencies, please install them with a different package manager like pip or apt-get depending on your platform. A flag also exists to bypass installing the R packages for those formulas that have R dependencies (--bypass-r-packages).

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homebrew-biobakery's Issues

Problem with brew install metaphlan2

HI,

I am installing complete biobakery tool suite using brew. I am encountering problem while installing metaphlan2. Brew is downloading metaphlan2 archive from "http://huttenhower.sph.harvard.edu/metaphlan2_downloads/metaphlan2-2.6.0.tar.gz".

However, this link is not active and hence brew install command stucks. I have verified the link by checking it in browser, but it is dead.
Also, the link of metaphlan2 is dead "http://huttenhower.sph.harvard.edu/metaphlan2".

Executing "brew install biobakery/biobakery/humann2" results in Python.h error

hi, everybody,
I have a problem when " brew install biobakery/biobakery/humann2"
looks like the 'python2' can NOT find the python.h

the system is CentOS 6.5

I have searched
#14
numpy: builds and installs after standalone brew
thefuck depends python-dev and psutil => :python
Executing "brew install biobakery_tool_suite" results in Python.h error #2
but can NOT find the reason.

below is the install log , env , and the file 's location.
1.install log
2.brew config
3.which python2
4.the Python.h 's location
5. the libpython2.7.so 's location

--------------1.install log :------------
==> Downloading https://pypi.python.org/packages/43/07/ec41577c3c1f9b578875ade8ed549d14fc2944c13cb7504579d542b62a69/humann2-0.11.1.tar.gz
Already downloaded: /home/test/.cache/Homebrew/humann2-0.11.1.tar.gz
==> Downloading https://pypi.python.org/packages/67/ab/41e4b42e0519d868347d2cf1051a05ce0170632039c053dee8ffe8b43b0b/numpy-1.8.2.tar.gz
Already downloaded: /home/test/.cache/Homebrew/humann2--numpy-1.8.2.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/home/test/.linuxbrew/Cellar/humann2/0.11.1/libexec --single-version-externally-managed --record=installed.txt
Last 15 lines from /home/test/.cache/Homebrew/Logs/humann2/01.python2:
File "/tmp/humann2--numpy-20180314-25181-13t03la/numpy-1.8.2/numpy/distutils/command/build_src.py", line 153, in run
self.build_sources()
File "/tmp/humann2--numpy-20180314-25181-13t03la/numpy-1.8.2/numpy/distutils/command/build_src.py", line 170, in build_sources
self.build_extension_sources(ext)
File "/tmp/humann2--numpy-20180314-25181-13t03la/numpy-1.8.2/numpy/distutils/command/build_src.py", line 329, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/tmp/humann2--numpy-20180314-25181-13t03la/numpy-1.8.2/numpy/distutils/command/build_src.py", line 386, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 428, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 42, in check_types
out = check_types(*a, **kw)
File "numpy/core/setup.py", line 289, in check_types
"Cannot compile 'Python.h'. Perhaps you need to "
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.
------------ 2.brew config -------------
HOMEBREW_VERSION: >=1.4.0 (shallow or no git repository)
ORIGIN: https://github.com/Linuxbrew/brew
HEAD: 42f6c7af3280bbf4329272e708d5710500c02fee
Last commit: 7 days ago
Core tap ORIGIN: https://github.com/Linuxbrew/homebrew-core
Core tap HEAD: 241a09f87d0978518840ece6062402b72e6d5953
Core tap last commit: 10 hours ago
HOMEBREW_PREFIX: /home/test/.linuxbrew
HOMEBREW_REPOSITORY: /home/test/.linuxbrew/Homebrew
HOMEBREW_CELLAR: /home/test/.linuxbrew/Cellar
HOMEBREW_BUILD_FROM_SOURCE: 1
HOMEBREW_CACHE: /home/test/.cache/Homebrew
HOMEBREW_CELLAR: /home/test/.linuxbrew/Cellar
HOMEBREW_MAKE_JOBS: 1
HOMEBREW_NO_ANALYTICS_THIS_RUN: 1
HOMEBREW_PREFIX: /home/test/.linuxbrew
HOMEBREW_REPOSITORY: /home/test/.linuxbrew/Homebrew
HOMEBREW_RUBY_WARNINGS: -W0
CPU: single-core 64-bit sandybridge
Homebrew Ruby: 2.3.3 => /home/test/.linuxbrew/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/bin/ruby
Clang: N/A
Git: 2.16.2 => /home/test/.linuxbrew/bin/git
Curl: 7.19.7 => /usr/bin/curl
Perl: /home/test/.linuxbrew/bin/perl => /home/test/.linuxbrew/Cellar/perl/5.26.1_1/bin/perl
Python: /home/test/.linuxbrew/opt/python/libexec/bin/python => /home/test/.linuxbrew/Cellar/python/3.6.4_5/bin/python3.6
Ruby: /usr/bin/ruby
Java: N/A
Kernel: Linux 2.6.32-696.18.7.1.el6.ucloud.x86_64 x86_64 GNU/Linux
OS: CentOS release 6.5 (Final)
Host glibc: 2.12
/usr/bin/gcc: 4.4.7
glibc: 2.23
gcc: 5.5.0_1
xorg: N/A
------------ 3. which python2 ------------
which python2
~/.linuxbrew/bin/python2
--------- 4.the Python.h 's location ---------
ls -l .linuxbrew/include/python2.7/Python.h
-rw-r--r-- 1 test test 4329 Mar 12 18:35 .linuxbrew/include/python2.7/Python.h
---------- 5. the libpython2.7.so 's location --------
ls .linuxbrew/lib/libpython2.7.so -l
lrwxrwxrwx 1 test test 47 Mar 12 18:35 .linuxbrew/lib/libpython2.7.so -> ../Cellar/python@2/2.7.14_4/lib/libpython2.7.so

what I have try:
##2
Executing "brew install biobakery_tool_suite" results in Python.h error #2 said we can use " yum install python-devel " to solved this problem . I have tried , but fail .
" brew install biobakery/biobakery/humann2" 's output is the same error.

another try: try install /home/test/.cache/Homebrew/humann2--numpy-1.8.2.tar.gz to see the error detial.

cd /home/test/.cache/Homebrew/
tar xzvf humann2--numpy-1.8.2.tar.gz
cd numpy-1.8.2
python setupegg.py install

------------install log ----------

python setupegg.py install
Running from numpy source directory.
non-existing path in 'numpy/distutils': 'site.cfg'
F2PY Version 2
blas_opt_info:
blas_mkl_info:
libraries mkl,vml,guide not found in ['/home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE

openblas_info:
libraries not found in ['/home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE

atlas_blas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in ['/home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']
NOT AVAILABLE

atlas_blas_info:
libraries f77blas,cblas,atlas not found in ['/home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64/sse2', '/usr/lib64', '/usr/lib']
NOT AVAILABLE

/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/system_info.py:1521: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.doc)
blas_info:
FOUND:
libraries = ['blas']
library_dirs = ['/usr/lib64']
language = f77

FOUND:
libraries = ['blas']
library_dirs = ['/usr/lib64']
define_macros = [('NO_ATLAS_INFO', 1)]
language = f77

non-existing path in 'numpy/lib': 'benchmarks'
lapack_opt_info:
lapack_mkl_info:
mkl_info:
libraries mkl,vml,guide not found in ['/home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib', '/usr/local/lib64', '/usr/local/lib', '/usr/lib64', '/usr/lib']
NOT AVAILABLE

NOT AVAILABLE

atlas_threads_info:
Setting PTATLAS=ATLAS
libraries ptf77blas,ptcblas,atlas not found in /home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib
libraries lapack_atlas not found in /home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib64
libraries lapack_atlas not found in /usr/local/lib64
libraries ptf77blas,ptcblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries ptf77blas,ptcblas,atlas not found in /usr/lib64/sse2
libraries lapack_atlas not found in /usr/lib64/sse2
libraries ptf77blas,ptcblas,atlas not found in /usr/lib64
libraries lapack_atlas not found in /usr/lib64
libraries ptf77blas,ptcblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_threads_info
NOT AVAILABLE

atlas_info:
libraries f77blas,cblas,atlas not found in /home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib
libraries lapack_atlas not found in /home/test/.linuxbrew/bin/../Cellar/python@2/2.7.14_4/lib
libraries f77blas,cblas,atlas not found in /usr/local/lib64
libraries lapack_atlas not found in /usr/local/lib64
libraries f77blas,cblas,atlas not found in /usr/local/lib
libraries lapack_atlas not found in /usr/local/lib
libraries f77blas,cblas,atlas not found in /usr/lib64/sse2
libraries lapack_atlas not found in /usr/lib64/sse2
libraries f77blas,cblas,atlas not found in /usr/lib64
libraries lapack_atlas not found in /usr/lib64
libraries f77blas,cblas,atlas not found in /usr/lib
libraries lapack_atlas not found in /usr/lib
numpy.distutils.system_info.atlas_info
NOT AVAILABLE

/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/system_info.py:1427: UserWarning:
Atlas (http://math-atlas.sourceforge.net/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [atlas]) or by setting
the ATLAS environment variable.
warnings.warn(AtlasNotFoundError.doc)
lapack_info:
FOUND:
libraries = ['lapack']
library_dirs = ['/usr/lib64']
language = f77

FOUND:
libraries = ['lapack', 'blas']
library_dirs = ['/usr/lib64']
define_macros = [('NO_ATLAS_INFO', 1)]
language = f77

