Commit 2cf16262 authored by Mihai's avatar Mihai

Update practicals including also #1

parent 9948b0de
\documentclass{article} \documentclass{article}
\usepackage{graphicx} \usepackage{graphicx}
\usepackage[hidelinks]{hyperref} \usepackage[hidelinks]{hyperref}
\usepackage{../shared/handouts} \usepackage{../shared/handouts}
\input{../shared/shared} \usepackage{xcolor}
\input{../shared/shared}
\usepackage[utf8]{inputenc} \usepackage[utf8]{inputenc}
\pagenumbering{arabic} \pagenumbering{arabic}
...@@ -14,7 +15,7 @@ ...@@ -14,7 +15,7 @@
\newcommand\cleartooddpage{\clearpage \newcommand\cleartooddpage{\clearpage
\ifodd\value{page}\else\null\clearpage\fi} \ifodd\value{page}\else\null\clearpage\fi}
\begin{document} \begin{document}
\vspace*{3cm} \vspace*{3cm}
...@@ -39,18 +40,18 @@ ...@@ -39,18 +40,18 @@
Welcome to the \textbf{Practical Linux} course! Welcome to the \textbf{Practical Linux} course!
\medskip \medskip
Designed for researchers, including PhD students and postdocs, this course Designed for researchers, including PhD students and postdocs, this course
provides attendees with an introduction to the Linux operating system. Linux provides attendees with an introduction to the Linux operating system. Linux
powers more than 90\% of the world’s supercomputers, most internet servers, powers more than 90\% of the world’s supercomputers, most internet servers,
and more than a billion Android devices. Additionally, bioinformatics depends and more than a billion Android devices. Additionally, bioinformatics depends
heavily on Linux since a lot of scientific software is written specifically heavily on Linux since a lot of scientific software is written specifically
for it. for it.
\medskip \medskip
This short and concise hands-on course will teach you how to effectively use This short and concise hands-on course will teach you how to effectively use
Linux using the command line interface. You will be able to swiftly start using Linux using the command line interface. You will be able to swiftly start using
Linux both on a server, e.g., the LUMC Shark cluster, as well as on your personal Linux both on a server, e.g., the LUMC Shark cluster, as well as on your personal
computer. computer.
\medskip \medskip
Learning outcomes: Learning outcomes:
...@@ -90,7 +91,7 @@ The entire course material is available online at the following address:\\ ...@@ -90,7 +91,7 @@ The entire course material is available online at the following address:\\
\clearpage \clearpage
\begin{center} \begin{center}
{\bf Practical 1}\\ {\bf Practical 1}\\
\medskip \medskip
Connecting to Other Machines Connecting to Other Machines
\end{center} \end{center}
...@@ -101,7 +102,7 @@ The entire course material is available online at the following address:\\ ...@@ -101,7 +102,7 @@ The entire course material is available online at the following address:\\
\clearpage \clearpage
\begin{center} \begin{center}
{\bf Practical 2}\\ {\bf Practical 2}\\
\medskip \medskip
Core 1 Core 1
\end{center} \end{center}
...@@ -112,7 +113,7 @@ The entire course material is available online at the following address:\\ ...@@ -112,7 +113,7 @@ The entire course material is available online at the following address:\\
\clearpage \clearpage
\begin{center} \begin{center}
{\bf Practical 3}\\ {\bf Practical 3}\\
\medskip \medskip
Core 2 Core 2
\end{center} \end{center}
...@@ -123,7 +124,7 @@ The entire course material is available online at the following address:\\ ...@@ -123,7 +124,7 @@ The entire course material is available online at the following address:\\
\clearpage \clearpage
\begin{center} \begin{center}
{\bf Practical 4}\\ {\bf Practical 4}\\
\medskip \medskip
User Environment User Environment
\end{center} \end{center}
...@@ -134,7 +135,7 @@ The entire course material is available online at the following address:\\ ...@@ -134,7 +135,7 @@ The entire course material is available online at the following address:\\
\cleartooddpage \cleartooddpage
\begin{center} \begin{center}
{\bf Commands Cheat Sheet}\\ {\bf Commands Cheat Sheet}\\
\end{center} \end{center}
\bigskip \bigskip
......
...@@ -10,6 +10,8 @@ ...@@ -10,6 +10,8 @@
\usepackage{multicol} \usepackage{multicol}
\usepackage{enumitem} \usepackage{enumitem}
\usepackage{xcolor}
\input{../shared/variables.tex} \input{../shared/variables.tex}
\input{../shared/shared.tex} \input{../shared/shared.tex}
......
