Answers.Body: <p>I've had many issues with installing blasr on my own, but it's a breeze using (bio)conda, see <a href="https://anaconda.org/bioconda/blasr" rel="nofollow noreferrer">https://anaconda.org/bioconda/blasr</a></p>
  
  <pre><code>conda install -c bioconda blasr 
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-25T15:42:05.590Z
Answers.Text: I added my trial with conda in my question. Did it succeed on Max OSX for you?
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-25T16:02:19.663Z
Answers.Text: I tried in on a GNU/Linux server and got this message after firing up blasr's help: blasr -h
  blasr: error while loading shared libraries: libhdf5_cpp.so.12: cannot open shared object file: No such file or directory
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-25T17:05:45.473Z
Answers.Text: This seems like a missing library on the server. Did you try to install (or get installed) packages related to `libhdf5`?
Answers.UserDisplayName: llrs
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-26T07:44:08.310Z
Answers.Text: @charlesdarwin I used conda to install it on CentOS Linux, and it indeed seems unavailable for Mac OSX. Oops, sorry!
Answers.UserDisplayName: Wouter De Coster
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-25T11:34:43.123Z
Answers.LastActivityDate: 2018-01-25T11:34:43.123Z
Answers.UserDisplayName: Wouter De Coster
Answers.Body: <p>is there reason why you want to compile it by your own? You can install blasr though <a href="https://brew.sh/" rel="nofollow noreferrer">homebrew</a> and <a href="https://github.com/brewsci/homebrew-science" rel="nofollow noreferrer">brewsci/science</a> tap :</p>
  
  <pre><code>brew tap brewsci/science
  brew install blasr
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-24T22:01:50.643Z
Answers.Text: I edited my question to include the error from homebrew.
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-25T12:43:01.937Z
Answers.Text: Unfortunately I do not know what is this error, I guess it will be some Xcode-Homebrew versions incompatibility. Best would be to ask directly at github page of homebrew.
Answers.UserDisplayName: Kamil S Jaron
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-24T13:34:56.503Z
Answers.LastActivityDate: 2018-01-24T13:49:13.163Z
Answers.LastEditDate: 2018-01-24T13:49:13.163Z
Answers.UserDisplayName: Kamil S Jaron
Answers.Body: <p>The path of least resistance is probably to run the software inside a container. If you install <a href="https://store.docker.com/editions/community/docker-ce-desktop-mac" rel="nofollow noreferrer">docker</a>, you can just do the following:</p>
  
  <pre><code>git clone https://github.com/muccg/docker-blasr.git
  docker-blasr/bin/blasr
  </code></pre>
  
  <p>(this worked for me on OSX 10.11.6)</p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-25T16:27:52.093Z
Answers.LastActivityDate: 2018-01-25T16:27:52.093Z
Answers.UserDisplayName: heathobrien
Body: <p>I am trying to install blasr on mac osx.</p>
  
  <p>I followed the steps <a href="https://github.com/PacificBiosciences/pitchfork/wiki" rel="nofollow noreferrer">here</a></p>
  