/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/dist.py:267: UserWarning: Unknown distribution option: 'define_macros'
warnings.warn(msg)
running install
running bdist_egg
running egg_info
running build_src
build_src
building py_modules sources
creating build
creating build/src.linux-x86_64-2.7
creating build/src.linux-x86_64-2.7/numpy
creating build/src.linux-x86_64-2.7/numpy/distutils
building library "npymath" sources
customize Gnu95FCompiler
Found executable /home/test/.linuxbrew/bin/gfortran
customize Gnu95FCompiler
customize Gnu95FCompiler using config
C compiler: gcc-5 -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC

compile options: '-Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -Inumpy/core/include -c'
gcc-5: _configtest.c
_configtest.c:1:20: fatal error: Python.h: No such file or directory
compilation terminated.
_configtest.c:1:20: fatal error: Python.h: No such file or directory
compilation terminated.
failure.
removing: _configtest.c _configtest.o
Traceback (most recent call last):
File "setupegg.py", line 25, in
exec(compile(open('setup.py').read(), 'setup.py', 'exec'))
File "setup.py", line 239, in
setup_package()
File "setup.py", line 231, in setup_package
setup(**metadata)
File "/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/core.py", line 169, in setup
return old_setup(**new_attr)
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/site-packages/setuptools/init.py", line 129, in setup
return distutils.core.setup(**attrs)
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/core.py", line 151, in setup
dist.run_commands()
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/dist.py", line 953, in run_commands
self.run_command(cmd)
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/command/install.py", line 59, in run
r = self.setuptools_run()
File "/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/command/install.py", line 53, in setuptools_run
self.do_egg_install()
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/site-packages/setuptools/command/install.py", line 109, in do_egg_install
self.run_command('bdist_egg')
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/site-packages/setuptools/command/bdist_egg.py", line 163, in run
self.run_command("egg_info")
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/command/egg_info.py", line 10, in run
self.run_command("build_src")
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/cmd.py", line 326, in run_command
self.distribution.run_command(command)
File "/home/test/.linuxbrew/Cellar/python@2/2.7.14_4/lib/python2.7/distutils/dist.py", line 972, in run_command
cmd_obj.run()
File "/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/command/build_src.py", line 153, in run
self.build_sources()
File "/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/command/build_src.py", line 170, in build_sources
self.build_extension_sources(ext)
File "/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/command/build_src.py", line 329, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/home/test/.cache/Homebrew/numpy-1.8.2/numpy/distutils/command/build_src.py", line 386, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 428, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 42, in check_types
out = check_types(*a, **kw)
File "numpy/core/setup.py", line 289, in check_types
"Cannot compile 'Python.h'. Perhaps you need to "
SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

still can NOT find the reason.
can anyone help ?

error in brew install

I'm trying to install a software through home-brew, but I'm getting the error below.
I already tried to update brew and pip and to install gcc.

brew install strainphlan

....
==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/strainphlan/2.5.0-6462147/libexec/vendor --single-version-exter
Last 15 lines from /Users/francescadefilippis/Library/Logs/Homebrew/strainphlan/11.python:
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PGroupFCompiler
Could not locate executable pgfortran
don't know how to compile Fortran code on platform 'posix'
building 'dfftpack' library
error: library dfftpack has Fortran sources but no Fortran compiler found

Error when installing strainphlan

After successfully installing all dependencies, I get the following when trying to install strainphlan itself:

==> Installing biobakery/biobakery/strainphlan
Warning: Use bowtie2 instead of deprecated homebrew/science/bowtie2
Warning: Use bowtie2 instead of deprecated homebrew/science/bowtie2
Warning: Use bowtie2 instead of deprecated homebrew/science/bowtie2
Warning: Use bowtie2 instead of deprecated homebrew/science/bowtie2
Warning: Use bowtie2 instead of deprecated homebrew/science/bowtie2
==> Downloading http://huttenhower.sph.harvard.edu/metaphlan2_downloads/strainphlan-2.6.0.tar.gz
######################################################################## 100.0%
==> Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/strainphlan_homebrew_counter.txt
==> Downloading from https://bbuseruploads.s3.amazonaws.com/3a01cee1-3a04-4efc-9fd1-2172c21956d9/downloads/b00b4953-42c8-4435-b2c5-07fe1436cdbc/strainphlan_homebrew_counter.txt?Signature=3%2ByD1%2BnZ%2FHWi
######################################################################## 100.0%
==> rm *counter.txt
==> Downloading https://github.com/stamatak/standard-RAxML/archive/v8.1.15.tar.gz
==> Downloading from https://codeload.github.com/stamatak/standard-RAxML/tar.gz/v8.1.15
######################################################################## 100.0%
==> make -f Makefile.gcc
==> make -f Makefile.PTHREADS.gcc
==> make -f Makefile.SSE3.PTHREADS.gcc
==> Downloading https://github.com/samtools/samtools/archive/0.1.19.tar.gz
==> Downloading from https://codeload.github.com/samtools/samtools/tar.gz/0.1.19
######################################################################## 100.0%
==> make
==> make -C bcftools
==> cp samtools bcftools/bcftools bcftools/vcfutils.pl /exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/bin/
==> cp misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/bin/
==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz
######################################################################## 100.0%
==> python2 -c import setuptools... --no-user-cfg install --prefix=/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor --single-version-externally
==> Downloading https://pypi.python.org/packages/source/p/pandas/pandas-0.13.1.tar.gz
######################################################################## 100.0%
==> python2 -c import setuptools... --no-user-cfg install --prefix=/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor --single-version-externally
Last 15 lines from /home/achitzan/.cache/Homebrew/Logs/strainphlan/10.python2:
File "/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/python/2.7.14/lib/python2.7/site-packages/pkg_resources/init.py", line 1220, in resource_filename
return get_provider(package_or_requirement).get_resource_filename(
File "/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/python/2.7.14/lib/python2.7/site-packages/pkg_resources/init.py", line 440, in get_provider
import(moduleOrReq)
File "/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/init.py", line 180, in
from . import add_newdocs
File "/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in
from numpy.lib import add_newdoc
File "/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/lib/init.py", line 8, in
from .type_check import *
File "/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/lib/type_check.py", line 11, in
import numpy.core.numeric as _nx
File "/exports/sg/eddie/iti/groups/researchservices/achitzan/brew/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/core/init.py", line 14, in
from . import multiarray
ImportError: libtatlas.so.3: cannot open shared object file: No such file or directory

If lbtatlas is a dependency, I don't understand why brew didn't install it. Please help!

hclust2 installation

I tried to install hclust2 with: brew install hclust2.
But i get an error:
ImportError: /lib/x86_64-linux-gnu/libm.so.6: version `GLIBC_2.23' not found (required by /home/linuxbrew/.linuxbrew/Cellar/gcc/5.4.0/lib/libquadmath.so.0)
with: brew install glibc
i get: Warning: glibc 2.23 is already installed
First GLIBC_2.23 is not found and then is already installed.
Any suggestions?
Thanks

brew install breadcrumbs

[server ~]$brew install breadcrumbs
Updating Homebrew...
==> Installing breadcrumbs from biobakery/biobakery
==> Installing dependencies for biobakery/biobakery/breadcrumbs: sqlite
==> Installing biobakery/biobakery/breadcrumbs dependency: sqlite
==> Downloading https://linuxbrew.bintray.com/bottles/sqlite-3.28.0.x86_64_linux.bottle.tar.gz
==> Downloading from https://akamai.bintray.com/35/352c75c01430b2b66a7922175009a1f0fbf3c83b9908eb9a1af362477b6221e2?__gda__=exp=1555932616~hmac=342
######################################################################## 100.0%
==> Pouring sqlite-3.28.0.x86_64_linux.bottle.tar.gz
🍺 /data/marshpc/apps/biobakery/brew/linuxbrew/Cellar/sqlite/3.28.0: 13 files, 4.5MB
==> Installing biobakery/biobakery/breadcrumbs
==> Downloading https://bitbucket.org/biobakery/breadcrumbs/downloads/breadcrumbs-v0.92.tar.gz
Already downloaded: /home/users/hpcmgr/.cache/Homebrew/downloads/dade2d261a07445a5beaf22cb4ca390d1e669a2891b97b5fb914d3aa9d013930--breadcrumbs-v0.92.tar.gz
==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.gz
Already downloaded: /home/users/hpcmgr/.cache/Homebrew/downloads/32246c557b05158cfbb1b88f4aa555c35a721709caa7c670e99fe38e923a59fc--numpy-1.7.1.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/data/marshpc/apps/biobakery/brew/linuxbrew/Cellar/breadcrumbs/0.92/libexec --in
==> Downloading https://pypi.python.org/packages/source/s/scipy/scipy-0.12.0.tar.gz
Already downloaded: /home/users/hpcmgr/.cache/Homebrew/downloads/9957d16b3f57d822d8b05f6f90017aabbdbfffca982b51fa9fbc241800f94282--scipy-0.12.0.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/data/marshpc/apps/biobakery/brew/linuxbrew/Cellar/breadcrumbs/0.92/libexec --in
Last 15 lines from /home/users/hpcmgr/.cache/Homebrew/Logs/breadcrumbs/02.python2:
.replace('\r\n', '\n'), file, 'exec'))
--no-user-cfg
install
--prefix=/data/marshpc/apps/biobakery/brew/linuxbrew/Cellar/breadcrumbs/0.92/libexec
--install-scripts=/data/marshpc/apps/biobakery/brew/linuxbrew/Cellar/breadcrumbs/0.92/libexec/bin
--single-version-externally-managed
--record=installed.txt

Traceback (most recent call last):
File "", line 4, in
File "setup.py", line 165, in
setup_package()
File "setup.py", line 145, in setup_package
from numpy.distutils.core import setup
ImportError: No module named numpy.distutils.core

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

Error when installing biobakery with linuxbrew

I built linuxbrew and biobakery from scratch in my own account and got errors. This server is running a recently updated RedHat Enterprise Linux 7.4
Linuxbrew and hello installed without issues:
Specifically I got errors when building strainphlan

Here is when I tried to install just strainphlan

[cgchildr@compile ~]$ brew install strainphlan
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (homebrew/core).
No changes to formulae.

