Question: 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)][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][2]

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.

[1]: http://www.clustal.org/omega/clustal-omega-1.2.1.tar.gz
[2]: http://prdownloads.sourceforge.net/argtable/argtable2-13.tar.gz

Answer: 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][1]. If you are on OS X Yosemite, you might use [these instructions][2] to set up the CLT. Or you can just download and install CLT [via the Apple Developer Connection site][3].

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
```

[1]: http://osxdaily.com/2014/02/12/install-command-line-tools-mac-os-x/
[2]: http://railsapps.github.io/xcode-command-line-tools.html
[3]: https://developer.apple.com/library/ios/technotes/tn2339/_index.html#//apple_ref/doc/uid/DTS40014588-CH1-DOWNLOADING_COMMAND_LINE_TOOLS_IS_NOT_AVAILABLE_IN_XCODE_FOR_OS_X_10_9__HOW_CAN_I_INSTALL_THEM_ON_MY_MACHINE_