  <p>I get the error below after using the 'make' command:</p>
  
  <pre><code>make PREFIX=/tmp/pitchfork blasr
  Cloning into 'pitchfork'...
  remote: Counting objects: 10203, done.
  remote: Compressing objects: 100% (51/51), done.
  remote: Total 10203 (delta 25), reused 51 (delta 18), pack-reused 10128
  Receiving objects: 100% (10203/10203), 1.16 MiB | 207.00 KiB/s, done.
  Resolving deltas: 100% (5413/5413), done.
  /Applications/Xcode.app/Contents/Developer/usr/bin/make -f mk/init.mk init
  /Users/cr517/Documents/pitchfork/bin/checkSystem
  /Users/cr517/Documents/pitchfork/bin/checkCC gcc
  mkdir -p "/Users/cr517/Documents/pitchfork/workspace"
  mkdir -p "/Users/cr517/Documents/pitchfork/distfiles"
  mkdir -p "/Users/cr517/Documents/pitchfork/staging"
  mkdir -p "/tmp/pitchfork/bin"
  mkdir -p "/tmp/pitchfork/etc"
  mkdir -p "/tmp/pitchfork/include"
  mkdir -p "/tmp/pitchfork/lib"
  mkdir -p "/tmp/pitchfork/lib/pkgconfig"
  mkdir -p "/tmp/pitchfork/share"
  mkdir -p "/tmp/pitchfork/var/pkg"
  echo "export DYLD_LIBRARY_PATH=/tmp/pitchfork/lib:\$DYLD_LIBRARY_PATH"|sed -e 's/::*/:/g' &gt; "/tmp/pitchfork/setup-env.sh"
  echo "export PATH=/tmp/pitchfork/bin:\$PATH"|sed -e 's/::*/:/g' &gt;&gt; "/tmp/pitchfork/setup-env.sh"
  echo "OLDPS1=\$PS1" &gt;&gt; "/tmp/pitchfork/setup-env.sh"
  echo "[[ \"\$PS1\" ]] &amp;&amp; PS1=\"pitchfork($(/Users/cr517/Documents/pitchfork/bin/pitchfork short-branch)) \$PS1\" || PS1=\($(/Users/cr517/Documents/pitchfork/bin/pitchfork short-branch)\)" &gt;&gt; "/tmp/pitchfork/setup-env.sh"
  touch mk//../initialized.o
  /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/zlib do-install
  make[1]: Nothing to be done for `do-install'.
  /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/libbzip2 do-install
  rm -rf /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6
  mkdir -p /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/pkgconfig /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/include /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/bin
  cp -aL /usr/bin/bzip2 /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/bin/
  cp -aL /usr/include/bzlib.h /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/include
  cp -aL /usr/lib/libbz2.* /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib
  ln -sfn libbz2.dylib.1.0 /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/libbz2.dylib.1
  ln -sfn libbz2.dylib.1   /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/libbz2.dylib
  sed -e "s@^prefix=.*@prefix=/tmp/pitchfork@" bzip2.pc &gt; /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/pkgconfig/bzip2.pc
  cd /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6 &amp;&amp; tar cf - * | tar xf - -C /tmp/pitchfork
  find /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6 ! -type d|awk -F '/Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/' '{print $2}' &gt; /tmp/pitchfork/var/pkg/libbzip2-1.0.6
  /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/boost do-install
  /Users/cr517/Documents/pitchfork/bin/pitchfork fetch --url https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
  fetching https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
  {'url': 'https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz', 'subcommand': 'fetch'}
  Traceback (most recent call last):
    File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 525, in &lt;module&gt;
      sys.exit(main())
    File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 518, in main
      pitchfork(pargs)
    File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 444, in pitchfork
      raise Exception("[ERROR] %s" % ''.join(_err))
  Exception: [ERROR] --2018-01-24 00:35:30--  https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
  Resolving prdownloads.sourceforge.net... 216.34.181.59
  Connecting to prdownloads.sourceforge.net|216.34.181.59|:443... connected.
  ERROR: cannot verify prdownloads.sourceforge.net's certificate, issued by ‘CN=COMODO RSA Domain Validation Secure Server CA,O=COMODO CA Limited,L=Salford,ST=Greater Manchester,C=GB’:
    Unable to locally verify the issuer's authority.
  To connect to prdownloads.sourceforge.net insecurely, use `--no-check-certificate'.
  make[1]: *** [boost_1_60_0.tar.gz] Error 1
  make: *** [boost] Error 2
  </code></pre>
  
  <p>I think the important info is here:</p>
  
  <pre><code>raise Exception("[ERROR] %s" % ''.join(_err))
      Exception: [ERROR] --2018-01-24 00:35:30--  https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
      Resolving prdownloads.sourceforge.net... 216.34.181.59
      Connecting to prdownloads.sourceforge.net|216.34.181.59|:443... connected.
      ERROR: cannot verify prdownloads.sourceforge.net's certificate, issued by ‘CN=COMODO RSA Domain Validation Secure Server CA,O=COMODO CA Limited,L=Salford,ST=Greater Manchester,C=GB’:
        Unable to locally verify the issuer's authority.
      To connect to prdownloads.sourceforge.net insecurely, use `--no-check-certificate'.
  </code></pre>
  
  <p>but how can I specify the --no-check-certificate option? That's not a make option, I've tried it.</p>
  
  <p>I tried homebrew but got this message:</p>
  
  <pre><code>Updating Homebrew...
  ==&gt; Auto-updated Homebrew!
  Updated 2 taps (caskroom/cask, caskroom/versions).
  Warning: Calling 'depends_on :mysql' is deprecated!
  Use 'depends_on "mysql"' instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blat.rb:19:in `&lt;class:Blat&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling 'depends_on :python3' is deprecated!
  Use 'depends_on "python3"' instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/matplotlib.rb:56:in `&lt;class:Matplotlib&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in &lt;class:Plink&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in &lt;class:Plink&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in &lt;class:Plink&gt;'
  Please report this to the brewsci/science tap!
  
