Download Clustal Omega on Mac OS

Question

[thorerges]

Hello Everyone,

I have a very basic question. Having little experience in Command Line, I am stumped on practically the first step. I am downloading the following file from the Clustal Omega website: Source code .tar.gz (1.2.1)

However, to run this in terminal, I have to install argtable2. So I went and downloaded the following from the website: argtable2-13.tar.gz

I placed both these into a single folder, and in terminal setup the directory to the argtable2 folder via

cd /filepath

and typed:

./configure

A ton of checks are done which ends like this:

configure: creating ./config.status
config.status: creating Makefile
config.status: creating example/Makefile
config.status: creating src/Makefile
config.status: creating doc/Makefile
config.status: creating doc/argtable2.3
config.status: creating doc/argtable2.html
config.status: creating tests/Makefile
config.status: creating argtable2.pc
config.status: creating argtable2-uninstalled.pc
config.status: creating src/config.h
config.status: src/config.h is unchanged
config.status: executing depfiles commands
config.status: executing libtool commands
nat-oitwireless-inside-vapornet100-c-20170:argtable2-13 Plosslab$ make
Making all in src
/Library/Developer/CommandLineTools/usr/bin/make  all-am
Making all in tests
make[1]: Nothing to be done for `all'.
Making all in doc
cp argtable2.3 argtable.3    
make[1]: Nothing to be done for `all-am'.

I then set the directory to the clustalO folder and configure and it ends like this:

Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path

The INSTALL text file says I should type this line:

./configure CFLAGS='-I/opt/local/include' LDFLAGS='-L/opt/local/lib'

I then get the following error:

configure: error: Could not find argtable2.h. Try $ ./configure CFLAGS='-Iyour-argtable2-include-path

I try to follow the recommendation as such:

./configure CFLAGS='-/lab/argtable2-13'

And finally I get the following error, and I am stumped:

checking whether the C compiler works... no
configure: error: in `/Users/lab/argtable2-13':
configure: error: C compiler cannot create executables

Anyone have any ideas as to why this isn't working? Did I download the wrong version of argtable? Am I typing in the wrong commands? Any advice would be thoroughly appreciated.

[Ram]

Looks like you either don't have permissions in the argtable dir or the argtable dir has its include elsewhere. Could you paste the output of ls -lR ~/lab/argtable2-13 please?

[thorerges]

ls: /Users/lab/lab/argtable2-13: No such file or directory

​Is what I get, strange that the file "lab" shows up twice, even though its one folder.

[thorerges]

So I typed this command in

ls -lR ~/argtable2-13

I am getting a ton of lines (about 100), is there anything I should be looking for in this?

[Ram]

Try Andreas' solution from below. We can debug further if that doesn't work. I am trying to verify the directory structure and look into your permissions on the argtable directory - especially if you have write and execute permissions on appropriate files. You can either copy paste the output of the command I gave you here or look for permissions by yourself.

Just check if you have a readable 'include' dir within the argtable dir and the argtable dir itself is w+x

[Alex Reynolds]

Do you have Xcode and its command-line utilities installed? You may need a C compiler (which is part of Xcode and its command-line utilities). See: https://developer.apple.com/library/ios/technotes/tn2339/_index.html

[thorerges]

Ok I have tried this approach. I followed this answer to actually get Xcode because I use 10.9.3, basically up until

sudo make install

http://stackoverflow.com/questions/19579401/php-xdebug-on-os-x-10-9-mavericks/19664507#19664507

It looks ok, I get the following output:

$ xcode-select --install
xcode-select: note: install requested for command line developer tools

I try to configure the clustalo file again and I get the exact same error.

checking for C compiler default output file name... 
configure: error: in `/Users/lab/clustalo':
configure: error: C compiler cannot create executables
See `config.log' for more details.

[Alex Reynolds]

I'm not really sure what to suggest other than to look at the config.log file and see what's going on there.

[Ram]

Maybe OP has an older version of XCode and needs to install CLT for the latest version? Maybe check gcc --version?

[Andreas]

Please clarify whether you want to compile Clustal Omega or just use it. The download link you provided is for the binary.

PS: OP changed link to source code

Answer 1

[Alex Reynolds]

What works for me:

1. Install Xcode and then install the command-line utilities, which adds Clang and Clang++ and related tools (basically, the equivalent of the GCC compiler kit for the purposes of compiling and building C and C++ projects).