==> Installing strainphlan from biobakery/biobakery
==> Downloading http://huttenhower.sph.harvard.edu/metaphlan2_downloads/strainphlan-2.6.0.tar.gz
Already downloaded: /home/cgchildr/.cache/Homebrew/strainphlan-2.6.0.tar.gz
==> Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/strainphlan_homebrew_counter.txt
Already downloaded: /home/cgchildr/.cache/Homebrew/strainphlan--counter-homebrew.txt
==> rm *counter.txt
==> Downloading https://github.com/stamatak/standard-RAxML/archive/v8.1.15.tar.gz
Already downloaded: /home/cgchildr/.cache/Homebrew/strainphlan--raxml-8.1.15.tar.gz
==> make -f Makefile.gcc
==> make -f Makefile.PTHREADS.gcc
==> make -f Makefile.SSE3.PTHREADS.gcc
==> Downloading https://github.com/samtools/samtools/archive/0.1.19.tar.gz
Already downloaded: /home/cgchildr/.cache/Homebrew/strainphlan--samtools.v0.1.19-0.1.19.tar.gz
==> make
==> make -C bcftools
==> cp samtools bcftools/bcftools bcftools/vcfutils.pl /home/cgchildr/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/bin/
==> cp misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /home/cgchildr/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/bin/
==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz
Already downloaded: /home/cgchildr/.cache/Homebrew/strainphlan--numpy-1.11.0.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/home/cgchildr/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor --single-version-external
==> Downloading https://pypi.python.org/packages/source/p/pandas/pandas-0.13.1.tar.gz
Already downloaded: /home/cgchildr/.cache/Homebrew/strainphlan--pandas-0.13.1.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/home/cgchildr/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor --single-version-external
==> Downloading https://pypi.python.org/packages/source/s/scipy/scipy-0.12.0.tar.gz
Already downloaded: /home/cgchildr/.cache/Homebrew/strainphlan--scipy-0.12.0.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/home/cgchildr/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor --single-version-external
Last 15 lines from /home/cgchildr/.cache/Homebrew/Logs/strainphlan/11.python2:
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://github.com/Homebrew/homebrew/issues for instructions.
scipy/special/amos/zunhj.f:1:0:

   SUBROUTINE ZUNHJ(ZR, ZI, FNU, IPMTR, TOL, PHIR, PHII, ARGR, ARGI,

^
internal compiler error: Illegal instruction
0x7f6f413fc08f ???
/tmp/glibc-20170905-4944-6pb7q1/glibc-2.23/signal/../sysdeps/unix/sysv/linux/x86_64/sigaction.c:0
Please submit a full bug report,
with preprocessed source if appropriate.
Please include the complete backtrace with any bug report.
See https://github.com/Homebrew/homebrew/issues for instructions.
error: Command "/home/cgchildr/.linuxbrew/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -I/home/cgchildr/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib64/python2.7/site-packages/numpy/core/include -c -c scipy/special/amos/zunhj.f -o build/temp.linux-x86_64-2.7/scipy/special/amos/zunhj.o" failed with exit status 1

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

Failure to install Maaslin on Mac

$ brew install maaslin
==> Installing maaslin from biobakery/biobakery
==> Downloading https://bitbucket.org/biobakery/maaslin/downloads/Maaslin_0.0.5.tar.gz
Already downloaded: /Users/kev/Library/Caches/Homebrew/maaslin-0.0.5.tar.gz
==> Downloading https://pypi.python.org/packages/source/b/blist/blist-1.3.6.tar.gz
Already downloaded: /Users/kev/Library/Caches/Homebrew/maaslin--blist-1.3.6.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/maaslin/0.0.5/libexec/vendor --single-version-externally-managed --record=installed.txt
Last 15 lines from /Users/kev/Library/Logs/Homebrew/maaslin/01.python2:
2018-04-27 11:06:53 -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/maaslin/0.0.5/libexec/vendor
--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

This time, it doesn't even mention what the problem is, but non of the maaslin scripts from here are available. This time, the solution from #18 (ignoring dependencies) does not work.

2018-04-27|11:06:55 iamc kev$ brew install maaslin --ignore-dependencies
==> Installing maaslin from biobakery/biobakery
==> Downloading https://bitbucket.org/biobakery/maaslin/downloads/Maaslin_0.0.5.tar.gz
Already downloaded: /Users/kev/Library/Caches/Homebrew/maaslin-0.0.5.tar.gz
==> Downloading https://pypi.python.org/packages/source/b/blist/blist-1.3.6.tar.gz
Already downloaded: /Users/kev/Library/Caches/Homebrew/maaslin--blist-1.3.6.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/maaslin/0.0.5/libexec/vendor --single-version-externally-managed --record=installed.txt
Last 15 lines from /Users/kev/Library/Logs/Homebrew/maaslin/01.python2:
2018-04-27 11:07:43 -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/maaslin/0.0.5/libexec/vendor
--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

Error message with HUMAnN2

Hello,

After installing HUMAnN2, I get the following error message trying to run the first command (inputting sample files):

"CRITICAL ERROR: The metaphlan2.py executable can not be found. Please check the install."

I have installed metaphlan2 and python, and I am not sure how to troubleshoot this- can you please help me understand what could be causing this issue? Thank you.

Best,
Christine

Installation failed

Hei,
to install metaphlan2, I was using the command

$ brew tap biobakery/biobakery
followed by
$ brew install metaphlan2

everything seems to work correctly; but at the end , I get the following error messages:

Last 15 lines from /home/SKNBE/.cache/Homebrew/Logs/metaphlan2/02.python2:
gcc-7: build/src.linux-x86_64-2.7/numpy/core/src/multiarray/nditer_templ.c
gcc-7: numpy/core/src/multiarray/python_xerbla.c
gcc-7: numpy/core/src/multiarray/ucsnarrow.c
gcc-7: build/src.linux-x86_64-2.7/numpy/core/src/multiarray/einsum.c
gcc-7: numpy/core/src/multiarray/number.c
gcc-7: numpy/core/src/multiarray/numpyos.c
numpy/core/src/multiarray/numpyos.c:18:10: fatal error: xlocale.h: No such file or directory
#include <xlocale.h>

compilation terminated.
numpy/core/src/multiarray/numpyos.c:18:10: fatal error: xlocale.h: No such file or directory
#include <xlocale.h>

compilation terminated.
error: Command "gcc-7 -fno-strict-aliasing -g -O2 -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -DNO_ATLAS_INFO=1 -DHAVE_CBLAS -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/home/linuxbrew/.linuxbrew/include -I/home/linuxbrew/.linuxbrew/opt/openssl/include -I/home/linuxbrew/.linuxbrew/opt/sqlite/include -I/home/linuxbrew/.linuxbrew/opt/python@2/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c numpy/core/src/multiarray/numpyos.c -o build/temp.linux-x86_64-2.7/numpy/core/src/multiarray/numpyos.o" failed with exit status 1

Errors with installing lefse

Hi,

I tried to homebrew to install lefse, got error messages as
Last 15 lines from /Users/mengwu/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, png

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

Error: A newer Command Line Tools release is available.
Update them from Software Update in the App Store.

Could you please help.

Thanks,
Meng

hclust2 install Error:SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

I have three python version in ubuntu, 2.7\3.5\3.6
when I use command: brew install hclust2

so I execute: sudo apt-get install python-dev
but show
python-dev is already the newest version

Failed to install GraPhlAn on Mac OS

When I try to install GarPhlAn on my MacOS Sierra system, version 10.12.6, following this command,
$ brew tap biobakery/biobakery
$ brew install graphlan
Here are the errors

==> Installing graphlan from biobakery/biobakery
==> Downloading https://bitbucket.org/nsegata/graphlan/get/d2ec14e3f75c.tar.gz
Already downloaded: /Users/Bubble/Library/Caches/Homebrew/graphlan-0.9.7.tar.gz
==> Downloading https://bitbucket.org/cibiocm/export2graphlan/get/b2e0ba667186.tar.gz
Already downloaded: /Users/Bubble/Library/Caches/Homebrew/graphlan--export2graphlan-667186.tar.gz
==> Downloading https://bitbucket.org/nsegata/hclust2/get/277c0d6a1d52.tar.gz
Already downloaded: /Users/Bubble/Library/Caches/Homebrew/graphlan--hclust2-52.tar.gz
==> mkdir /usr/local/Cellar/graphlan/0.9.7/libexec/hclust2
==> mv /usr/local/Cellar/graphlan/0.9.7/libexec/.py /usr/local/Cellar/graphlan/0.9.7/libexec/hclust2/
==> Downloading https://bitbucket.org/nsegata/pyphlan/get/eae40ebc0030.tar.gz
Already downloaded: /Users/Bubble/Library/Caches/Homebrew/graphlan--pyphlan-0030.tar.gz
==> mkdir /usr/local/Cellar/graphlan/0.9.7/libexec/pyphlan
==> mv /usr/local/Cellar/graphlan/0.9.7/libexec/.py /usr/local/Cellar/graphlan/0.9.7/libexec/pyphlan/
==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz
Already downloaded: /Users/Bubble/Library/Caches/Homebrew/graphlan--numpy-1.11.0.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/graphlan/0.9.7/libexec --single-version-externally-managed --record=installed.txt
Last 15 lines from /Users/Bubble/Library/Logs/Homebrew/graphlan/05.python2:
2018-05-13 14:34:41 +0800

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/graphlan/0.9.7/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

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

Besides, the default python version is 2.7.14. So is there anyone can help me to solve this problem, appreciate your time.

homebrew/science is deprecated and unusable

Many (edit: 5. workflows.rb, panphlan.rb, shortbred.rb, strainphlan.rb, metaphlan2.rb) formula in this repository have dependencies from homebrew/science. However, as-of Jan 1 that is no longer available. See this PR for details.