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  ==&gt; Installing blasr from brewsci/science
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  Warning: Calling &lt;&lt;-EOS.undent is deprecated!
  Use &lt;&lt;~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in &lt;class:Blasr&gt;'
  Please report this to the brewsci/science tap!
  
  ==&gt; Downloading https://github.com/PacificBiosciences/blasr/archive/smrtanalysis
  Already downloaded: /Users/cr517/Library/Caches/Homebrew/blasr-2.2.tar.gz
  ==&gt; make STATIC= HDF5INCLUDEDIR=/usr/local/opt/hdf5/include HDF5LIBDIR=/usr/loca
  Last 15 lines from /Users/cr517/Library/Logs/Homebrew/blasr/01.make:
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4912:1: note: candidate template ignored: could not match 'shared_ptr&lt;type-parameter-0-0&gt;' against 'const RegionAnnotation'
  operator&lt;(const shared_ptr&lt;_Tp&gt;&amp; __x, const shared_ptr&lt;_Up&gt;&amp; __y) _NOEXCEPT
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4977:1: note: candidate template ignored: could not match 'shared_ptr&lt;type-parameter-0-0&gt;' against 'const RegionAnnotation'
  operator&lt;(const shared_ptr&lt;_Tp&gt;&amp; __x, nullptr_t) _NOEXCEPT
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4985:1: note: candidate template ignored: could not match 'shared_ptr&lt;type-parameter-0-0&gt;' against 'const int'
  operator&lt;(nullptr_t, const shared_ptr&lt;_Tp&gt;&amp; __x) _NOEXCEPT
  ^
  1 error generated.
  make[1]: *** [bin/KBandMatcher.o] Error 1
  make: *** [alignment-build] Error 2
  make: *** [sequtils-build] Error 2
  clang++  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include bin/PrintPBBWT.o -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -lz -lpthread
  clang++  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include bin/BWTQuery.o -o bin/bwtquery -L/usr/local/opt/hdf5/lib -lz -lpthread
  
  If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
  https://github.com/brewsci/homebrew-science/issues
  </code></pre>
  
  <p>I still need to report the issue at the provided address.</p>
  
  <p>I tried Anaconda 'conda install -c bioconda blasr ':</p>
  
  <pre><code>PackageNotFoundError: Packages missing in current channels:
  
    - blasr
  
  We have searched for the packages in the following channels:
  
    - https://conda.anaconda.org/bioconda/osx-64
    - https://conda.anaconda.org/bioconda/noarch
    - https://conda.anaconda.org/conda-forge/osx-64
    - https://conda.anaconda.org/conda-forge/noarch
    - https://conda.anaconda.org/r/osx-64
    - https://conda.anaconda.org/r/noarch
    - https://repo.continuum.io/pkgs/main/osx-64
    - https://repo.continuum.io/pkgs/main/noarch
    - https://repo.continuum.io/pkgs/free/osx-64
    - https://repo.continuum.io/pkgs/free/noarch
    - https://repo.continuum.io/pkgs/r/osx-64
    - https://repo.continuum.io/pkgs/r/noarch
    - https://repo.continuum.io/pkgs/pro/osx-64
    - https://repo.continuum.io/pkgs/pro/noarch
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-24T08:04:55.097Z
Comments.Text: You need to have the certificate to download (securely) the files. Maybe you can try to do download it via wget to obtain the certificate and then check again with make to install it
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T15:44:33.123Z
Comments.Text: according to [this](https://anaconda.org/bioconda/blasr), there's only a conda recipe for linux-64, not osx-64
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T16:03:34.987Z
Comments.Text: @heathobrien, ok, but I've got this error after I install it on Linux. blasr -h
  blasr: error while loading shared libraries: libhdf5_cpp.so.12: cannot open shared object file: No such file or directory
Comments.UserDisplayName: Biomagician
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-01-25T16:10:43.323Z
Comments.Text: If I were you, I'd give this a try: https://github.com/muccg/docker-blasr
Comments.UserDisplayName: heathobrien
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2022-06-24T06:29:45.247Z
Comments.Text: • update •`conda install -c bioconda blasr`,  okay in June 2022 on z shell of macos
Comments.UserDisplayName: envs_h_gang_5
Tags: <errors><pacbio><software-installation><blasr>
Title: How to install blasr on Mac OS X?
ThreadText: # How to install blasr on Mac OS X?
  
