Notebook

The Linux Commandline (bash)¶

8/29/2023¶

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Linux¶

Happy Birthday Linux! Here's your cake:

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Installing (Linux)¶

For this class we expect you to do your work on your own computing resources.

Your code will be evaluated using Ubuntu 22.04. You use the system package manager (apt) and the python package manager (pip) to install additional software needed for the course. sudo runs a command with super user privileges.

sudo apt install git vim wget python-pip ipython-notebook python-tk clustalw libcairo2 libcairo2-dev libxml2 libxml2-dev cmake libeigen3-dev swig graphviz python-pygraphviz imagemagick python3-openbabel

sudo pip3 install pysb matplotlib biopython prody MDAnalysis cython sklearn Pillow py3Dmol pandas pydotplus pydot bionetgen

macOS¶

Macs also have a built-in commandline (Terminal.app). Many of the packages we use are also available of OS X. However, keep in mind your assignments must run properly on Ubuntu 22.04.

MacPorts is most convenient for installing software (https://www.macports.org), but not all packages that we use are readily available.

Windows¶

As of Windows 10, can install Linux Subsystem. In theory should work just like Ubuntu and is much less cumbersome to use than the Windows shell.

Colab¶

Google Colab provides a cloud-based solution from running python. You can run bash commands by prefixing them with !.

Since your colab runtime will eventually timeout, we strongly recommend install Jupyter notebook locally on your own machine rather than using cloud resources.

Commands¶

The first word you type is the program you want to run. bash will search PATH environment variable for an appropriately named executable and run it with the specified arguments.

ipython - start interactive python shell (more later)

ssh hostname - connect to hostname passwd - change your password nano - a user-friendly text editor

A BASH cheatsheet¶ https://mscbio2025.github.io/notes/bash_cheatsheet.pdf ls - directory listing¶ $ ls -l total 8 -rw-rw-r-- 1 dkoes dkoes 19 Sep 3 09:08 hello.txt drwxrwxr-x 2 dkoes dkoes 4096 Sep 3 09:08 lecture $ pwd /home/dkoes/intro $ cd lecture/../.. $ pwd In [3]: %%html <div id="question1" style="width: 500px"></div> <script> jQuery('#question1').asker({ id: "cdquestion", question: "What prints out?", answers: ["~/","/home/dkoes", "/home/dkoes/intro","/home/dkoes/intro/lecture","An Error"], extra: ["","","","","",""], server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi", charter: chartmaker}) $(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide(); </script> $ ls -l total 8 -rw-rw-r-- 1 dkoes dkoes 19 Sep 3 09:08 hello.txt drwxrwxr-x 2 dkoes dkoes 4096 Sep 3 09:08 lecture $ ls *.txt In [4]: %%html <div id="question2" style="width: 500px"></div> <script> jQuery('#question2').asker({ id: "lsquestion", question: "What prints out?", answers: ["hello.txt","*.txt", "hello.txt lecture", "An Error"], extra: ["","","","","",""], server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi", charter: chartmaker}) $(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide(); </script> Spacing Out¶ du - disk usage of files/directores [dkoes@n052 tmp]$ du -s 146564 . [dkoes@n052 tmp]$ du -sh 144M . [dkoes@n052 tmp]$ du -sh intro 4.0K intro df - usage of full disk [dkoes@n052 tmp]$ df -h . Filesystem Size Used Avail Use% Mounted on pulsar:/home 37T 28T 9.3T 75% /net/pulsar/home Dude, where's my stuff?¶ locate find a file system wide find search directory tree which print location of a command man print manual page of a command Save the Environment¶ NAME=value set NAME equal to value No spaces around equals export NAME=value set NAME equal to value and make it stick $ dereference variable user@python$ X=3 user@python$ echo $X 3 user@python$ X=hello user@python$ echo $X hello user@python$ echo X X Getting at your variables¶ In [5]: %%html <div id="questionvarprint" style="width: 500px; "></div> <script> jQuery('#questionvarprint').asker({ id: "varquestion", question: "Which does <b>not</b> print the value of X?", answers: ["echo $X","echo ${X}","echo '$X'","echo \"$X\""], extra: ["","","","","",""], server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi", charter: chartmaker}) $(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide(); </script> $ ls -l total 8 -rw-rw-r-- 1 dkoes dkoes 19 Sep 3 09:08 hello.txt drwxrwxr-x 2 dkoes dkoes 4096 Sep 3 09:08 lecture $ ls '*.txt' In [6]: %%html <div id="questionls2" style="width: 500px"></div> <script> jQuery('#questionls2').asker({ id: "ls2question", question: "What prints out?", answers: ["hello.txt","*.txt", "hello.txt lecture", "An Error"], extra: ["","","","","",""], server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi", charter: chartmaker}) $(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide(); </script> Capturing Output¶ `cmd` evaluates to output of cmd $ FILES=`ls` $ echo $FILES hello.txt lecture Your Environment¶ env list all set environment variables PATH where shell searches for commands LD_LIBRARY_PATH library search path PYTHONPATH where python searches for modules .bashrc initialization file for bash - set PATH etc here History¶ history show commands previously issued up arrow cycle through previous commands Ctrl-R search through history for command AWESOME .bash_history file that stores the history HISTCONTROL environment variable that sets history options: ignoredups HISTSIZE size of history buffer Shortcuts¶ Tab autocomplete Ctrl-D EOF/logout/exit Ctrl-A go to beginning of line Ctrl-E go to end of line alias new=cmd make a nickname for a command $ alias l='ls -l' $ alias $ l Loops¶ for i in x y z do echo $i done for i in *.txt do echo $i done Lots more... (TLDP) String Manipulation¶ http://tldp.org/LDP/abs/html/string-manipulation.html $ i="ovolo" $ echo ${i%o} In [7]: %%html <div id="stringm" style="width: 500px"></div> <script> jQuery('#stringm').asker({ id: "stringm", question: "What prints out?", answers: ["ovolo","volo", "ovol","vl","An Error"], server: "https://bits.csb.pitt.edu/asker.js/example/asker.cgi", charter: chartmaker}) $(".jp-InputArea .o:contains(html)").closest('.jp-InputArea').hide(); </script> Batch processing files¶ for file in *.png do convert $file ${file%.png}.tif done Assignment 1¶ Due in a week Use GradeScope to hand-in Test your code before submitting