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‎presentation/linux_bash_metacentrum_course.tex

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@@ -4011,21 +4011,21 @@ \subsection{Packages}
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\item System has list of applications available
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\item Updates and bug fixes are installed for all applications using one interface (GUI or command line) --- very reliable
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\item Packages are digitally signed --- security
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\item User can set custom repositories to get new packages
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\item User can set custom repositories to get more package resources
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\item Repositories can be added whenever needed --- check documentation for your distribution (at least basic \enquote{how-to})
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\end{itemize}
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\item The most different task among distributions
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\item The most different task among Linux distributions
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\item Packages have dependencies --- required shared libraries and so on --- use package manager and try to avoid downloading packages from the internet outside repositories
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\item \alert{Read manual for your distribution!}
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\item Package is basically an archive and system has configured directories where to unpack it --- binaries are commonly in \texttt{/usr/bin/}, shared libraries in \texttt{/usr/lib} and \texttt{/sr/lib64}, data in \texttt{/var},~\ldots
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\item Package is basically an archive and system has configured directories where to unpack it --- binaries are commonly in \texttt{/usr/bin/}, shared libraries in \texttt{/usr/lib} and \texttt{/usr/lib64}, data in \texttt{/var},~\ldots
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\item User should not care where parts of packages go to --- system is taking the care --- user can only damage it
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\item Shared libraries are installed automatically whenever required
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\item As all files are placed in standard defined directories, it is very simple to use them also for another applications
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\item Applications not available in repositories, neither as distributional package should be installed into \texttt{$\sim$/bin} for current user or \texttt{/usr/local} for all users (binaries then go into \texttt{/usr/local/bin} and so on)
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\item Common distributions use to provide convenient graphical tool to manage software
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\begin{itemize}
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\item Ubuntu Software Center
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\item Synaptic --- feature rich, graphical, advances, for any DEB distribution
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\item Synaptic --- feature rich, graphical, advances, for any DEB distribution (Debian, Ubuntu, Mint,~\ldots)
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\item Aptitude --- feature rich, command-line, advanced, for any DEB distribution (more advanced version of Apt)
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\item DPKG --- low-level, any DEB-based distribution
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\item YaST Software for openSUSE (feature rich, graphical as well as command-line)
@@ -4048,29 +4048,31 @@ \subsection{Packages}
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\begin{frame}[allowframebreaks]{Package management in command line in openSUSE and SLE (basic commands)}
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\begin{itemize}
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\item Root password is required: use \texttt{sudo\ldots} or \texttt{su}~-
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\item Root password is required: use \texttt{sudo\ldots} or \texttt{su~-}
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\item Package name \texttt{*.rpm}
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\item \texttt{zypper in \textit{package}} --- install \textit{package}
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\item \texttt{zypper rm \textit{package}} --- remove \textit{package}
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\item \texttt{zypper ref} --- refresh repositories
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\item \texttt{zypper up} --- update
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\item \texttt{zypper dup} -- upgrade to newer release of whole distribution
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\item \texttt{zypper ps -s} -- check which running applications (including SystemD services) should be restarted after update of packages
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\item \texttt{zypper se \textit{term}} --- search \textit{term}
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\item \texttt{zypper} \texttt{pa -{-}orphaned -{-}unneeded} --- list packages, which can be safely removed
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\item \texttt{zypper pa -{-}orphaned -{-}unneeded} --- list packages, which can be safely removed
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\item \texttt{yast sw\_single} --- interactive manager
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\item \texttt{zypper lr} --- list repositories
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\item \texttt{zypper ar \textit{repository}} --- add \textit{repository} (URL of remote \texttt{*.repo} file)
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\item \texttt{zypper rr \textit{repository}} --- remove \textit{repository} (name according to \texttt{zypper lr})
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\item \texttt{zypper mr \textit{repository}} --- modify \textit{repository} (see \texttt{man zypper} first or use \texttt{yast sw\_single})
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\item \texttt{zypper pa \textit{package}} --- get information about particular \textit{package} or another query (e.g. list of dependencies, see \texttt{man zypper})
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\item \texttt{rpmconfigcheck} --- check which configuration files in \texttt{/etc} have new version after update of some software --- compare respective configuration files with new \texttt{*.rpmnew} files
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\item \texttt{rpm*} commands for other tasks
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\item \texttt{man zypper}, \texttt{man rpm} --- usage help