Change of links for blast downloads

On my Mac curl is failing on downloading the blast executable in blast.rb for Macs: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.3.0/ncbi-blast-2.3.0+-universal-macosx.tar.gz

I believe the urls should now use https:// rather than ftp://

strainphlan via biobakery_tool_suite fails to find /usr/lib64/liblapack.so.3

RHEL6/CentOS6 /w linuxbrew. I have tried the lapack-devel system package (which provides /usr/lib64/liblapack.so.3) as well as brew install lapack (which provides ~/.linuxbrew/Cellar/lapack/3.8.0/lib64/liblapack.so.3) and strainphlan fails to build with the following:

Build logs here.

==> python2 -c import setuptools... --no-user-cfg install --prefix=/home/testuser/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor --single-version-externally-managed --record=installed.txt
Last 15 lines from /home/testuser/.cache/Homebrew/Logs/strainphlan/10.python2:
  File "/home/testuser/.linuxbrew/Cellar/python/2.7.14/lib/python2.7/site-packages/pkg_resources/__init__.py", line 440, in get_provider
    __import__(moduleOrReq)
  File "/home/testuser/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/__init__.py", line 180, in <module>
    from . import add_newdocs
  File "/home/testuser/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "/home/testuser/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/lib/__init__.py", line 18, in <module>
    from .polynomial import *
  File "/home/testuser/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/lib/polynomial.py", line 20, in <module>
    from numpy.linalg import eigvals, lstsq, inv
  File "/home/testuser/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/linalg/__init__.py", line 51, in <module>
    from .linalg import *
  File "/home/testuser/.linuxbrew/Cellar/strainphlan/2.6.0/libexec/vendor/lib/python2.7/site-packages/numpy/linalg/linalg.py", line 29, in <module>
    from numpy.linalg import lapack_lite, _umath_linalg
ImportError: liblapack.so.3: cannot open shared object file: No such file or directory

The most recent Dockerfile I have tried contains both methods (RPM as well as brew install):

FROM centos:centos6

ADD RPMs/*.rpm /tmp/RPMs/
RUN yum localinstall -y /tmp/RPMs/*.rpm &&\
    rm -vf /tmp/RPMs/*.rpm &&\
    rmdir -v /tmp/RPMs
RUN yum makecache fast &&\
    yum -y upgrade &&\
    yum -y install coreutils curl file git python-setuptools '@Development Tools' blas-devel lapack-devel freetype-devel &&\
    yum clean all
RUN localedef -v -c -i en_US -f UTF-8 en_US.UTF-8 || true
ENV LC_ALL='en_US.UTF-8'

RUN useradd -m -U testuser
USER testuser
WORKDIR /home/testuser

RUN git clone https://github.com/Linuxbrew/brew.git .linuxbrew
RUN echo 'export PATH="${HOME}/.linuxbrew/bin:${HOME}/.linuxbrew/sbin:$PATH"' >> .bashrc &&\
    echo 'export MANPATH="$(brew --prefix)/share/man:${MANPATH}"' >> .bashrc &&\
    echo 'export INFOPATH="$(brew --prefix)/share/info:${INFOPATH}"' >> .bashrc &&\
    echo 'export HOMEBREW_MAKE_JOBS="$(/usr/bin/nproc)"' >> .bashrc

# using this dumb formatting to ensure the above environment vars are in effect, without resorting to ENV
RUN ["/bin/bash", "-l", "-c", "HOMEBREW_NO_AUTO_UPDATE=1 brew config"]
RUN ["/bin/bash", "-l", "-c", "HOMEBREW_NO_AUTO_UPDATE=1 HOMEBREW_BUILD_FROM_SOURCE=1 brew install gcc --without-glibc"]
RUN ["/bin/bash", "-l", "-c", "HOMEBREW_NO_AUTO_UPDATE=1 brew install glibc"]
RUN ["/bin/bash", "-l", "-c", "HOMEBREW_NO_AUTO_UPDATE=1 brew remove gcc"]
RUN ["/bin/bash", "-l", "-c", "HOMEBREW_NO_AUTO_UPDATE=1 brew install gcc"]
RUN ["/bin/bash", "-l", "-c", "localedef -v -c -i en_US -f UTF-8 en_US.UTF-8 || true"]
RUN ["/bin/bash", "-l", "-c", "HOMEBREW_NO_AUTO_UPDATE=1 brew install git"]
RUN ["/bin/bash", "-l", "-c", "brew update"]
RUN ["/bin/bash", "-l", "-c", "brew tap biobakery/biobakery"]
RUN ["/bin/bash", "-l", "-c", "brew install lapack"]
#RUN ["/bin/bash", "-l", "-c", "brew install biobakery_tool_suite"]

#RUN ["/bin/bash", "-l", "-c", "rm -rf $(brew --cache)"]
CMD ["/bin/bash", "-i"]

brew install metaphlan2 error

==> python2 -c import setuptools... --no-user-cfg install --prefix=/home/admin/.linuxbrew/Cellar/metaphlan2/2.6.0/libexe
Last 15 lines from /home/admin/.cache/Homebrew/Logs/metaphlan2/04.python2:
File "/home/admin/.linuxbrew/Cellar/metaphlan2/2.6.0/libexec/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 972, in get_subpackage
caller_level = caller_level + 1)
File "/home/admin/.linuxbrew/Cellar/metaphlan2/2.6.0/libexec/lib/python2.7/site-packages/numpy/distutils/misc_util.py", line 909, in _get_configuration_from_setup_py
config = setup_module.configuration(*args)
File "scipy/integrate/setup.py", line 12, in configuration
blas_opt = get_info('blas_opt',notfound_action=2)
File "/home/admin/.linuxbrew/Cellar/metaphlan2/2.6.0/libexec/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 372, in get_info
return cl().get_info(notfound_action)
File "/home/admin/.linuxbrew/Cellar/metaphlan2/2.6.0/libexec/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 566, in get_info
raise self.notfounderror(self.notfounderror.doc)
numpy.distutils.system_info.BlasNotFoundError:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.

Problems installing lefse using brew

I'm attempting to install lefse on Mac OS X 10.13, using the instructions on the biobakery README using brew but have run into similar failures noted in past bug reports. I am now trying to install using the recommended --without-dependencies flag, but I now see this:

$ brew install lefse --without-dependencies
Updating Homebrew...
==> Auto-updated Homebrew!
Updated 1 tap (caskroom/cask).
No changes to formulae.

==> Installing lefse from biobakery/biobakery
==> Downloading https://bitbucket.org/nsegata/lefse/get/e3cabe93a0d1.tar.gz
Already downloaded: /Users/cjfields/Library/Caches/Homebrew/lefse-1.0.0-dev-e3cabe9.tar.gz
==> R -q -e install.packages('splines', lib='/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/R/library', repos='http://cran.r-project.org')
Last 15 lines from /Users/cjfields/Library/Logs/Homebrew/lefse/01.R:
2018-05-12 11:10:25 -0500

R
-q
-e
install.packages('splines', lib='/usr/local/Cellar/lefse/1.0.0-dev-e3cabe9/libexec/R/library', repos='http://cran.r-project.org')


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

It seems the brew installation is really finicky on Mac, should we switch to the bioconda installation?

Required packages could not be built

Hello,

I'm trying to install Lefse using Homebrew and I get this error at the end:

============================================================================
* The following required packages can not be built:
* freetype, png

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

I then used brew to install freetype (which completed successfully), but when I ran the brew install for lefse again I got the same error except png is no longer a problem. It is only freetype. My brew is up to date, so I'm unsure what the issue is.

Any help on getting this lefse install working would be greatly appreciated!

Thanks,
Samantha

Issue with LEfSe installation

Hi,

I am trying to install lefse on my mac but it give me this error:

brew install biobakery/biobakery/lefse
==> Installing lefse from biobakery/biobakery
==> Downloading https://bitbucket.org/nsegata/lefse/get/e3cabe93a0d1.tar.gz
Already downloaded: /Users/Faisal/Library/Caches/Homebrew/downloads/860fb6bb11236559bfa7d18011e886d06aa99f4210dda2e24876068236b9c1f1--nsegata-lefse-e3cabe93a0d1.tar.gz
==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz
Already downloaded: /Users/Faisal/Library/Caches/Homebrew/downloads/179cce20524ad92a21a0b3252a0f9d0e9138b63153280bf8e6900ef6a9972a8d--numpy-1.11.0.tar.gz
==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cab
==> Downloading https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.5.1.tar.gz
Already downloaded: /Users/Faisal/Library/Caches/Homebrew/downloads/c6e0b40cfa64e5575033cb0251e797ef358bd9ef40ad024fa431ada84d1b8765--matplotlib-1.5.1.tar.gz
==> python -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/lefse/1.0.0-dev-e3cab
Last 15 lines from /Users/Faisal/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

I tried to install freetype by brew install freetype and try to reinstall lefse but I still get the same issue!

