I am trying to download STAR for RNA seq. After I installed gcc 8.2, and inputting this command on terminal
make STARforMacStatic CXX=/Users/local/Cellar/gcc/8.3.0/bin/g++-8
It keeps responding
make: *** No rule to make target `STARforMacStatic'. Stop.
How do I get this work?
These days, you really don't need to be downloading and manually managing things like gcc or building STAR. Instead, install Bioconda (i.e., Miniconda + bioconda and conda-forge channels), then it's just a matter of
conda install star
If you use brew (like sugest README file), this path (CXX=/Users/local/Cellar/gcc/8.3.0/bin/g++-8).
Copy and paste command from README file:
$make STARforMacStatic CXX=/usr/local/Cellar/gcc/8.2.0/bin/g++-8
Path to brew files is /usr/local/Cellar. Mine:
alex#vosjod:/usr/local/Cellar$ ls -1
adns
aom
bash-completion
bashmarks
ctags
erlang
exiftool
ffmpeg
fontconfig
freetype
frei0r
fribidi
gdbm
gettext
git
gmp
gnupg
gnutls
go
icu4c
jpeg
...
Related
I am having a problem where I can't specify options for installing a formula with brew.
Specifically
brew install gnuplot --with-qt results in a invalid option: --with-qt and when I look at brew info gnuplot there is no option available:
$ brew info gnuplot
gnuplot: stable 5.2.6 (bottled), HEAD
Command-driven, interactive function plotting
http://www.gnuplot.info/
Not installed
From: https://github.com/Homebrew/homebrew-core/blob/master/Formula/gnuplot.rb
==> Dependencies
Build: pkg-config ✔
Required: gd ✔, libcerf ✔, lua ✔, pango ✔, qt ✔, readline ✔
==> Options
--HEAD
Install HEAD version
However, I get all indication from the documentation, and thousands of Andrew Ng's machine learning course students that there are some optional flags I could specify. I've tried all sorts of updating and upgrading, and nothing under brew doctor seems to be relevant. I've installed very many things with brew in the past (though ultimately I'm not very sure of the inner workings)
$ brew --version
Homebrew 2.0.1
Homebrew/homebrew-core (git revision 1204; last commit 2019-02-09)
Homebrew/homebrew-cask (git revision 8d29a; last commit 2019-02-09)
mac os 10.14.2 Mojave
Any ideas on where to start investigating would be helpful.
Unfortunately, options have been removed recently, more about it can be found here: Remove all options from Homebrew/homebrew-core formulae
My recommendation would be to use MacPorts as it's generally much easier to install.
$ port variant gnuplot
gnuplot has the variants:
[+]aquaterm: Enable AquaTerm terminal
[+]luaterm: Enable lua-based terminals
old_bitmap_terminals: Enable PBM (Portable Bit Map) and other older bitmap terminals
[+]pangocairo: Enable cairo-based terminals
qt: Enable qt terminal with Qt 4
* conflicts with qt5
qt5: Enable qt terminal with Qt 5
* conflicts with qt
universal: Build for multiple architectures
[+]wxwidgets: Enable wxt terminal
[+]x11: Enable X11 support
Note: In the description it states that qt conflicts with qt5, so you'll want to use one or the other.
So based upon that output you can see there are several "variants" available to install. To use qt:
$ sudo port install gnuplot +qt
If you also wanted to install x11 with qt you could do:
$ sudo port install gnuplot +qt +x11
For now, the option --with-qt is applied by default when you do brew install gnuplot.