If you are on OS X Mavericks, you can install the command-line tools directly via the Terminal via these instructions. If you are on OS X Yosemite, you might use these instructions to set up the CLT. Or you can just download and install CLT via the Apple Developer Connection site.

2. Once the CLT are installed, install Homebrew:

$ ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

3. Use Homebrew to install argtable:

$ brew install argtable

4. Once argtable is installed, download source for Clustal Omega, unpack it and compile it:

$ wget -qO- http://www.clustal.org/omega/clustal-omega-1.2.1.tar.gz > clustal-omega-1.2.1.tar.gz
$ tar zxvf clustal-omega-1.2.1.tar.gz
...
$ cd clustal-omega-1.2.1
$ ./configure CFLAGS="-I/usr/local/include" LDFLAGS="-L/usr/local/lib" --prefix="/usr/local"
...
$ make
...
$ sudo make install
...

Clustal Omega is now in /usr/local/bin:

$ which clustalo
/usr/local/bin/clustalo
$ clustalo --version
1.2.1

[cjcoope2]

Took me 2 days to find your response, and now ClustalO is working like a charm. Thank you for this!

[Ram]

I wished to avoid homebrew as OP is a command line beginner, but I guess it solves most problems!

[thorerges]

Thank you so much for this, I am beginning to think I have been denied access somehow. After installing argtable (at least according to your instructions), I try the following command:

$ wget -qO- http://www.clustal.org/omega/clustal-omega-1.2.1.tar.gz > clustal-omega-1.2.1.tar.gz

The result I get is:

-bash: clustal-omega-1.2.1.tar.gz: Permission denied

I am not sure what is the cause of this, I might have to figure out whether I have permission or not. Or perhaps I just don't have GNU Wget? I have to give it a shot.

[Alex Reynolds]

You probably have wget or you'd get a different error.

Most likely, you are in a directory where your user account does not have permissions to write data. So change to a directory where you do have write permission. You could do something like:

$ cd

to get to your home directory, for instance. Or you could do all of this work in the /tmp directory:

$ cd /tmp

If you still get permission errors, you should speak to your system administrator and find out if there are problems with your account.

[Alastair]

This worked perfectly, thank you!!

Answer 2

[Andreas]

The link you used is for the ClustalO executable file. There's no need to run configure or install anything. From the Clustal website: "UNIX and Mac users should rename the downloaded file to clustalo and place in the location of their choice. This file may need to be made executable e.g.: chmod u+x clustalo"

It seems you additionally downloaded the source code which you have to compile first after installing some dependencies. It's easier to download the binary as you already did and make it executable as described above. Afterwards you just have to type ./clustalo

Andreas

PS: OP changed link to source code

Answer 3

[Alex Reynolds]

If you want to avoid Homebrew for installing argtable, you can compile it directly:

1. Install wget, if necessary:

$ brew install wget

2. Download source code for argtable:

$ wget -qO- http://prdownloads.sourceforge.net/argtable/argtable2-13.tar.gz > argtable2-13.tar.gz
...
$ tar zxvf argtable2-13.tar.gz
...

3. Configure the build script, using /usr/local as the prefix:

$ cd argtable2-13
$ ./configure --prefix="/usr/local"

4. Build and install:

$ make
...
$ sudo make install

5. Build and install clustalo per instructions in previous answer (pointing CFLAGS and LDFLAGS to /usr/local subdirectories)

[thorerges]

Thank you so much! I got it to work! Much appreciated everyone!

Answer 4

[Nate]

For anyone hoping to install on newer mac arm64 / M1 / M2 platforms so you can have a native version—and if you also are using Homebrew —you may need to change your links to the lib and include folders. This is only true if you've followed Homebrew's recommended install for arm64/M1 platforms which puts everything in /opt/homebrew/... instead of /usr/local/homebrew... like it used to in the past.

Here's the sequence of commands that worked for me:

brew install argtable
./configure CFLAGS='-I/opt/homebrew/include' LDFLAGS='-L/opt/homebrew/lib'
make
make install

NOTE: This will still install to /usr/local/bin, which is fine as long as that's in your $PATH variable.