...@@ -140,35 +140,63 @@ This will include: ...@@ -140,35 +140,63 @@ This will include:
\begin{enumerate} \begin{enumerate}
\item Print the \textbf{project\_genetics/README.md} file contents. (\textcolor{command-color}{\lstinline{cat}}) \item Print the \textbf{project\_genetics/README.md} file contents. (\textcolor{command-color}{\lstinline{cat}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item Open the \textbf{project\_genetics/README.md} file with \textcolor{command-color}{\lstinline{nano}} and edit it according to what it is mentioned inside it. (make use of key combinations in \textcolor{command-color}{\lstinline{nano}}, e.g., \textcolor{command-color}{\lstinline{Ctrl-k, Ctrl-x, ...}}; see cheat sheet) \item Open the \textbf{project\_genetics/README.md} file with \textcolor{command-color}{\lstinline{nano}} and edit it according to what it is mentioned inside it. (make use of key combinations in \textcolor{command-color}{\lstinline{nano}}, e.g., \textcolor{command-color}{\lstinline{Ctrl-k, Ctrl-x, ...}}; see cheat sheet)
\vspace{-0.6cm} \vspace{-0.6cm}
\item Print again the \textbf{project\_genetics/README.md} file content to check the changes. (\textcolor{command-color}{\lstinline{cat}}) \item Print again the \textbf{project\_genetics/README.md} file content to check the changes. (\textcolor{command-color}{\lstinline{cat}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item Inspect the \textbf{project\_genetics/data/orchids.gb} file content first with the \textcolor{command-color}{\lstinline{cat}} command and after that with the \textcolor{command-color}{\lstinline{less}} command in order to see the differences between the two commands. \item Inspect the \textbf{project\_genetics/data/orchids.gb} file content first with the \textcolor{command-color}{\lstinline{cat}} command and after that with the \textcolor{command-color}{\lstinline{less}} command in order to see the differences between the two commands.
\vspace{-0.1cm} \vspace{-0.1cm}
\item Search for the appearences of \textbf{LOCUS} within the \textbf{project\_genetics/data/orchids.gb}. (\textcolor{command-color}{\lstinline{grep}}) \item Search for the appearences of \textbf{LOCUS} within the \textbf{project\_genetics/data/orchids.gb}. (\textcolor{command-color}{\lstinline{grep}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item Search for the appearences of \textbf{ORGANISM} within all the \textbf{.gb} files in the \textbf{project\_genetics/data} directory. (\textcolor{command-color}{\lstinline{grep, *}}) \item Search for the appearences of \textbf{ORGANISM} within all the \textbf{.gb} files in the \textbf{project\_genetics/data} directory. (\textcolor{command-color}{\lstinline{grep, *}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item Open the \textbf{manual} page of \textbf{grep} and search for the \textbf{option} on how to \textbf{suppress the prefixing of file names on output}. (\textcolor{command-color}{\lstinline{man}}; use the \textcolor{command-color}{\lstinline{/}} key to search for keywords inside the manual page) \item Open the \textbf{manual} page of \textbf{grep} and search for the \textbf{option} on how to \textbf{suppress the prefixing of file names on output}. (\textcolor{command-color}{\lstinline{man}}; use the \textcolor{command-color}{\lstinline{/}} key to search for keywords inside the manual page)
\vspace{-0.1cm} \vspace{-0.1cm}
\item Make use of the previous \textbf{grep} command found \textbf{option} in the search for the appearences of \textbf{ORGANISM} within the all \textbf{.gb} files in \textbf{project\_genetics/data}. \item Make use of the previous \textbf{grep} command found \textbf{option} in the search for the appearences of \textbf{ORGANISM} within the all \textbf{.gb} files in \textbf{project\_genetics/data}.
\vspace{-0.1cm} \vspace{-0.1cm}
\item Rerun the previous command and redirect its output to a file named \textbf{organisms.txt} inside the \textbf{project\_genetics/data} directory. (\textcolor{command-color}{\lstinline{grep, *, >}}) \item Rerun the previous command and redirect its output to a file named \textbf{organisms.txt} inside the \textbf{project\_genetics/data} directory. (\textcolor{command-color}{\lstinline{grep, *, >}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item Check the content of the newly \textbf{organisms.txt} created file. (\textcolor{command-color}{\lstinline{cat}} or \textcolor{command-color}{\lstinline{less}})
\item Check the content of the newly \textbf{organisms.txt} created file.
(\cmd{cat} or \cmd{less})
\vspace{-0.1cm}
\item Make sure that your working directory is \textbf{project\_genetics/data}.\\
Run the \textbf{project\_genetics/src/script.sh} script. Some error message
should appear indicating that the resource was not found.
\item Edit the \textbf{project\_genetics/src/script.sh} file and update the URL
after the \cmdarg{wget} command such that \textbf{important} is replaced with
\textbf{unimportant}. Save the file and close the editor.
\vspace{-0.1cm} \vspace{-0.1cm}
\item Make sure that your current directory is \textbf{project\_genetics/data} and run the \textbf{project\_genetics/src/script.sh} script.
A new file \textbf{lost\_orchid.gb} should appear now in the \textbf{project\_genetics/data} directory. \item Make sure that your working directory is \textbf{project\_genetics/data}.\\
Run again the \textbf{project\_genetics/src/script.sh} script.