  (Asked by: username_0 on 2018-01-24)
  
  I am trying to install blasr on mac osx.
  
  I followed the steps [here](https://github.com/PacificBiosciences/pitchfork/wiki)
  
  I get the error below after using the 'make' command:
  
  ```
  make PREFIX=/tmp/pitchfork blasr
  Cloning into 'pitchfork'...
  remote: Counting objects: 10203, done.
  remote: Compressing objects: 100% (51/51), done.
  remote: Total 10203 (delta 25), reused 51 (delta 18), pack-reused 10128
  Receiving objects: 100% (10203/10203), 1.16 MiB | 207.00 KiB/s, done.
  Resolving deltas: 100% (5413/5413), done.
  /Applications/Xcode.app/Contents/Developer/usr/bin/make -f mk/init.mk init
  /Users/cr517/Documents/pitchfork/bin/checkSystem
  /Users/cr517/Documents/pitchfork/bin/checkCC gcc
  mkdir -p "/Users/cr517/Documents/pitchfork/workspace"
  mkdir -p "/Users/cr517/Documents/pitchfork/distfiles"
  mkdir -p "/Users/cr517/Documents/pitchfork/staging"
  mkdir -p "/tmp/pitchfork/bin"
  mkdir -p "/tmp/pitchfork/etc"
  mkdir -p "/tmp/pitchfork/include"
  mkdir -p "/tmp/pitchfork/lib"
  mkdir -p "/tmp/pitchfork/lib/pkgconfig"
  mkdir -p "/tmp/pitchfork/share"
  mkdir -p "/tmp/pitchfork/var/pkg"
  echo "export DYLD_LIBRARY_PATH=/tmp/pitchfork/lib:\$DYLD_LIBRARY_PATH"|sed -e 's/::*/:/g' > "/tmp/pitchfork/setup-env.sh"
  echo "export PATH=/tmp/pitchfork/bin:\$PATH"|sed -e 's/::*/:/g' >> "/tmp/pitchfork/setup-env.sh"
  echo "OLDPS1=\$PS1" >> "/tmp/pitchfork/setup-env.sh"
  echo "[[ \"\$PS1\" ]] && PS1=\"pitchfork($(/Users/cr517/Documents/pitchfork/bin/pitchfork short-branch)) \$PS1\" || PS1=\($(/Users/cr517/Documents/pitchfork/bin/pitchfork short-branch)\)" >> "/tmp/pitchfork/setup-env.sh"
  touch mk//../initialized.o
  /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/zlib do-install
  make[1]: Nothing to be done for `do-install'.
  /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/libbzip2 do-install
  rm -rf /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6
  mkdir -p /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/pkgconfig /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/include /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/bin
  cp -aL /usr/bin/bzip2 /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/bin/
  cp -aL /usr/include/bzlib.h /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/include
  cp -aL /usr/lib/libbz2.* /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib
  ln -sfn libbz2.dylib.1.0 /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/libbz2.dylib.1
  ln -sfn libbz2.dylib.1   /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/libbz2.dylib
  sed -e "s@^prefix=.*@prefix=/tmp/pitchfork@" bzip2.pc > /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/lib/pkgconfig/bzip2.pc
  cd /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6 && tar cf - * | tar xf - -C /tmp/pitchfork
  find /Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6 ! -type d|awk -F '/Users/cr517/Documents/pitchfork/staging/libbzip2-1.0.6/' '{print $2}' > /tmp/pitchfork/var/pkg/libbzip2-1.0.6
  /Applications/Xcode.app/Contents/Developer/usr/bin/make -C ports/thirdparty/boost do-install
  /Users/cr517/Documents/pitchfork/bin/pitchfork fetch --url https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
  fetching https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
  {'url': 'https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz', 'subcommand': 'fetch'}
  Traceback (most recent call last):
    File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 525, in <module>
      sys.exit(main())
    File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 518, in main
      pitchfork(pargs)
    File "/Users/cr517/Documents/pitchfork/bin/pitchfork", line 444, in pitchfork
      raise Exception("[ERROR] %s" % ''.join(_err))
  Exception: [ERROR] --2018-01-24 00:35:30--  https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
  Resolving prdownloads.sourceforge.net... 216.34.181.59
  Connecting to prdownloads.sourceforge.net|216.34.181.59|:443... connected.
  ERROR: cannot verify prdownloads.sourceforge.net's certificate, issued by ‘CN=COMODO RSA Domain Validation Secure Server CA,O=COMODO CA Limited,L=Salford,ST=Greater Manchester,C=GB’:
    Unable to locally verify the issuer's authority.
  To connect to prdownloads.sourceforge.net insecurely, use `--no-check-certificate'.
  make[1]: *** [boost_1_60_0.tar.gz] Error 1
  make: *** [boost] Error 2
  
  ```
  