As you can see in the following source code of gnuplot hombrew formula.
args = %W[
--disable-dependency-tracking
--disable-silent-rules
--prefix=#{prefix}
--with-readline=#{Formula["readline"].opt_prefix}
--without-tutorial
--disable-wxwidgets
--with-qt
--without-x
]
system "./configure", *args
This can be changed in the future. You can check the source code of gnuplot formula here:
https://github.com/Homebrew/homebrew-core/blob/master/Formula/gnuplot.rb
I am trying to install gphoto2 on my macbook pro. I installed the tar.gz from their website and from terminal I cd Downloads and run ./configure as the README file recommends doing. I keep receiving this error:
checking for pkg-config... false
configure: error:
*** Build requires pkg-config
***
*** Possible solutions:
*** - set PKG_CONFIG to where your pkg-config is located
*** - set PATH to include the directory where pkg-config is installed
*** - get it from http://freedesktop.org/software/pkgconfig/ and install it
I have Xcode 6 installed, as well as Command Line tools (tested it by running gcc in terminal). What am I doing wrong? What should I do?
Also, should I install gphoto2 or libgphoto2?
I wouldn't bother faffing around with building it yourself. I would install homebrew from here.
Then you can simply do
brew install gphoto2
and you will also have a decent package manager if you want to install other cool stuff later on - e.g. ImageMagick, gawk, GNU sed, swatch, youtube-downloader, wxWidgets, vips, redis, sox, ffmpeg. To find other cool stuff that can be managed with homebrew just do
brew search
I am trying to install ROOT (cern.root.ch). When I run ./configure , I get a message that libX11 is missing and must be installed.
I did some research and found that I need to install
) XQuartz (I already have the latest version.)
) Command line tools in Xcode.
I tried installing Command Line Tools from apple's developer website. The installation goes through smoothly but how do I know whether it has been installed? I still get libX11 missing error with root's configure command.
I also tried xcode-select --install and it once went through smoothly and then later again gives error saying this package is no longer maintained - or something of that sort.
I understand I may have multiple installations... But I am still facing the problem of not having libX11 and not being able to install ROOT.
Thanks,
Hershal.
This link and the one referenced in it suggests you use homebrew (brew) to install it
$ ruby <(curl -fsS https://raw.github.com/mxcl/homebrew/go)
$ brew doctor
Remember to add the Homebrew directory to your PATH by adding the directory (found with brew --prefix) to your .bashrc, .zshrc or whatever shell file you’re using (.bashrc is the OS X default). We’ll also add the XQuartz binaries to the PATH in case anything needs them in the future.
export PATH=/usr/local/bin:/opt/X11/bin:$PATH
Start a new Terminal session to pick up the changes.
Now that Homebrew is installed, we can use it to install the required dependencies. Each may take some time as Homebrew generally compiles from source.
$ brew install gfortran # Fortran compiler
$ brew install python # Python interpreter
$ brew install pcre # Regular Expressions library
$ brew install fftw # Fast Fourier Transforms
$ brew install cmake # Cross-platform make
install root
$ brew tap homebrew/science
$ brew install --with-cocoa root
You don't say whether you have installed XCode as well as the commandline tools but I think you will need it
I am trying to install tesseract on my mac using homeBrew. When I try installing, everything seems to be good but I get the following error/message:
Warning: Could not link leptonica. Unlinking...
Error: The `brew link` step did not complete successfully
The formula built, but is not symlinked into /usr/local
You can try again using `brew link leptonica'
When I try running a tesseract function, I get the following error:
Tesseract Open Source OCR Engine v3.02.02 with Leptonica
Error in pixReadStreamPng: function not present
Error in pixReadStream: png: no pix returned
Error in pixRead: pix not read
Unsupported image type.
I have image magick installed and the command I used to install tesseract was:
brew install tesseract
Can anyone please tell me what I can do to get tesseract working? Thank you!
EDIT
When I run brew link leptonica, I get the following error:
Could not symlink file: /usr/local/Cellar/leptonica/1.69/bin/yuvtest
Target /usr/local/bin/yuvtest already exists. You may need to delete it.
Now, as of September 2019, there are no longer any optional install flags available
brew options tesseract
yield nothing. But,
brew info tesseract
yields the following key info:
This formula contains only the "eng", "osd", and "snum" language data files.
If you need all the other supported languages, `brew install tesseract-lang`.