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\end{itemize}
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\end{frame}
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\begin{frame}[allowframebreaks]{Package management in command line in Debian/Ubuntu and derivatives (basic commands)}
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\begin{itemize}
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\item Root password is required: use \texttt{sudo\ldots} or \texttt{su}~-
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\item Root password is required: use \texttt{sudo\ldots} or \texttt{su~-}
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\item Package name \texttt{*.deb}
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\item \texttt{apt install \textit{package}} --- install \textit{package}
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\item \texttt{apt remove \textit{package}} --- remove \textit{package}
@@ -4085,7 +4087,7 @@ \subsection{Packages}
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\item \texttt{dpkg-*}, \texttt{apt-*} commands for other tasks
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\item \texttt{aptitude} is used in similar way as \texttt{apt} (e.g. \texttt{aptitude install \textit{package}},~\ldots)
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\item Similar tasks can be done with \texttt{apt}, \texttt{apt-get}, or \texttt{aptitude}
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\item \texttt{man aptitude}, \texttt{man apt-XXX} (e.g. \texttt{man apt}), \texttt{man dpkg-XXX}, \texttt{man apt} --- usage help
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\item \texttt{man aptitude}, \texttt{man apt-XXX}, \texttt{man dpkg-XXX}, \texttt{man apt} --- usage help
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\end{itemize}
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\end{frame}
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@@ -4106,18 +4108,18 @@ \subsection{Packages}
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\item \texttt{rpm -e \textit{package}} --- remove \textit{package}
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\item \texttt{rpm*} commands for other tasks
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\item In older releases of Fedora, RedHat and CENTOS, \texttt{yum} is used instead of \texttt{dnf} in nearly identical way
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\item \texttt{man dnf} (or \texttt{man dnf}), \texttt{man rpm} --- usage help
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\item \texttt{man dnf} (or \texttt{man yum}), \texttt{man rpm} --- usage help
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\end{itemize}
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\end{frame}
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\begin{frame}{Graphical package managers I}{Ubuntu Software, and Synaptic and text-based Aptitude for all DEB-based distributions}
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\begin{center}
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\includegraphics[width=\textwidth-4cm]{software_managers_ubuntu_deb.png}
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\includegraphics[height=6cm]{software_managers_ubuntu_deb.png}
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\end{center}
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\end{frame}
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\begin{frame}{Graphical package managers II}{GNOME Software in Fedora and YaST in openSUSE}
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\includegraphics[width=\textwidth-2cm]{software_managers_fedora_suse.png}
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\includegraphics[height=5.5cm]{software_managers_fedora_suse.png}
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\begin{itemize}
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\item Practically every common general distribution has some graphical tool\ldots{ }Explore it\ldots
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\end{itemize}
@@ -4137,7 +4139,7 @@ \subsection{Compilation}
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\begin{frame}[fragile]{Basics of compilation}
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\begin{itemize}
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\item Some software is distributed only as source code written in languages like C or C++ --- user has to compile it to get binary executable
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\item Some software is distributed only as source code (e.g. downloaded from GitHub) written in languages like C or C++ --- user has to compile it to get binary executable
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\item Compilation creates binary specific for particular operating system and hardware platform --- can be tuned for optimal performance
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\item Interpreted languages like Bash, Perl, Python or Java don't have to be compiled (but it is possible) --- they need their interpreter to run, relative easily portable among hardware platforms and OS
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\item Applications requiring compilation usually have good instructions
@@ -4157,8 +4159,8 @@ \subsection{Compilation}
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\item You need to install compilation tools for your distribution and programming languages you are going to use
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\item Commonly, extra dependencies are required to compile the application
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\begin{itemize}
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\item Packages for compilation use to end with -\texttt{dev} or -\texttt{devel} (e.g. if the software requires package \texttt{zlib} to run, install also its developmental version \texttt{zlib-dev(el)} to be able to compile it)
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\item All requirements should be listed in README or INSTALL documents of particular package --- user must install them manually\ldots
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\item Packages for compilation use to end with \texttt{-dev} or \texttt{-devel} (e.g. if the software requires package \texttt{zlib} to run, install also its developmental version \texttt{zlib-dev(el)} to be able to compile it)
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\item All requirements should be listed in README and/or INSTALL documents of particular package --- user must install them manually\ldots
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\end{itemize}
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\end{itemize}
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\vfill
@@ -4167,7 +4169,7 @@ \subsection{Compilation}
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zypper in -t pattern devel_basis devel_C_C++
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# Debian, Ubuntu and derivatives like Linux Mint and others
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apt-get install build-essential # Or "aptitude install build-essential"
