How to install blasr on Mac OS X?

Question

I am trying to install blasr on mac osx.

I followed the steps here

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

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 — llrs, Jan 24, 2018 at 8:04
according to this, there's only a conda recipe for linux-64, not osx-64 — heathobrien, Jan 25, 2018 at 15:44
@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 — Biomagician, Jan 25, 2018 at 16:03
If I were you, I'd give this a try: github.com/muccg/docker-blasr — heathobrien, Jan 25, 2018 at 16:10
• update •conda install -c bioconda blasr, okay in June 2022 on z shell of macos — envs_h_gang_5, Jun 24, 2022 at 6:29

heathobrien · Accepted Answer · 2018-01-25 16:27:52Z

3

The path of least resistance is probably to run the software inside a container. If you install docker, 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)

answered Jan 25, 2018 at 16:27

heathobrien

1,8167 silver badges16 bronze badges

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Wouter De Coster · Accepted Answer · 2018-01-25 11:34:43Z

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

answered Jan 25, 2018 at 11:34

Wouter De Coster

1,3147 silver badges12 bronze badges

$\begingroup$ I added my trial with conda in my question. Did it succeed on Max OSX for you? $\endgroup$
– Biomagician
Jan 25, 2018 at 15:42
$\begingroup$ 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 $\endgroup$
– Biomagician
Jan 25, 2018 at 16:02
$\begingroup$ This seems like a missing library on the server. Did you try to install (or get installed) packages related to libhdf5? $\endgroup$
– llrs
Jan 25, 2018 at 17:05
$\begingroup$ @charlesdarwin I used conda to install it on CentOS Linux, and it indeed seems unavailable for Mac OSX. Oops, sorry! $\endgroup$
– Wouter De Coster
Jan 26, 2018 at 7:44

Add a comment |

llrs · Accepted Answer · 2018-01-24 13:49:13Z

1

is there reason why you want to compile it by your own? You can install blasr though homebrew and brewsci/science tap :

brew tap brewsci/science
brew install blasr

edited Jan 24, 2018 at 13:49

llrs

4,6921 gold badge18 silver badges42 bronze badges

answered Jan 24, 2018 at 13:34

Kamil S Jaron

5,4971 gold badge23 silver badges59 bronze badges

$\begingroup$ I edited my question to include the error from homebrew. $\endgroup$
– Biomagician
Jan 24, 2018 at 22:01
$\begingroup$ 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. $\endgroup$
– Kamil S Jaron
Jan 25, 2018 at 12:43

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