This time the script should have successfully run and a new file named
\textbf{lost\_orchid.gb} should have appeared in your working directory, i.e.,
\textbf{project\_genetics/data}.
\vspace{-0.1cm} \vspace{-0.1cm}
\item Append the contents of \textbf{lost\_orchid.gb} to the \textbf{orchids.gb} file. (\textcolor{command-color}{\lstinline{cat, >>}}) \item Append the contents of \textbf{lost\_orchid.gb} to the \textbf{orchids.gb} file. (\textcolor{command-color}{\lstinline{cat, >>}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item Remove the \textbf{lost\_orchid.gb} file. (\textcolor{command-color}{\lstinline{rm}}) \item Remove the \textbf{lost\_orchid.gb} file. (\textcolor{command-color}{\lstinline{rm}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item Print the first three organisms from the \textbf{organisms.txt}. (\textcolor{command-color}{\lstinline{head}}) \item Print the first three organisms from the \textbf{organisms.txt}. (\textcolor{command-color}{\lstinline{head}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item What is the total number of organisms that appear in the \textbf{organisms.txt} file? (\textcolor{command-color}{\lstinline{wc}}) \item What is the total number of organisms that appear in the \textbf{organisms.txt} file? (\textcolor{command-color}{\lstinline{wc}})
\vspace{-0.1cm} \vspace{-0.1cm}
\item What is the disk usage of the data folder? (\textcolor{command-color}{\lstinline{du}}) \item What is the disk usage of the data folder? (\textcolor{command-color}{\lstinline{du}})
\end{enumerate} \end{enumerate}
......
LOCUS Z78533 740 bp DNA linear PLN 30-NOV-2006
DEFINITION C.irapeanum 5.8S rRNA gene and ITS1 and ITS2 DNA.
ACCESSION Z78533
VERSION Z78533.1
KEYWORDS 5.8S ribosomal RNA; 5.8S rRNA gene; internal transcribed spacer;
ITS1; ITS2.
SOURCE Cypripedium irapeanum
ORGANISM Cypripedium irapeanum
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Asparagales; Orchidaceae;
Cypripedioideae; Cypripedium.
REFERENCE 1
AUTHORS Cox,A.V., Pridgeon,A.M., Albert,V.A. and Chase,M.W.
TITLE Phylogenetics of the slipper orchids (Cypripedioideae:
Orchidaceae): nuclear rDNA ITS sequences
JOURNAL Unpublished
REFERENCE 2 (bases 1 to 740)
AUTHORS Cox,A.V.
TITLE Direct Submission
JOURNAL Submitted (19-AUG-1996) Cox A.V., Royal Botanic Gardens, Kew,
Richmond, Surrey TW9 3AB, UK
FEATURES Location/Qualifiers
source 1..740
/organism="Cypripedium irapeanum"
/mol_type="genomic DNA"
/db_xref="taxon:49711"
misc_feature 1..380
/note="internal transcribed spacer 1"
gene 381..550
/gene="5.8S rRNA"
rRNA 381..550
/gene="5.8S rRNA"
/product="5.8S ribosomal RNA"
misc_feature 551..740
/note="internal transcribed spacer 2"
ORIGIN
1 cgtaacaagg tttccgtagg tgaacctgcg gaaggatcat tgatgagacc gtggaataaa
61 cgatcgagtg aatccggagg accggtgtac tcagctcacc gggggcattg ctcccgtggt
121 gaccctgatt tgttgttggg ccgcctcggg agcgtccatg gcgggtttga acctctagcc
181 cggcgcagtt tgggcgccaa gccatatgaa agcatcaccg gcgaatggca ttgtcttccc
241 caaaacccgg agcggcggcg tgctgtcgcg tgcccaatga attttgatga ctctcgcaaa
301 cgggaatctt ggctctttgc atcggatgga aggacgcagc gaaatgcgat aagtggtgtg
361 aattgcaaga tcccgtgaac catcgagtct tttgaacgca agttgcgccc gaggccatca
421 ggctaagggc acgcctgctt gggcgtcgcg cttcgtctct ctcctgccaa tgcttgcccg
481 gcatacagcc aggccggcgt ggtgcggatg tgaaagattg gccccttgtg cctaggtgcg
541 gcgggtccaa gagctggtgt tttgatggcc cggaacccgg caagaggtgg acggatgctg
601 gcagcagctg ccgtgcgaat cccccatgtt gtcgtgcttg tcggacaggc aggagaaccc
661 ttccgaaccc caatggaggg cggttgaccg ccattcggat gtgaccccag gtcaggcggg
721 ggcacccgct gagtttacgc
//
#!/bin/bash #!/bin/bash
wget https://barmsijs.lumc.nl/HG/courses/practical-linux/lost_orchid.gb wget https://git.lumc.nl/courses/practical-linux-course/raw/master/practical_files/project_x/important/lost_orchid.gb
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