Under development
Setup:
We recommend you follow this course in a jupyter notebook which includes the course material and it's own terminal. If for whatever reason you don't see below for setup on your own machine.
Jupyter Notebook¶
Jupyter notebooks contain bash 'magic' which executes terminal commands within the jupyter interface. We have modified one of these for the purpose of this training, so where you see %%bash2 this is what you should run in a terminal.
In [1]:
%%bash2
# This is a comment
echo "This will be output"
This will be output
Slide Type
You can also use the %%bash2 magic to keep your solutions to exercises in the notebook as a record. They will still be executed at the command line, so be careful! We can extract the files for this training by unzipping the data-shell.zip file in the repository. This can be done by executing the cell below:
In [2]:
%%bash2 --dir ~/library/data
unzip data-shell.zip
A
Archive: data-shell.zip inflating: data-shell/notes.txt inflating: data-shell/.bash_profile inflating: data-shell/creatures/unicorn.dat inflating: data-shell/creatures/basilisk.dat inflating: data-shell/data/pdb/quinine.pdb inflating: data-shell/data/pdb/lactose.pdb inflating: data-shell/data/pdb/pyridoxal.pdb inflating: data-shell/data/pdb/lactic-acid.pdb inflating: data-shell/data/pdb/methanol.pdb inflating: data-shell/data/pdb/tnt.pdb inflating: data-shell/data/pdb/vanillin.pdb inflating: data-shell/data/pdb/glycol.pdb inflating: data-shell/data/pdb/tuberin.pdb inflating: data-shell/data/pdb/tyrian-purple.pdb inflating: data-shell/data/pdb/aldrin.pdb inflating: data-shell/data/pdb/mustard.pdb inflating: data-shell/data/pdb/strychnine.pdb inflating: data-shell/data/pdb/cyclobutane.pdb inflating: data-shell/data/pdb/cyclohexanol.pdb inflating: data-shell/data/pdb/thiamine.pdb inflating: data-shell/data/pdb/vinyl-chloride.pdb inflating: data-shell/data/pdb/propane.pdb inflating: data-shell/data/pdb/mint.pdb inflating: data-shell/data/pdb/menthol.pdb inflating: data-shell/data/pdb/octane.pdb inflating: data-shell/data/pdb/camphene.pdb inflating: data-shell/data/pdb/cinnamaldehyde.pdb inflating: data-shell/data/pdb/codeine.pdb inflating: data-shell/data/pdb/maltose.pdb inflating: data-shell/data/pdb/heme.pdb inflating: data-shell/data/pdb/ethane.pdb inflating: data-shell/data/pdb/ascorbic-acid.pdb inflating: data-shell/data/pdb/testosterone.pdb inflating: data-shell/data/pdb/vitamin-a.pdb inflating: data-shell/data/pdb/lsd.pdb inflating: data-shell/data/pdb/citronellal.pdb inflating: data-shell/data/pdb/benzaldehyde.pdb inflating: data-shell/data/pdb/nerol.pdb inflating: data-shell/data/pdb/morphine.pdb inflating: data-shell/data/pdb/ethylcyclohexane.pdb inflating: data-shell/data/pdb/norethindrone.pdb inflating: data-shell/data/pdb/lanoxin.pdb inflating: data-shell/data/pdb/cyclopropane.pdb inflating: data-shell/data/pdb/styrene.pdb inflating: data-shell/data/pdb/ammonia.pdb inflating: data-shell/data/pdb/cubane.pdb inflating: data-shell/data/pdb/pentane.pdb inflating: data-shell/data/pdb/ethanol.pdb inflating: data-shell/data/pdb/methane.pdb inflating: data-shell/data/pdb/sucrose.pdb inflating: data-shell/data/pdb/cholesterol.pdb inflating: data-shell/data/pdb/piperine.pdb inflating: data-shell/data/amino-acids.txt inflating: data-shell/data/planets.txt inflating: data-shell/data/salmon.txt inflating: data-shell/data/animals.txt inflating: data-shell/data/elements/Tl.xml inflating: data-shell/data/elements/Co.xml inflating: data-shell/data/elements/Na.xml inflating: data-shell/data/elements/Np.xml inflating: data-shell/data/elements/Xe.xml inflating: data-shell/data/elements/Fr.xml inflating: data-shell/data/elements/Er.xml inflating: data-shell/data/elements/Md.xml inflating: data-shell/data/elements/Sc.xml inflating: data-shell/data/elements/Cl.xml inflating: data-shell/data/elements/Mo.xml inflating: data-shell/data/elements/Hg.xml inflating: data-shell/data/elements/Ba.xml inflating: data-shell/data/elements/Cu.xml inflating: data-shell/data/elements/Tc.xml inflating: data-shell/data/elements/Re.xml inflating: data-shell/data/elements/H.xml inflating: data-shell/data/elements/Nb.xml inflating: data-shell/data/elements/Cd.xml inflating: data-shell/data/elements/Gd.xml inflating: data-shell/data/elements/Bi.xml inflating: data-shell/data/elements/C.xml inflating: data-shell/data/elements/Zr.xml inflating: data-shell/data/elements/Li.xml inflating: data-shell/data/elements/Ti.xml inflating: data-shell/data/elements/Sr.xml inflating: data-shell/data/elements/Ac.xml inflating: data-shell/data/elements/Lu.xml inflating: data-shell/data/elements/Fm.xml inflating: data-shell/data/elements/Pa.xml inflating: data-shell/data/elements/Os.xml inflating: data-shell/data/elements/Pu.xml inflating: data-shell/data/elements/Mg.xml inflating: data-shell/data/elements/Es.xml inflating: data-shell/data/elements/O.xml inflating: data-shell/data/elements/Ru.xml inflating: data-shell/data/elements/Eu.xml inflating: data-shell/data/elements/F.xml inflating: data-shell/data/elements/Pr.xml inflating: data-shell/data/elements/Al.xml inflating: data-shell/data/elements/Te.xml inflating: data-shell/data/elements/Pt.xml inflating: data-shell/data/elements/B.xml inflating: data-shell/data/elements/Pd.xml inflating: data-shell/data/elements/Ce.xml inflating: data-shell/data/elements/At.xml inflating: data-shell/data/elements/Au.xml inflating: data-shell/data/elements/W.xml inflating: data-shell/data/elements/Am.xml inflating: data-shell/data/elements/Cm.xml inflating: data-shell/data/elements/Ga.xml inflating: data-shell/data/elements/As.xml inflating: data-shell/data/elements/Cf.xml inflating: data-shell/data/elements/Hf.xml inflating: data-shell/data/elements/V.xml inflating: data-shell/data/elements/Fe.xml inflating: data-shell/data/elements/I.xml inflating: data-shell/data/elements/Tm.xml inflating: data-shell/data/elements/He.xml inflating: data-shell/data/elements/Se.xml inflating: data-shell/data/elements/Ho.xml inflating: data-shell/data/elements/S.xml inflating: data-shell/data/elements/Kr.xml inflating: data-shell/data/elements/Sm.xml inflating: data-shell/data/elements/Zn.xml inflating: data-shell/data/elements/Ta.xml inflating: data-shell/data/elements/Si.xml inflating: data-shell/data/elements/Ni.xml inflating: data-shell/data/elements/Y.xml inflating: data-shell/data/elements/K.xml inflating: data-shell/data/elements/In.xml inflating: data-shell/data/elements/Ra.xml inflating: data-shell/data/elements/Th.xml inflating: data-shell/data/elements/No.xml inflating: data-shell/data/elements/Dy.xml inflating: data-shell/data/elements/Bk.xml inflating: data-shell/data/elements/Ge.xml inflating: data-shell/data/elements/Rn.xml inflating: data-shell/data/elements/Nd.xml inflating: data-shell/data/elements/Pm.xml inflating: data-shell/data/elements/Ag.xml inflating: data-shell/data/elements/Rh.xml inflating: data-shell/data/elements/La.xml inflating: data-shell/data/elements/Br.xml inflating: data-shell/data/elements/Ir.xml inflating: data-shell/data/elements/Tb.xml inflating: data-shell/data/elements/P.xml inflating: data-shell/data/elements/Mn.xml inflating: data-shell/data/elements/Ar.xml inflating: data-shell/data/elements/Rb.xml inflating: data-shell/data/elements/Sn.xml inflating: data-shell/data/elements/Yb.xml inflating: data-shell/data/elements/Po.xml inflating: data-shell/data/elements/Pb.xml inflating: data-shell/data/elements/Sb.xml inflating: data-shell/data/elements/Cs.xml inflating: data-shell/data/elements/Be.xml inflating: data-shell/data/elements/N.xml inflating: data-shell/data/elements/Cr.xml inflating: data-shell/data/elements/Ca.xml inflating: data-shell/data/elements/U.xml inflating: data-shell/data/elements/Lr.xml inflating: data-shell/data/elements/Ne.xml inflating: data-shell/data/sunspot.txt inflating: data-shell/data/morse.txt inflating: data-shell/data/animal-counts/animals.txt inflating: data-shell/writing/haiku.txt inflating: data-shell/writing/data/LittleWomen.txt inflating: data-shell/writing/data/one.txt inflating: data-shell/writing/data/two.txt extracting: data-shell/writing/thesis/empty-draft.md extracting: data-shell/writing/tools/old/oldtool inflating: data-shell/writing/tools/format extracting: data-shell/writing/tools/stats inflating: data-shell/solar.pdf inflating: data-shell/north-pacific-gyre/2012-07-03/goodiff inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01978B.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01729B.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE02043B.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01751B.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01978A.txt inflating: data-shell/north-pacific-gyre/2012-07-03/goostats inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01971Z.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01843A.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01729A.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01736A.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE02043A.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE02040B.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01843B.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE02040A.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01751A.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE02018B.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE02040Z.txt inflating: data-shell/north-pacific-gyre/2012-07-03/NENE01812A.txt inflating: data-shell/pizza.cfg inflating: data-shell/molecules/propane.pdb inflating: data-shell/molecules/octane.pdb inflating: data-shell/molecules/ethane.pdb inflating: data-shell/molecules/cubane.pdb inflating: data-shell/molecules/pentane.pdb inflating: data-shell/molecules/methane.pdb [Errno 2] No such file or directory: 'replace data-shell/notes.txt? [y]es, [n]o, [A]ll, [N]one, [r]ename:'
Slide Type
We can check this has suceeded by changing into the newly created data-shell directory, using the bash2 magic and listing the contents (see the first lesson for more information).
In [3]:
%%bash2 --dir ~/library/data/data-shell
ls
creatures data molecules north-pacific-gyre notes.txt pizza.cfg solar.pdf thesis writing
You are now ready to begin lesson 1.