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# Red Hat, CENTOS, Fedora and derivatives (2 options)
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# Red Hat, CENTOS, Fedora and derivatives (2 options - dnf or yum)
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dnf groupinstall "Development Tools" "C Development Tools and Libraries"
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yum groupinstall "Development Tools" "C Development Tools and Libraries"
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\end{bashcode}
@@ -4197,22 +4199,22 @@ \subsection{Compilation}
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\begin{frame}[fragile]{Compilation of SAMtools}
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\begin{itemize}
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\item See \url{http://www.htslib.org/download/}
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\item Ensure packages \texttt{zlib} and \texttt{zlib-dev(el) }are installed --- required for running and compilation, see \href{https://github.com/samtools/samtools/blob/master/INSTALL}{INSTALL} and \href{https://github.com/samtools/samtools/blob/master/README}{README}
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\item Ensure packages \texttt{zlib} and \texttt{zlib-dev(el)} are installed --- required for running and compilation, see \href{https://github.com/samtools/samtools/blob/master/INSTALL}{INSTALL} and \href{https://github.com/samtools/samtools/blob/master/README}{README}
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\end{itemize}
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\vfill
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\begin{bashcode}
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wget https://github.com/samtools/samtools/releases/download/1.10/
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samtools-1.10.tar.bz2 # Download SAMtools
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tar xjvf samtools-1.10.tar.bz2 # Unpack the archive
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cd samtools-1.10/ # Go to the unpacked directory
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./configure # Configure settings for compilation
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./configure --help # See various configuring options
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./configure # Configure settings for compilation (default settings)
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./configure --without-curses # Compile without ncurses support
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make # Compile the software - check if there is error
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# Ensure developmental files for zlib (and ncurses) are available
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make install # Copy products into final location - default /usr/local
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make prefix=/where/to/install install # Install into custom location
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make prefix=/home/$USER/bin install # Binary is in /home/$USER/bin/bin
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sudo make install # Copy products into final location - default /usr/local
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sudo make prefix=/where/to/install install # Install into custom location
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make prefix=/home/$USER/bin install # Binary into /home/$USER/bin/bin
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make clean # Cleanup - final files are already in the destination
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\end{bashcode}
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\end{frame}
@@ -4250,7 +4252,7 @@ \subsection{Windows applications}
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\item They must be written in portable language like Java or script like Perl, Python or BASH
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\item Otherwise we need an emulator --- not everything works
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\end{itemize}
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\item Windows 10 has \href{https://docs.microsoft.com/windows/wsl/install-win10}{possibility to run Linux applications}, other option (for more Windows versions) is \href{https://www.cygwin.com/}{Cygwin} (application must be specially compiled to support Cygwin)
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\item Windows 10 has \href{https://docs.microsoft.com/windows/wsl/install-win10}{possibility to run Linux applications}, other option (for more Windows versions) is \href{https://www.cygwin.com/}{Cygwin} (application must be specially compiled to work on Cygwin)
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\item To run Windows applications on Linux use \href{https://www.winehq.org/}{Wine}
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\begin{itemize}
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\item Search for packages named \texttt{wine} and install it
@@ -4274,14 +4276,14 @@ \subsection{Windows applications}
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\item For many Windows-only applications there are fully comparable alternatives
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\end{itemize}
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\item Some applications do not work under Wine (from various reasons), some complex packages are \href{https://www.codeweavers.com/}{supported commercially} (I~have no experience with it)
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\item Wine is well compatible with rest of the Linux hosting system, it is considerable to install Windows in e.g. VirtualBox (or another virtualization platform), if needed
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\item Wine is well compatible with rest of the Linux hosting system, but it is also considerable to install Windows in e.g. VirtualBox (or another virtualization platform), if needed
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\end{itemize}
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\end{frame}
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\begin{frame}{winefile, winetricks and winecfg}
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\begin{center}
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\includegraphics[width=\textwidth-3.5cm]{wine.png}
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\includegraphics[height=3.25cm]{wine.png}
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\end{center}
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\begin{flushright}
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\texttt{winefile}, \texttt{winetricks} and \texttt{winecfg}
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\end{flushright}
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\end{frame}
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\section{MetaCentrum}

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