Therefore, to get all of the languages installed, you need to now install a separate library called tesseract-lang.
Updated installation:
brew install tesseract
brew install tesseract-lang
Hope this helps.
old in case this is useful:
Now, as of January 2019, Tesseract installs fine via homebrew, as long as you have xquartz installed first, brew cask install xquartz. Then you can do the following: brew install tesseract --with-all-languages --with-serial-num-pack --with-training-tools
After installing / removing and re-installing tesseract i found the solution for the same problem you have. On your terminal logs, while installing tesseract, you will see:
Error: The brew link step did not complete successfully
The formula built, but is not symlinked into /usr/local
Could not symlink bin/convertfilestopdf
Target /usr/local/bin/convertfilestopdf
already exists.
You may want to remove it:
rm '/usr/local/bin/convertfilestopdf'
To force the link and overwrite all conflicting files:
brew link --overwrite leptonica
To list all files that would be deleted:
brew link --overwrite --dry-run leptonica
What i did was running: brew link --overwrite leptonica
"Linking /usr/local/Cellar/leptonica/1.71_1... 45 symlinks created"
Everything should work perfectly.
Hope this can be a help for you
It sounds a bit silly, but have you tried deleting yuvtest? I just tried it myself - the file is automatically generated by brew link leptonica. As for why it isn't working, is it possible you had some version of leptonica/tesseract installed previously? Another reasonable guess at a fix would be
brew uninstall tesseract; brew install tesseract
So far as I know, image magick being installed shouldn't matter for tesseract. They don't have anything in common.
Tesseract is now dependent on Leptonica being installed.
The error messages you are seeing relate to these files:
Leptonica is configured to handle image I/O using these external libraries: libjpeg, libtiff, libpng, libz, libgif, libwebp.
These libraries are easy to obtain. For example, using the debian package manager:
sudo apt-get install
where = {libpng12-dev, libjpeg62-dev, libtiff4-dev}.
Source: Leptonica unofficial documentation
I found that homebrew would install some but not all of the libraries.
Trying to follow the directions from: http://github.com/zeromq/jzmq
I installed pkg-config using Homebrew and then I run the following commands:
./autogen.sh
./configure
The configure fails with:
checking how to hardcode library paths into programs... immediate
./configure: line 15263: syntax error near unexpected token `newline'
./configure: line 15263: ` PKG_CHECK_MODULES('
A better solution is:
eval `brew --config | grep HOMEBREW_PREFIX | sed 's/: /=/'`
sudo bash -c 'echo '$HOMEBREW_PREFIX/share/aclocal' >> `aclocal --print-ac-dir`/dirlist'
This will allow the version of aclocal that ships with OSX to find any macros installed by homebrew packages.
With homebrew, the key is the warning message:
~/code/foss/java/jzmq$ brew install pkg-config
==> Downloading http://pkg-config.freedesktop.org/releases/pkg-config-0.25.tar.gz
==> ./configure --disable-debug --prefix=/usr/local/Cellar/pkg-config/0.25 --with-pc-path=/usr/local/lib/pkgconfig:/usr/lib/pkgconfig:/usr/X11/lib/pkgconfig
==> make install
Warning: m4 macros were installed to "share/aclocal".
Homebrew does not append "/usr/local/share/aclocal"
to "/usr/share/aclocal/dirlist". If an autoconf script you use
requires these m4 macros, you'll need to add this path manually.
==> Summary
/usr/local/Cellar/pkg-config/0.25: 8 files, 232K, built in 19 seconds
If you look at /usr/local/Cellar/pkg-config/0.25/share/aclocal/, you will see:
$ ls /usr/local/Cellar/pkg-config/0.25/share/aclocal/
pkg.m4
You need to append /usr/local/Cellar/pkg-config/0.25/share/aclocal/ to /usr/share/aclocal/dirlist,like this:
$ cat /usr/share/aclocal/dirlist
/usr/local/share/aclocal
/usr/local/Cellar/pkg-config/0.25/share/aclocal/
And then re-run autogen and the other steps.