Any way to solve this issue?

Thanks,

Provide option to skip counter for less public network areas.

Hi, I'm here to report that the counter url https://bitbucket.org/biobakery/metaphlan2/downloads/metaphlan2_homebrew_counter.txt is being blocked by the China goverment. This means all computers in China cannot install metaphlan2 directly from homebrew.

Would do please provide an option to skip downloading from https://bitbucket.org ?

freetype dependency

Hello,
my attempts to install metaphlan2 via linuxbrew constantly end up with:

"*The following required packages can not be built:

freetype"

Any ideas or help?

Thank you,
Ralf

Install issue with starainphlan

Hello, I have been really trying to install strainphlan on my MAC and it kept giving me an error message.

Please note my system below:

python --version:
Python 2.7.15
brew link python
Error: No such keg: /usr/local/Cellar/python
brew link python2
Warning: Already linked: /usr/local/Cellar/python@2/2.7.15_1

Last 15 lines from /Users/myname/Library/Logs/Homebrew/strainphlan/10.python2:
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PGroupFCompiler
Could not locate executable pgfortran
don't know how to compile Fortran code on platform 'posix'
building 'dfftpack' library
error: library dfftpack has Fortran sources but no Fortran compiler found
/usr/local/Homebrew/Library/Homebrew/utils/fork.rb:49:in write': Broken pipe (Errno::EPIPE) from /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:49:in puts'
from /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:49:in rescue in block (3 levels) in safe_fork' from /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:31:in block (3 levels) in safe_fork'
from /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:30:in fork' from /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:30:in block (2 levels) in safe_fork'
from /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:27:in open' from /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:27:in block in safe_fork'
from /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/tmpdir.rb:89:in mktmpdir' from /usr/local/Homebrew/Library/Homebrew/utils/fork.rb:26:in safe_fork'
from /usr/local/Homebrew/Library/Homebrew/formula_installer.rb:719:in build' from /usr/local/Homebrew/Library/Homebrew/formula_installer.rb:311:in install'
from /usr/local/Homebrew/Library/Homebrew/cmd/install.rb:321:in install_formula' from /usr/local/Homebrew/Library/Homebrew/cmd/install.rb:253:in block in install'
from /usr/local/Homebrew/Library/Homebrew/cmd/install.rb:251:in each' from /usr/local/Homebrew/Library/Homebrew/cmd/install.rb:251:in install'
from /usr/local/Homebrew/Library/Homebrew/brew.rb:89:in `

I have been really trying to download the strainphaln using all kinds of methods (including docker and install using --without-dependencies), but nothing giving me any luck. Could you please help me to resolve this issue? Thanks.

Weird installation errors on Mac (humann2 and metaphlan2)

Metaphlan2

$ brew install metaphlan2
==> Installing metaphlan2 from biobakery/biobakery
==> Downloading http://huttenhower.sph.harvard.edu/metaphlan2_downloads/metaphlan2-2.6.0.tar.gz
######################################################################## 100.0%
Please install python2
$ python --version
Python 2.7.10
$ python2 --version
Python 2.7.14

For the record, Mac OSX has python 2.7 installed as part of the system software, so all OSX installations should have it. I also have an additional python2 installed through homebrew, but I tried this on a system that doesn't, and got the same message.

Humann2

$ brew install humann2
Error: Formulae found in multiple taps:
       * biobakery/biobakery/humann2
       * brewsci/science/humann2

Please use the fully-qualified name e.g. biobakery/biobakery/humann2 to refer the formula.
$ brew install biobakery/biobakery/humann2
==> Installing humann2 from biobakery/biobakery
==> Installing dependencies for biobakery/biobakery/humann2: biobakery/biobakery/metaphlan2
==> Installing biobakery/biobakery/humann2 dependency: biobakery/biobakery/metaphlan2
==> Downloading http://huttenhower.sph.harvard.edu/metaphlan2_downloads/metaphlan2-2.6.0.tar.gz
Already downloaded: /Users/kev/Library/Caches/Homebrew/metaphlan2-2.6.0.tar.gz
Please install python2

The one in brewsci/science seems to work for both humann2 and (because it's installed as a dependency) metaphlan2. Though I think it's installing the python3 version.

Problem installing Maaslin

Hello I'm trying to use Homebrew to install maaslin and the installation is having a problem that I'm not able to identify.

I am running MAC High Sierra v. 10.13.6.

This is the command I used to install:
brew install biobakery/biobakery/maaslin

This is the output from running the above command:

==> Installing maaslin from biobakery/biobakery
==> Downloading https://bitbucket.org/biobakery/maaslin/downloads/Maaslin_0.0.5.tar.gz
Already downloaded: /Users/kirbylab/Library/Caches/Homebrew/maaslin-0.0.5.tar.gz
==> Downloading https://pypi.python.org/packages/source/b/blist/blist-1.3.6.tar.gz
Already downloaded: /Users/kirbylab/Library/Caches/Homebrew/maaslin--blist-1.3.6.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/maaslin/0.0.5/libexec/vendor --single-version-externally-managed --record=installed.txt
Last 15 lines from /Users/kirbylab/Library/Logs/Homebrew/maaslin/01.python2:
2018-07-24 15:11:12 -0500

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/maaslin/0.0.5/libexec/vendor
--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

Thank you,
Samantha

error in 'brew install biobakery_tool_suite' in biobakery vagrant image

when i download the vm box and build a image of biobakery tool suite, i met lots error. first one is the homebrew install. in the orign .sh script, there install linuxbrew by git form github. but the last install command of brew is different. i install the last brew in the vm box success. although this, i meet this error. i have not a computer background, i don't know how to fix this.
so, everyone, please help me.

vagrant@biobakery:~$ brew install biobakery_tool_suite
Updating Homebrew...
==> Installing biobakery_tool_suite from biobakery/biobakery
==> Installing dependencies for biobakery/biobakery/biobakery_tool_suite: biobakery/biobakery/maaslin, brewsci/bio/cd-hit, biobakery/biobakery/shortbred, biobakery/biobakery/sparsedossa, biobakery/biobakery/ppanini, biobakery/biobakery/lefse, biobakery/biobakery/graphlan, gsl, mpich, biobakery/biobakery/micropita, biobakery/biobakery/breadcrumbs, biobakery/biobakery/halla, biobakery/biobakery/hclust2, curl, htslib, homebrew/core/samtools, biobakery/biobakery/panphlan, argtable, brewsci/bio/clustal-omega, brewsci/science/ea-utils and biobakery/biobakery/workflows
==> Installing biobakery/biobakery/biobakery_tool_suite dependency: biobakery/biobakery
==> Downloading https://bitbucket.org/biobakery/maaslin/downloads/Maaslin_0.0.5.tar.gz
Already downloaded: /home/vagrant/.cache/Homebrew/downloads/4ec06b0d2772dacccb83c119f9d8a3713cc21982aec8c0b3fe509dcf8b17b275--Maaslin_0.0.5.tar.gz
==> Downloading https://pypi.python.org/packages/source/b/blist/blist-1.3.6.tar.gz
Already downloaded: /home/vagrant/.cache/Homebrew/downloads/cdf77dd62b0f649ae008841e9f0ca0280a93a6cd9e63174be75e5736217d31dd--blist-1.3.6.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/home/linuxbrew/.linuxbre
==> R -q -e install.packages('foreach', lib='/home/linuxbrew/.linuxbrew/Cellar/maaslin/0.0.5
==> Downloading https://cran.r-project.org/src/contrib/Archive/gam/gam_1.14.tar.gz
Already downloaded: /home/vagrant/.cache/Homebrew/downloads/a6ff89450e1700acf081356ce47237ad4d1e6f84c246b2289d365057ebf6bfca--gam_1.14.tar.gz
==> R CMD INSTALL .
Last 15 lines from /home/vagrant/.cache/Homebrew/Logs/maaslin/03.R:
** libs
gfortran -fpic -g -O2 -fstack-protector-strong -c backfit.f -o backfit.o
gfortran -fpic -g -O2 -fstack-protector-strong -c backlo.f -o backlo.o
gfortran -fpic -g -O2 -fstack-protector-strong -c bsplvd.f -o bsplvd.o
gfortran -fpic -g -O2 -fstack-protector-strong -c bvalue.f -o bvalue.o
gfortran -fpic -g -O2 -fstack-protector-strong -c bvalus.f -o bvalus.o
gfortran -fpic -g -O2 -fstack-protector-strong -c linear.f -o linear.o
gfortran -fpic -g -O2 -fstack-protector-strong -c lo.f -o lo.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c loessc.c -o loessc.o
loessc.c:43:15: fatal error: R.h: No such file or directory
compilation terminated.
/usr/lib/R/etc/Makeconf:159: recipe for target 'loessc.o' failed
make: *** [loessc.o] Error 1
ERROR: compilation failed for package ‘gam’

removing ‘/home/linuxbrew/.linuxbrew/Cellar/maaslin/0.0.5/libexec/gam’

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

freetype needed as dependency, already installed

I've been banging my head against this error for a while:

==> Installing lefse from biobakery/biobakery
==> Downloading https://bitbucket.org/nsegata/lefse/get/e3cabe93a0d1.tar.gz
Already downloaded: /Users/trane/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/trane/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-
==> Downloading https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.5.1.tar.gz
Already downloaded: /Users/trane/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-
Last 15 lines from /Users/trane/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

➜  brew install freetype
Warning: freetype 2.8 is already installed

My anaconda, LaTeX, and other dependencies seem to be working fine.

