Prerequisites for building software/conda packages

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---

# Prerequisites for building software/conda packages

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  <a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-abretaud"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" />
    Anthony Bretaudeau</a>
  
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---

### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- What does 'installing a software' means on a Linux architecture?

- Why my compilations always fail?

- How to solve common compiling and installation issues?

---

### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Learn how to compile and install tools using standard procedures.

- Learn needed tricks to write conda build.sh files.

---

### Environment variables

```sh
$ MY_NAME="Bobby"
$ echo $MY_NAME
Bobby
```

```sh
$ MY_DATE=$(date)
$ echo $MY_DATE
Wed Feb 14 12:12:21 CET 2018
```

Use export to make sure the variable is accessible to any script/program you run from the current shell.

```sh
$ export MY_DATE=$(date)
$ echo $MY_DATE
Wed Feb 14 12:12:21 CET 2018
$ bash some_script.sh # some_script.sh will have access to $MY_DATE
```

Many environment variables predefined in a shell: PATH, HOSTNAME, HOME, LANG, USER, ...

---

### Show me the PATH

```sh
$ the_binary --help
```

How does the system knows where to find the binary?

PATH is an environment variable defining possible locations of binaries.

```sh
$ echo $PATH
/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
```

Paths separated by `:`, ordered list (highest priority first).

As all environment variable, you can redefine it:

```sh
$ export PATH="/opt/xxx/bin/:$PATH"
$ echo $PATH
/opt/xxx/bin/:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin
```

---

### Show me the PATH

The command `which` lets you know which binary will be used by your shell.

```sh
$ which the_binary
/opt/xxx/bin/the_binary
```

It throws an error if the binary is not "in the PATH".

```sh
$ export PATH="/usr/bin/"
$ echo $PATH
/usr/bin
```
```sh
$ which the_binary
/usr/bin/which: no the_binary in (/usr/bin)
```

---

### Thinking outside the PATH

What if you want to run a binary only located in the current working directory?

```sh
$ ls
my_binary
$ my_binary --help
bash: my_binary: command not found...
```

You need to add `./` to explicitly tell the shell to run the file from working directory:

```sh
$ ./my_binary --help
It works!
```

`./` is just the relative path to `my_binary`, it could be a more complicated one, or an absolute path:

```sh
$ ../somewhere/my_binary --help
It works!
$ /home/someone/womewhere/my_binary --help
It works!
```

---

### Installing a single binary

Just a single executable file (binary, script).

You only need to copy it to a `bin` directory and make sure permissions are set:

```sh
$ cp the_binary /usr/local/bin
$ chmod a+x /usr/local/bin/the_binary
```

Other possible `bin` directories:

```sh
/bin            = reserved for system
/usr/bin        = installed by package manager (apt, yum, ...)
/usr/local/bin  = manually installed binaries
/opt/xxx/bin    = manually installed binaries (xxx=path)
/yyy/bin        = a bin directory wherever you like (yyy=path)
```

.center[.footnote[If you install a precompiled binary, make sure that it was compiled for the same architecture as your system (e.g. x86_64)]]

---

### Compiling a single binary

In the following slides we consider a program written in `C`.

Usually, compilation is done with `make`.

```sh
$ ls
Makefile    my_program.c
```
```sh
$ make
```
```sh
$ ls
Makefile    my_program.c    my_binary
```

`make` will read the instructions defined in the file `Makefile` and run the compiler automatically to produce the binary.

You can then copy the binary to a bin dir.

Some exotic tools come with other scripts or methods for compiling, read the README or INSTALL files.

---

### Compiling a library

Libraries are reusable chunks of code. They are not executable as is. They are compiled similarly as binaries.

```sh
$ ls
Makefile    my_lib.c    my_lib.h
```
```sh
$ make
```
```sh
$ ls
Makefile    my_lib.c    my_lib.h    libmy.so.1.2.8
```

`.h` files are code files defining which functions are provided by the library.

`.so` are compiled binary code. Their file name structure is important: `libXXXX.so.version`.

---

### Installing a library

```sh
$ cp libmy.so.1.2.8 /usr/local/lib/
```

Some symbolic links need to be created:

```sh
$ ln -s /usr/local/lib/libmy.so.1.2.8 /usr/local/lib/libmy.so
$ ln -s /usr/local/lib/libmy.so.1.2.8 /usr/local/lib/libmy.so.1
```

You also need to install `headers` in a `include` dir:

```sh
$ cp my_lib.h /usr/local/include/
```

Other possible `lib` (or `lib64`) directories (same principle for `include`):

```sh
/lib(64)            = reserved for system
/usr/lib(64)        = installed by package manager (apt, yum, ...)
/usr/local/lib(64)  = manually installed
/opt/xxx/lib(64)    = manually installed (xxx=path)
/yyy/lib(64)        = a lib directory wherever you like (yyy=path)
```

---

### make install

Copying/symlinking manually each file is painful.

Running `make install` usually install everything automatically for you.

```sh
$ make
$ make install
```

By default, installs to `/usr/local`. We will see how to change this later.

---

### Compiling a binary that uses an external library

For example, if your program relies on `zlib` to read or create gzipped files.

`make` needs to know where are the `.h` and `.so` files to compile your program properly.