  I think the important info is here:
  
  ```
  raise Exception("[ERROR] %s" % ''.join(_err))
      Exception: [ERROR] --2018-01-24 00:35:30--  https://prdownloads.sourceforge.net/boost/boost_1_60_0.tar.gz
      Resolving prdownloads.sourceforge.net... 216.34.181.59
      Connecting to prdownloads.sourceforge.net|216.34.181.59|:443... connected.
      ERROR: cannot verify prdownloads.sourceforge.net's certificate, issued by ‘CN=COMODO RSA Domain Validation Secure Server CA,O=COMODO CA Limited,L=Salford,ST=Greater Manchester,C=GB’:
        Unable to locally verify the issuer's authority.
      To connect to prdownloads.sourceforge.net insecurely, use `--no-check-certificate'.
  
  ```
  
  but how can I specify the --no-check-certificate option? That's not a make option, I've tried it.
  
  I tried homebrew but got this message:
  
  ```
  Updating Homebrew...
  ==> Auto-updated Homebrew!
  Updated 2 taps (caskroom/cask, caskroom/versions).
  Warning: Calling 'depends_on :mysql' is deprecated!
  Use 'depends_on "mysql"' instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blat.rb:19:in `<class:Blat>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling 'depends_on :python3' is deprecated!
  Use 'depends_on "python3"' instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/matplotlib.rb:56:in `<class:Matplotlib>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/plink.rb:23:in `block in <class:Plink>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  ==> Installing blasr from brewsci/science
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:27:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  Warning: Calling <<-EOS.undent is deprecated!
  Use <<~EOS instead.
  /usr/local/Homebrew/Library/Taps/brewsci/homebrew-science/Formula/blasr.rb:36:in `block in <class:Blasr>'
  Please report this to the brewsci/science tap!
  
  ==> Downloading https://github.com/PacificBiosciences/blasr/archive/smrtanalysis
  Already downloaded: /Users/cr517/Library/Caches/Homebrew/blasr-2.2.tar.gz
  ==> make STATIC= HDF5INCLUDEDIR=/usr/local/opt/hdf5/include HDF5LIBDIR=/usr/loca
  Last 15 lines from /Users/cr517/Library/Logs/Homebrew/blasr/01.make:
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4912:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const RegionAnnotation'
  operator<(const shared_ptr<_Tp>& __x, const shared_ptr<_Up>& __y) _NOEXCEPT
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4977:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const RegionAnnotation'
  operator<(const shared_ptr<_Tp>& __x, nullptr_t) _NOEXCEPT
  ^
  /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include/c++/v1/memory:4985:1: note: candidate template ignored: could not match 'shared_ptr<type-parameter-0-0>' against 'const int'
  operator<(nullptr_t, const shared_ptr<_Tp>& __x) _NOEXCEPT
  ^
  1 error generated.
  make[1]: *** [bin/KBandMatcher.o] Error 1
  make: *** [alignment-build] Error 2
  make: *** [sequtils-build] Error 2
  clang++  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include bin/PrintPBBWT.o -o bin/bwtpbPrint -L/usr/local/opt/hdf5/lib -lz -lpthread
  clang++  -O3 -Wno-div-by-zero -I ..//common -I /usr/local/opt/hdf5/include bin/BWTQuery.o -o bin/bwtquery -L/usr/local/opt/hdf5/lib -lz -lpthread
  
  If reporting this issue please do so at (not Homebrew/brew or Homebrew/core):
  https://github.com/brewsci/homebrew-science/issues
  
  ```
  
  I still need to report the issue at the provided address.
  