installation error

I was trying to install shortbred from homebrew but got error message:
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Ce
Last 15 lines from /Users/433d-mbp-01/Library/Logs/Homebrew/shortbred/01.python2:
2020-05-17 22:07:18 -0500

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/shortbred/0.9.3-dev-702e3ef/libexec
--install-scripts=/usr/local/Cellar/shortbred/0.9.3-dev-702e3ef/libexec/bin
--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

Heat-map generation error

/home/venkat/Desktop/Software/biobakery-metaphlan2-c3fb65390c21/utils/metaphla
n_hclust_heatmap.py --in merged_abundance_table.txt --out test.png
Traceback (most recent call last):
  File "/home/venkat/Desktop/Software/biobakery-metaphlan2-c3fb65390c21/utils/metaphlan_hclust_heatmap.py", line 481, in <module>
	tax_lev = pars['tax_lev']
  File "/home/venkat/Desktop/Software/biobakery-metaphlan2-c3fb65390c21/utils/metaphlan_hclust_heatmap.py", line 435, in hclust
	Y2 = sch.linkage(   Dt, method=method, metric=dist_func )
  File "/home/venkat/miniconda3/envs/python2/lib/python2.7/site-packages/scipy/cluster/hierarchy.py", line 676, in linkage
	raise ValueError("The condensed distance matrix must contain only finite values.")
ValueError: The condensed distance matrix must contain only finite values.

issues with install bio bakery

Similar to last comment about strainphlan installation, I used home-brew and have had the same problem.

python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Ce
Last 15 lines from /Users/wmcjrlee/Library/Logs/Homebrew/strainphlan/10.python2:
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PGroupFCompiler
Could not locate executable pgfortran
don't know how to compile Fortran code on platform 'posix'
building 'dfftpack' library
error: library dfftpack has Fortran sources but no Fortran compiler found

How can I get around this?

possible fix for missing xlocale.h error

Hi Lauren,

Fyi, when trying to install biobakery on an aws ec2 instance, I kept getting an error that the xlocale.h is missing, detailed message below. I applied the fix at the bottom of this message and it helped.

ERROR

==> python2 -c import setuptools... --no-user-cfg install --prefix=/home/ec2-user/.linuxbrew/Cellar/strainphlan/2.6.0/libexec --install-s
Last 15 lines from /home/ec2-user/.cache/Homebrew/Logs/strainphlan/09.python2:
gcc-7: numpy/core/src/multiarray/common.c
gcc-7: build/src.linux-x86_64-2.7/numpy/core/src/multiarray/nditer_templ.c
gcc-7: numpy/core/src/multiarray/ucsnarrow.c
gcc-7: build/src.linux-x86_64-2.7/numpy/core/src/multiarray/einsum.c
gcc-7: numpy/core/src/multiarray/number.c
gcc-7: numpy/core/src/multiarray/numpyos.c
numpy/core/src/multiarray/numpyos.c:18:10: fatal error: xlocale.h: No such file or directory
 #include <xlocale.h>
          ^~~~~~~~~~~
compilation terminated.
numpy/core/src/multiarray/numpyos.c:18:10: fatal error: xlocale.h: No such file or directory
 #include <xlocale.h>
          ^~~~~~~~~~~
compilation terminated.
error: Command "gcc-7 -fno-strict-aliasing -g -O2 -DNDEBUG -g -O3 -Wall -Wstrict-prototypes -fPIC -DHAVE_NPY_CONFIG_H=1 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE=1 -D_LARGEFILE64_SOURCE=1 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Inumpy/core/include -Ibuild/src.linux-x86_64-2.7/numpy/core/include/numpy -Inumpy/core/src/private -Inumpy/core/src -Inumpy/core -Inumpy/core/src/npymath -Inumpy/core/src/multiarray -Inumpy/core/src/umath -Inumpy/core/src/npysort -I/home/ec2-user/.linuxbrew/include -I/home/ec2-user/.linuxbrew/opt/openssl/include -I/home/ec2-user/.linuxbrew/opt/sqlite/include -I/home/ec2-user/.linuxbrew/Cellar/python@2/2.7.15_1/include/python2.7 -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -Ibuild/src.linux-x86_64-2.7/numpy/core/src/private -c numpy/core/src/multiarray/numpyos.c -o build/temp.linux-x86_64-2.7/numpy/core/src/multiarray/numpyos.o" failed with exit status 1

FIX
ln -s /usr/include/locale.h /usr/include/xlocale.h

Problem installing lefse tool

I am trying to instal the command line version of lefse since the galaxy server has not been working. I am following the directions here (and have successfully installed other tools such as picrust). I get the same error that has been discussed in length in issue #4 and was never resolved. Here is my error after running brew install lefse --verbose:

==> Downloading https://pypi.python.org/packages/source/m/matplotlib/matplotlib-1.5.1.tar.gz
Already downloaded: /Users/keri/Library/Caches/Homebrew/lefse--matplotlib-1.5.1.tar.gz
==> Verifying lefse--matplotlib-1.5.1.tar.gz checksum
tar xzf /Users/keri/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
IMPORTANT WARNING:
    pkg-config is not installed.
    matplotlib may not be able to find some of its dependencies
============================================================================
Edit setup.cfg to change the build options

BUILDING MATPLOTLIB
            matplotlib: yes [1.5.1]
                python: yes [2.7.10 (default, Feb  7 2017, 00:08:15)  [GCC
                        4.2.1 Compatible Apple LLVM 8.0.0 (clang-800.0.34)]]
              platform: yes [darwin]

REQUIRED DEPENDENCIES AND EXTENSIONS
                 numpy: yes [version 1.11.0]
              dateutil: yes [using dateutil version 1.5]
                  pytz: yes [using pytz version 2013.7]
                cycler: yes [cycler was not found. pip will attempt to
                        install it after matplotlib.]
               tornado: yes [tornado was not found. It is required for the
                        WebAgg backend. pip/easy_install may attempt to
                        install it after matplotlib.]
             pyparsing: yes [using pyparsing version 2.0.1]
                libagg: yes [pkg-config information for 'libagg' could not
                        be found. Using local copy.]
              freetype: no  [The C/C++ header for freetype2 (ft2build.h)
                        could not be found.  You may need to install the
                        development package.]
                   png: yes [pkg-config information for 'libpng' could not
                        be found. Using unknown version found on system.]
                 qhull: yes [pkg-config information for 'qhull' could not be
                        found. Using local copy.]

OPTIONAL SUBPACKAGES
           sample_data: yes [installing]
              toolkits: yes [installing]
                 tests: yes [nose 0.11.1 or later is required to run the
                        matplotlib test suite. Please install it with pip or
                        your preferred tool to run the test suite / mock is
                        required to run the matplotlib test suite. Please
                        install it with pip or your preferred tool to run
                        the test suite]
        toolkits_tests: yes [nose 0.11.1 or later is required to run the
                        matplotlib test suite. Please install it with pip or
                        your preferred tool to run the test suite / mock is
                        required to run the matplotlib test suite. Please
                        install it with pip or your preferred tool to run
                        the test suite]

OPTIONAL BACKEND EXTENSIONS
                macosx: yes [installing, darwin]
                qt5agg: no  [PyQt5 not found]
                qt4agg: no  [PySide not found; PyQt4 not found]
               gtk3agg: no  [Requires pygobject to be installed.]
             gtk3cairo: no  [Requires cairocffi or pycairo to be installed.]
                gtkagg: no  [Requires pygtk]
                 tkagg: yes [installing, version 81008]
                 wxagg: no  [requires wxPython]
                   gtk: no  [Requires pygtk]
                   agg: yes [installing]
                 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

==> Formula
Tap: biobakery/biobakery
Path: /usr/local/Homebrew/Library/Taps/biobakery/homebrew-biobakery/lefse.rb
==> Configuration
HOMEBREW_VERSION: 1.4.3
ORIGIN: https://github.com/Homebrew/brew
HEAD: 987805d3dcd4c8dbc70127399d4ea7aee8e98c21
Last commit: 9 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: 7342cb86eda94915ea52495ac9d6de9fed25cd9c
Core tap last commit: 5 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_ENABLE_AUTO_UPDATE_MIGRATION: 1
CPU: octa-core 64-bit sandybridge
Homebrew Ruby: 2.3.3 => /usr/local/Homebrew/Library/Homebrew/vendor/portable-ruby/2.3.3/bin/ruby
Clang: 9.0 build 900
Git: 2.14.3 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.54.0 => /usr/bin/curl
Perl: /usr/bin/perl
Python: /Users/keri/miniconda2/bin/python => /Users/keri/miniconda2/bin/python2.7
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: 1.8.0_102, 1.6.0_65-b14-468
macOS: 10.12.6-x86_64
Xcode: 9.2
CLT: 9.2.0.0.1.1510905681
X11: 2.7.9 => /opt/X11
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j8
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_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/bin:/bin:/usr/sbin:/sbin

Error: biobakery/biobakery/lefse 1.0.0-dev-e3cabe9 did not build
Logs:
     /Users/keri/Library/Logs/Homebrew/lefse/00.options.out
     /Users/keri/Library/Logs/Homebrew/lefse/01.python
     /Users/keri/Library/Logs/Homebrew/lefse/01.python.cc
     /Users/keri/Library/Logs/Homebrew/lefse/02.python
If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/biobakery/homebrew-biobakery/issues

I have tried the fix suggested in issue #4; however I ran into the exact same problem as the other user. On more thoughts on this?