Usually, a script named 'configure' is distributed with the program sources.

```sh
$ ls
configure   Makefile    my_program.c
```

This script explores the filesystem to find the needed `.h` and `.so` files. You can then run `make` and `make install` as usual.

```sh
$ ./configure
$ make
$ make install
```

Sometimes, `configure` is replaced by another software like cmake.

---

### Playing with ./configure

You can pass many options to the `configure` script.

A very common one is `--prefix` which allows to change the installation directory.

```sh
$ ./configure --prefix=/home/somewhere
$ make
$ make install
```

The binary will be installed in `/home/somewhere/bin/`

If you are compiling a library, files will be installed in `/home/somewhere/include/` and `/home/somewhere/lib(64)/`

---

### Playing with ./configure

You can pass many options to the `configure` script.

You can often disable or enable some software features this way.

```sh
$ ./configure --disable-gpu --enable-greedy-algorithm
$ make
$ make install
```

---

### Playing with ./configure

By default, `configure` only searches for `.h` and `.so` files in standard directories (`/usr/`, `/usr/local`).

If your program depends on a library installed in an exotic location, you need to specify it.

There might be a specific `configure` option.

```sh
$ ./configure --zlib-dir=/home/somewhere/zlib/
```

Or, you can define some standard environment variables:

```sh
$ export CFLAGS="-I/home/somewhere/zlib/include $CFLAGS"
$ export LDFLAGS="-L/home/somewhere/zlib/lib $LDFLAGS"
```

In some cases, you might need to define additional variables:

```sh
$ export CPATH="/home/somewhere/zlib/include:$CPATH"
$ export LIBRARY_PATH="/home/somewhere/zlib/lib:$LIBRARY_PATH"
```

---

### Playing with ./configure

The `CFLAGS` environment variable can also be used for other purposes like enabling some compiler optimisation, predefining some C macro or compiling with debugging symbols.

```sh
$ export CFLAGS="-I/home/somewhere/zlib/include -O2 -DDEBUG -g"
```

When you are compiling C++ code, you need to use `CXXFLAGS` instead of `CFLAGS`.

---

### Shebang

The first line of script is called the [shebang](https://en.wikipedia.org/wiki/Shebang_%28Unix%29).

```sh
#!/bin/bash
```

It determines how your script will be run when called in a shell.

```sh
$ my_script.sh
$ # is interpreted as
$ /bin/bash /usr/bin/my_script.sh
```

---

### Shebang

You need to write an absolute path in the shebang. But never do this:

```sh
#!/usr/bin/python
```

Because you are not sure /usr/bin/python will always be at this location. Preferred solution:

```sh
#!/usr/bin/env python
```

This will ensure to use the `python` found using the PATH environment variable.

`/bin/bash` or `/usr/bin/env` are considered to always be present.

---

### Python/Perl/R packages

Installing Python modules consists in placing the source files in the correct path inside the Python installation.

For example BioPython code will be installed in `/usr/lib/python3.6/site-packages/Bio/`

Some Python modules consists both of Python code and C code that need to be compiled.

Python modules are usually installed with specific setup mechanisms that take care of it all for you.

```sh
$ pip install my_module
```

```sh
$ cd my_module_src/
$ python setup.py install
```

Perl or R modules are installed in similar ways.

---

### Common error: Undefined symbol

Symptom: you get an `Undefined symbol` while running an installed program.

Cause: the program uses a library which is not available in the expected location.

To list all the libraries needed by the program and identify the one causing the problem:

```sh
$ ldd `which nano`
	linux-vdso.so.1 (0x00007ffdfb48c000)
	libmagic.so.1 => not found
	libncursesw.so.6 => /lib64/libncursesw.so.6 (0x00007f16cbb54000)
```

Make sure the library is correctly installed. If it is installed in an exotic location, use the `LD_LIBRARY_PATH` environment.

```sh
$ export LD_LIBRARY_PATH="/home/somewhere/magic/:$LD_LIBRARY_PATH"
$ ldd `which nano`
	linux-vdso.so.1 (0x00007ffdfb48c000)
	libmagic.so.1 => /home/somewhere/magic/lib/libmagic.so.1
	libncursesw.so.6 => /lib64/libncursesw.so.6 (0x00007f16cbb54000)
```

---
### <i class="fas fa-key" aria-hidden="true"></i><span class="visually-hidden">keypoints</span> Key points

- There is a common procedure to compile and install many tools: `./configure && make && make install`

- Some exotic tools require adjustements to compile or install properly

- Pay attention to INSTALL and README files, and to documentation

---

## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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  <a href="/training-material/hall-of-fame/abretaud/" class="contributor-badge contributor-abretaud"><img src="/training-material/assets/images/orcid.png" alt="orcid logo" width="36" height="36"/><img src="https://avatars.githubusercontent.com/abretaud?s=36" alt="Anthony Bretaudeau avatar" width="36" class="avatar" />
    Anthony Bretaudeau</a>
  
  <a href="/training-material/hall-of-fame/cmonjeau/" class="contributor-badge contributor-cmonjeau"><img src="https://avatars.githubusercontent.com/cmonjeau?s=36" alt="Cyril Monjeaud avatar" width="36" class="avatar" />
    Cyril Monjeaud</a>
  
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