  I tried Anaconda 'conda install -c bioconda blasr ':
  
  ```
  PackageNotFoundError: Packages missing in current channels:
  
    - blasr
  
  We have searched for the packages in the following channels:
  
    - https://conda.anaconda.org/bioconda/osx-64
    - https://conda.anaconda.org/bioconda/noarch
    - https://conda.anaconda.org/conda-forge/osx-64
    - https://conda.anaconda.org/conda-forge/noarch
    - https://conda.anaconda.org/r/osx-64
    - https://conda.anaconda.org/r/noarch
    - https://repo.continuum.io/pkgs/main/osx-64
    - https://repo.continuum.io/pkgs/main/noarch
    - https://repo.continuum.io/pkgs/free/osx-64
    - https://repo.continuum.io/pkgs/free/noarch
    - https://repo.continuum.io/pkgs/r/osx-64
    - https://repo.continuum.io/pkgs/r/noarch
    - https://repo.continuum.io/pkgs/pro/osx-64
    - https://repo.continuum.io/pkgs/pro/noarch
  
  ```
  
  **Tags:** errors, pacbio, software-installation, blasr
  
  > **Comments:**
  > **username_1**: You need to have the certificate to download (securely) the files. Maybe you can try to do download it via wget to obtain the certificate and then check again with make to install it  
  > **username_2**: according to [this](https://anaconda.org/bioconda/blasr), there's only a conda recipe for linux-64, not osx-64  
  > **username_0**: @username_2, ok, but I've got this error after I install it on Linux. blasr -h blasr: error while loading shared libraries: libhdf5_cpp.so.12: cannot open shared object file: No such file or directory  
  > **username_2**: If I were you, I'd give this a try: https://github.com/muccg/docker-blasr  
  > **username_3**: • update •`conda install -c bioconda blasr`,  okay in June 2022 on z shell of macos  
  
  ---
  
  ## 3 answers
  
  ### Answer by username_2 on 2018-01-25. Score: 3 | Accepted answer
  
  The path of least resistance is probably to run the software inside a container. If you install [docker](https://store.docker.com/editions/community/docker-ce-desktop-mac), you can just do the following:
  
  ```
  git clone https://github.com/muccg/docker-blasr.git
  docker-blasr/bin/blasr
  
  ```
  
  (this worked for me on OSX 10.11.6)
  
  
  ---
  
  ### Answer by username_4 on 2018-01-25. Score: 2
  
  I've had many issues with installing blasr on my own, but it's a breeze using (bio)conda, see <https://anaconda.org/bioconda/blasr>
  
  ```
  conda install -c bioconda blasr 
  
  ```
  
  > **Comments:**
  > **username_0**: I added my trial with conda in my question. Did it succeed on Max OSX for you?  
  > **username_0**: I tried in on a GNU/Linux server and got this message after firing up blasr's help: blasr -h blasr: error while loading shared libraries: libhdf5_cpp.so.12: cannot open shared object file: No such file or directory  
  > **username_1**: This seems like a missing library on the server. Did you try to install (or get installed) packages related to `libhdf5`?  
  > **username_4**: @charlesdarwin I used conda to install it on CentOS Linux, and it indeed seems unavailable for Mac OSX. Oops, sorry!  
  
  ---
  
  ### Answer by username_5 on 2018-01-24. Score: 1
  
  is there reason why you want to compile it by your own? You can install blasr though [homebrew](https://brew.sh/) and [brewsci/science](https://github.com/brewsci/homebrew-science) tap :
  
  ```
  brew tap brewsci/science
  brew install blasr
  
  ```
  
  > **Comments:**
  > **username_0**: I edited my question to include the error from homebrew.  
  > **username_5**: Unfortunately I do not know what is this error, I guess it will be some Xcode-Homebrew versions incompatibility. Best would be to ask directly at github page of homebrew.  
  
  ---
  
  