I made a simple list about jzmq building for MacOS.
Install brew
https://brew.sh
Install tools for jzmq building
brew install autoconf
brew install automake
brew install libtool
brew install pkg-config
brew install zeromq#3.2
Download jzmq source
https://github.com/zeromq/jzmq source download to ~/somewhere/jzmq
Add symbolic link to /usr/local/include
cd /usr/local/include
ln -s /usr/local/Cellar/zeromq\#3.2/3.2.5/include/zmq.h
ln -s /usr/local/Cellar/zeromq\#3.2/3.2.5/include/zmq_utils.h
Add symbolic linke to /usr/local/lib
cd /usr/local/lib
ln -s /usr/local/Cellar/zeromq\#3.2/3.2.5/lib/libzmq.3.dylib
ln -s /usr/local/Cellar/zeromq\#3.2/3.2.5/lib/libzmq.a
ln -s /usr/local/Cellar/zeromq\#3.2/3.2.5/lib/libmq.dylib
ln -s /usr/local/Cellar/zeromq\#3.2/3.2.5/lib/pkgconfig/
Build jzmq-jni
cd ~/somewhere/jzmq
cd jzmq-jni
./autogen.sh
./configure
make
make install
Add option to VM options
VM options -Djava.library.path=/usr/local/lib
From the zeromq mailing list:
Building 0MQ from the development
trunk on a UNIX style OS (Linux, OS X)
requires that pkg-config
(http://pkg-config.freedesktop.org/wiki/)
be installed. A regular source build
of 0MQ does not require pkg-config.
On Mac OS X, pkg-config does not come
with the system, so when you try to do
./configure you may see errors like:
./configure: line 23913: syntax error near unexpected token `GLIB,'
./configure: line 23913: `PKG_CHECK_MODULES(GLIB, glib-2.0 gthread-2.0)'
To resolve this, you need to install
the latest pkg-config:
tar xzf pkg-config-0.25.tar.gz
cd pkg-config-0.25
./configure --prefix=/usr/local/pkg-config-0.25 --datarootdir=/usr/share
make
sudo make install
Then you will need to put
/usr/local/pkg-config-0.25/bin on your
$PATH. It is important to include the
"--datarootdir=/usr/share" option,
which will install the pkg.m4 file in
/usr/share/aclocal, where aclocal will
be able to find it.
Then you can build 0MQ:
cd zeromq2
./autogen.sh # must do this again after installing pkg-config
./configure # add other options here
make
sudo make install
Edited to reflect latest pkg-config version (0.25).
I came here with the same question, and I don't feel this is answered. I also installed ZeroMQ and pkg-config via Homebrew. /usr/local/share/aclocal/pkg.m4 exists and comes from pkg-config 0.25. It seems that Homebrew has satisfied the requirements listed but it still fails.
Trying to compile jzmq on Mac OS X, proved to be a bit of a headache. I followed the instructions above. I was still getting following error
syntax error near unexpected token
`PKG_CHECK_MODULES
The instructions above tell you to copy the pkgk.m4 file into /usr/share/aclocal, but your directory might be different. Basically you need the dir that automake searches for macro definitions.
The _PKG_CHECK_MODULES_ macro is defined in the pkg.m4 file. This file must be installed in the appropriate directory, which is searched by automake. Somehow automake is installed twice on my OS X, one in /usr and another in /Developer/usr. Make sure you know which one it's using. Just do which automake. If yours in is /Developer/usr, then copy the pkg.m4 file to /Developer/usr/share/aclocal.
For me, the problem was that I didn't have pkg-config installed.
On Osx Mountain Lion I don't have the dirlist file as Phil Calçado said, but a simple symlink from /usr/local/Cellar/pkg-config/[version]/share/aclocal/pkg.m4 to /usr/share/aclocal made the trick and now jzmq build fine.