find / -name ft2build.h

/Users/keri/ds/macqiime/anaconda/include/freetype2/ft2build.h
/Users/keri/ds/macqiime/anaconda/pkgs/freetype-2.5.2-0/include/freetype2/ft2build.h
/Users/keri/ds/macqiime/anaconda/pkgs/freetype-2.5.2-2/include/freetype2/ft2build.h
/Users/keri/miniconda2/envs/qiime2-2017.10/include/freetype2/ft2build.h
/Users/keri/miniconda2/pkgs/freetype-2.7-1/include/freetype2/ft2build.h
/usr/local/Cellar/freetype/2.9/include/freetype2/ft2build.h

sudo ln -s /usr/local/Cellar/freetype/2.9/include/freetype2/ft2build.h /usr/include/

Password:
ln: /usr/include//ft2build.h: Operation not permitted

Problem installing biobakery tool suite on Mac

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

docker

Brewed strainphlan installation fails (Mac OS 10.14.3)

$ brew install strainphlan
==> Installing strainphlan from biobakery/biobakery
==> Downloading http://huttenhower.sph.harvard.edu/metaphlan2_downloads/strainphlan-2.6.0.tar.gz
Already downloaded: /Users/bede/Library/Caches/Homebrew/downloads/665a92b675629f1e4a81136ba2962c538a504a450e0e1379aeec9b65d152175a--strainphlan-2.6.0.tar.gz
==> Downloading https://bitbucket.org/biobakery/metaphlan2/downloads/strainphlan_homebrew_counter.txt
==> Downloading from https://bbuseruploads.s3.amazonaws.com/3a01cee1-3a04-4efc-9fd1-2172c21956d9/downloads/b00b4953-42c8-4435-b2c5-07fe1436cdbc/strainphlan_homebrew_counter.txt?Signature=o6w1DMFgMi%2BAJ
######################################################################## 100.0%
==> rm *counter.txt
==> Downloading https://github.com/stamatak/standard-RAxML/archive/v8.1.15.tar.gz
Already downloaded: /Users/bede/Library/Caches/Homebrew/downloads/8e2de4bccef007ed6cec726d90618179df6dec614f8edc30f0901f5973374459--standard-RAxML-8.1.15.tar.gz
==> make -f Makefile.gcc
==> make -f Makefile.PTHREADS.gcc
==> make -f Makefile.SSE3.PTHREADS.gcc
==> Downloading https://github.com/samtools/samtools/archive/0.1.19.tar.gz
Already downloaded: /Users/bede/Library/Caches/Homebrew/downloads/ecc8ea645f87a06b964bedbaab33eab6c5ec47e0aca745ce3b12113d19d74911--samtools-0.1.19.tar.gz
==> make
==> make -C bcftools
==> cp samtools bcftools/bcftools bcftools/vcfutils.pl /usr/local/Cellar/strainphlan/2.6.0/libexec/vendor/bin/
==> cp misc/maq2sam-long misc/maq2sam-short misc/md5fa misc/md5sum-lite misc/wgsim /usr/local/Cellar/strainphlan/2.6.0/libexec/vendor/bin/
==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.11.0.tar.gz
Already downloaded: /Users/bede/Library/Caches/Homebrew/downloads/179cce20524ad92a21a0b3252a0f9d0e9138b63153280bf8e6900ef6a9972a8d--numpy-1.11.0.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/strainphlan/2.6.0/libexec --install-scripts=/usr/local/Cellar/strainphlan/2.6.0/libexec/bin --single-version-external
Last 15 lines from /Users/bede/Library/Logs/Homebrew/strainphlan/09.python2:
2019-04-03 15:31:49 +0100

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
--install-scripts=/usr/local/Cellar/strainphlan/2.6.0/libexec/bin
--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

$

Executing "brew install biobakery_tool_suite" results in Python.h error

Following the directions in README.md, executing "brew install biobakery_tool_suite" command results in the following error pertaining to Python.h. "which python" and "python --version" confirm version as 2.7.11, and the command was executed in a vagrant VM:

<...snip...>
==> python -c import setuptools... --no-user-cfg install --prefix=/home/vagrant/
Last 15 lines from /home/vagrant/.cache/Homebrew/Logs/metaphlan2/01.python:
File "/tmp/metaphlan2--numpy20160509-26098-1x0zpd5/numpy-1.5.1/numpy/distutils/command/build_src.py", line 152, in run
self.build_sources()
File "/tmp/metaphlan2--numpy20160509-26098-1x0zpd5/numpy-1.5.1/numpy/distutils/command/build_src.py", line 169, in build_sources
self.build_extension_sources(ext)
File "/tmp/metaphlan2--numpy20160509-26098-1x0zpd5/numpy-1.5.1/numpy/distutils/command/build_src.py", line 328, in build_extension_sources
sources = self.generate_sources(sources, ext)
File "/tmp/metaphlan2--numpy20160509-26098-1x0zpd5/numpy-1.5.1/numpy/distutils/command/build_src.py", line 385, in generate_sources
source = func(extension, build_dir)
File "numpy/core/setup.py", line 402, in generate_config_h
moredefs, ignored = cocache.check_types(config_cmd, ext, build_dir)
File "numpy/core/setup.py", line 41, in check_types
out = check_types(_a, *_kw)
File "numpy/core/setup.py", line 263, in check_types
"Cannot compile 'Python.h'. Perhaps you need to "\

SystemError: Cannot compile 'Python.h'. Perhaps you need to install python-dev|python-devel.

The default install path is ~/.linuxbrew. I have verified the existence of Python.h, and I have tried soft-linking Python.h to ~/.linuxbrew/include. I have also tried to execute "brew install metaphlan2", and also executed "sudo yum install python-devel". None of these measures have resolved the problem.

Blas not found

File "scipy/integrate/setup.py", line 12, in configuration
blas_opt = get_info('blas_opt',notfound_action=2)
File "/home/venkat/.linuxbrew/Cellar/metaphlan2/2.6.0/libexec/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 372, in get_info
return cl().get_info(notfound_action)
File "/home/venkat/.linuxbrew/Cellar/metaphlan2/2.6.0/libexec/lib/python2.7/site-packages/numpy/distutils/system_info.py", line 566, in get_info
raise self.notfounderror(self.notfounderror.doc)
numpy.distutils.system_info.BlasNotFoundError:
Blas (http://www.netlib.org/blas/) libraries not found.
Directories to search for the libraries can be specified in the
numpy/distutils/site.cfg file (section [blas]) or by setting
the BLAS environment variable.

Failed to install hclust2 on Mac OS

hi,
I was trying to install hclust2 on my mac metaphlan-env. But I failed to install the hclust2.
Here are the logs:
(metaphlan-env) vcv075026:metaphlan a123$ brew install hclust2
==> Installing hclust2 from biobakery/biobakery
==> Installing dependencies for biobakery/biobakery/hclust2: bzip2
==> Installing biobakery/biobakery/hclust2 dependency: bzip2
==> Downloading https://homebrew.bintray.com/bottles/bzip2-1.0.6_1.mojave.bottle
######################################################################## 100.0%
==> Pouring bzip2-1.0.6_1.mojave.bottle.tar.gz
==> Caveats
bzip2 is keg-only, which means it was not symlinked into /usr/local,
because macOS already provides this software and installing another version in
parallel can cause all kinds of trouble.

If you need to have bzip2 first in your PATH run:
echo 'export PATH="/usr/local/opt/bzip2/bin:$PATH"' >> ~/.bash_profile

For compilers to find bzip2 you may need to set:
export LDFLAGS="-L/usr/local/opt/bzip2/lib"
export CPPFLAGS="-I/usr/local/opt/bzip2/include"

==> Summary
🍺 /usr/local/Cellar/bzip2/1.0.6_1: 26 files, 400.4KB
==> Installing biobakery/biobakery/hclust2
==> Downloading https://bitbucket.org/nsegata/hclust2/get/3d589ab2cb68.tar.gz
######################################################################## 100.0%
==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.
==> Downloading from https://files.pythonhosted.org/packages/84/fb/5e9dfeeb5d890
######################################################################## 100.0%
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Ce
Last 15 lines from /Users/a123/Library/Logs/Homebrew/hclust2/01.python2:
2018-11-26 08:35:58 -0800

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/hclust2/1.0.0-3d589ab/libexec
--install-scripts=/usr/local/Cellar/hclust2/1.0.0-3d589ab/libexec/bin
--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

Error: You have MacPorts or Fink installed:
/opt/local/bin/port

This can cause trouble. You don't have to uninstall them, but you may want to
temporarily move them out of the way, e.g.

sudo mv /opt/local ~/macports
(metaphlan-env) vcv075026:metaphlan a123$ sudo mv /opt/local ~/macports
Password:
(metaphlan-env) vcv075026:metaphlan a123$ brew install hclust2
==> Installing hclust2 from biobakery/biobakery
==> Downloading https://bitbucket.org/nsegata/hclust2/get/3d589ab2cb68.tar.gz
Already downloaded: /Users/a123/Library/Caches/Homebrew/downloads/fbb64c454c95e647ae50b5fc7db4af135f7a63e45a2ee555af40d5de5abd4797--nsegata-hclust2-3d589ab2cb68.tar.gz
==> Downloading https://pypi.python.org/packages/source/n/numpy/numpy-1.7.1.tar.
Already downloaded: /Users/a123/Library/Caches/Homebrew/downloads/32246c557b05158cfbb1b88f4aa555c35a721709caa7c670e99fe38e923a59fc--numpy-1.7.1.tar.gz
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Ce
Last 15 lines from /Users/a123/Library/Logs/Homebrew/hclust2/01.python2:
2018-11-26 08:41:30 -0800

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/hclust2/1.0.0-3d589ab/libexec
--install-scripts=/usr/local/Cellar/hclust2/1.0.0-3d589ab/libexec/bin
--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

(metaphlan-env) vcv075026:metaphlan a123$ brew install hclust2 --without-numpy
==> Installing hclust2 from biobakery/biobakery
==> Downloading https://bitbucket.org/nsegata/hclust2/get/3d589ab2cb68.tar.gz
Already downloaded: /Users/a123/Library/Caches/Homebrew/downloads/fbb64c454c95e647ae50b5fc7db4af135f7a63e45a2ee555af40d5de5abd4797--nsegata-hclust2-3d589ab2cb68.tar.gz
==> Downloading https://pypi.python.org/packages/source/s/scipy/scipy-0.12.0.tar.gz
==> Downloading from https://files.pythonhosted.org/packages/51/1c/d53b2c99f8dd94307ddc92772c7a696b045384c40e039240c24c3b2bae28/scipy-0.12.0.tar.gz
######################################################################## 100.0%
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/hclust2/1.0.0-3d589ab/libexec --install-scripts=/usr/local/Cellar/hclust2/1.0.0-3d589ab/libexec/bin --single-version-ex
Last 15 lines from /Users/a123/Library/Logs/Homebrew/hclust2/01.python2:
2018-11-26 08:44:24 -0800

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/hclust2/1.0.0-3d589ab/libexec
--install-scripts=/usr/local/Cellar/hclust2/1.0.0-3d589ab/libexec/bin
--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

(metaphlan-env) vcv075026:metaphlan a123$ brew install python
Error: python 3.7.0 is already installed
To upgrade to 3.7.1, run brew upgrade python
(metaphlan-env) vcv075026:metaphlan a123$ brew install hclust2 --without-numpy --verbose
==> Installing hclust2 from biobakery/biobakery
/usr/bin/sandbox-exec -f /private/tmp/homebrew20181126-40698-1bvuyn.sb nice /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby -W0 -I /usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/ruby-macho-2.1.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/rubocop-rspec-1.30.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/rubocop-0.60.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/unicode-display_width-1.4.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/ruby-progressbar-1.10.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/rainbow-3.0.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/powerpack-0.1.2/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/plist-3.4.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/parser-2.5.3.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/parallel-1.12.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/jaro_winkler-1.5.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/extensions/universal-darwin-18/2.3.0/jaro_winkler-1.5.1:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/backports-3.11.4/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/ast-2.4.0/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/activesupport-5.2.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/tzinfo-1.2.5/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/thread_safe-0.3.6/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/minitest-5.11.3/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/i18n-1.1.1/lib:/usr/local/Homebrew/Library/Homebrew/vendor/bundle-standalone/bundler/../ruby/2.3.0/gems/concurrent-ruby-1.0.5/lib:/Library/Ruby/Gems/2.3.0/gems/did_you_mean-1.0.0/lib:/Library/Ruby/Site/2.3.0:/Library/Ruby/Site/2.3.0/x86_64-darwin18:/Library/Ruby/Site/2.3.0/universal-darwin18:/Library/Ruby/Site:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/vendor_ruby/2.3.0:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/vendor_ruby/2.3.0/x86_64-darwin18:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/vendor_ruby/2.3.0/universal-darwin18:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/vendor_ruby:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/x86_64-darwin18:/System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/lib/ruby/2.3.0/universal-darwin18:/usr/local/Homebrew/Library/Homebrew -- /usr/local/Homebrew/Library/Homebrew/build.rb /usr/local/Homebrew/Library/Taps/biobakery/homebrew-biobakery/hclust2.rb --verbose --without-numpy
==> Downloading https://bitbucket.org/nsegata/hclust2/get/3d589ab2cb68.tar.gz
Already downloaded: /Users/a123/Library/Caches/Homebrew/downloads/fbb64c454c95e647ae50b5fc7db4af135f7a63e45a2ee555af40d5de5abd4797--nsegata-hclust2-3d589ab2cb68.tar.gz
==> Verifying fbb64c454c95e647ae50b5fc7db4af135f7a63e45a2ee555af40d5de5abd4797--nsegata-hclust2-3d589ab2cb68.tar.gz checksum
tar xf /Users/a123/Library/Caches/Homebrew/downloads/fbb64c454c95e647ae50b5fc7db4af135f7a63e45a2ee555af40d5de5abd4797--nsegata-hclust2-3d589ab2cb68.tar.gz -C /private/tmp/d20181126-40700-99cfwo
cp -pR /private/tmp/d20181126-40700-99cfwo/nsegata-hclust2-3d589ab2cb68/. /private/tmp/hclust2-20181126-40700-1nfmacm/nsegata-hclust2-3d589ab2cb68
chmod -Rf +w /private/tmp/d20181126-40700-99cfwo
==> Downloading https://pypi.python.org/packages/source/s/scipy/scipy-0.12.0.tar.gz
Already downloaded: /Users/a123/Library/Caches/Homebrew/downloads/9957d16b3f57d822d8b05f6f90017aabbdbfffca982b51fa9fbc241800f94282--scipy-0.12.0.tar.gz
==> Verifying 9957d16b3f57d822d8b05f6f90017aabbdbfffca982b51fa9fbc241800f94282--scipy-0.12.0.tar.gz checksum
tar xf /Users/a123/Library/Caches/Homebrew/downloads/9957d16b3f57d822d8b05f6f90017aabbdbfffca982b51fa9fbc241800f94282--scipy-0.12.0.tar.gz -C /private/tmp/d20181126-40700-1ps5ic0
cp -pR /private/tmp/d20181126-40700-1ps5ic0/scipy-0.12.0/. /private/tmp/hclust2--scipy-20181126-40700-jnet7e/scipy-0.12.0
chmod -Rf +w /private/tmp/d20181126-40700-1ps5ic0
==> python2 -c import setuptools... --no-user-cfg install --prefix=/usr/local/Cellar/hclust2/1.0.0-3d589ab/libexec --install-scripts=/usr/local/Cellar/hclust2/1.0.0-3d589ab/libexec/bin --single-version-externally-managed --record=installed.txt
Failed to execute: python2

==> Formula
Tap: biobakery/biobakery
Path: /usr/local/Homebrew/Library/Taps/biobakery/homebrew-biobakery/hclust2.rb
==> Configuration
HOMEBREW_VERSION: 1.8.4-3-g6f0ef7d
ORIGIN: https://github.com/Homebrew/brew
HEAD: 6f0ef7deecaf267277f315a4b70fb7277269728c
Last commit: 2 hours ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: e5def19d72af783c8c5e3e763afce0debb9dc51d
Core tap last commit: 2 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_DEV_CMD_RUN: 1
HOMEBREW_ENABLE_AUTO_UPDATE_MIGRATION: 1
CPU: quad-core 64-bit kabylake
Homebrew Ruby: 2.3.7 => /System/Library/Frameworks/Ruby.framework/Versions/2.3/usr/bin/ruby
Clang: 10.0 build 1000
Git: 2.17.2 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Curl: 7.54.0 => /usr/bin/curl
Java: 11
macOS: 10.14.1-x86_64
CLT: N/A
Xcode: 10.1
==> ENV
HOMEBREW_CC: clang
HOMEBREW_CXX: clang++
MAKEFLAGS: -j4
CMAKE_PREFIX_PATH: /usr/local/opt/bzip2:/usr/local
CMAKE_INCLUDE_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/libxml2:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/include/apache2:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Headers
CMAKE_LIBRARY_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks/OpenGL.framework/Versions/Current/Libraries
CMAKE_FRAMEWORK_PATH: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks
PKG_CONFIG_LIBDIR: /usr/lib/pkgconfig:/usr/local/Homebrew/Library/Homebrew/os/mac/pkgconfig/10.14
HOMEBREW_GIT: git
HOMEBREW_SDKROOT: /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk
ACLOCAL_PATH: /usr/local/share/aclocal
PATH: /usr/local/Homebrew/Library/Homebrew/shims/mac/super:/usr/local/opt/bzip2/bin:/usr/bin:/bin:/usr/sbin:/sbin

Error: biobakery/biobakery/hclust2 1.0.0-3d589ab did not build
Logs:
/Users/a123/Library/Logs/Homebrew/hclust2/00.options.out
/Users/a123/Library/Logs/Homebrew/hclust2/01.python2
If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
https://github.com/biobakery/homebrew-biobakery/issues

here are /Users/a123/Library/Logs/Homebrew/hclust2/00.options.out
/Users/a123/Library/Logs/Homebrew/hclust2/01.python2
👇
归档.zip

error: library dfftpack has Fortran sources but no Fortran compiler found

Hi. I am trying to install metaphlan2, but I get this issue:

Last 15 lines from /Users/natachacouto/Library/Logs/Homebrew/metaphlan2/04.python2:
customize IBMFCompiler
Could not locate executable xlf90
Could not locate executable xlf
customize IntelFCompiler
Could not locate executable ifort
Could not locate executable ifc
customize GnuFCompiler
Could not locate executable g77
customize G95FCompiler
Could not locate executable g95
customize PGroupFCompiler
Could not locate executable pgfortran
don't know how to compile Fortran code on platform 'posix'
building 'dfftpack' library
error: library dfftpack has Fortran sources but no Fortran compiler found

I have tried reinstalling gcc, linking it, but I can't get it working.
Can you help me?

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When I try to install GarPhlAn on my MacOS Sierra system, version 10.12.6, following this command, $ brew tap biobakery/biobakery $ brew install graphlan Here are the errors

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When I try to install GarPhlAn on my MacOS Sierra system, version 10.12.6, following this command,
$ brew tap biobakery/biobakery
$ brew install graphlan
Here are the errors