MATERI PERKULIAHAN BAGIAN II (Dilaksanakan setelah mid semester)

Pengenalan sistem operasi Linux dan Free & Open Source Software (FOSS)
Berbagai software aplikasi di Linux dan Windows untuk pengajaran dan penelitian kimia, klik DI SINI
Praktek instalasi linux (Ubuntu/Blankon)
Praktek instalasi software aplikasi kimia di Ubuntu/Blankon
Praktek menggunakan aplikasi kimia di Ubuntu/Blankon
Praktek instalasi software aplikasi elearning (moodle/Joomla/Edmodo/Wordpress/WebMO atau lainnya)
Praktek membuat blog pendidikan menggunakan Wordpress, klik DI SINI
Tutorial Membuat Blog Wordpress-1: Download DI SINI
Tutorial Membuat Blog Wordpress-2: Download DI SINI
Web Programming: HTML dan JavaScript: Download materi
Praktek pemrograman aplikasi Android menggunakan Eclipse. Klik link materi DI SINI

Senin, 28 November 2011

Memasang Link Aplikasi di Desktop

Untuk aplikasi yang dipasang sendiri terkadang hanya bisa dijalankan di terminal dengan memanggil nama aplikasinya. Cara ini mungkin tidak nyaman atau tidak praktis untuk yang tidak terbiasa kerja di terminal.

Di bawah ini disebutkan langkah-langkah untuk memasang link aplikasi tertentu di desktop sehingga mudah dijalankan:

1. Ketahui dulu di direktori mana aplikasi itu terpasang
2. Masuk ke desktop dan klik kanan sehingga muncul dialog box dan klik "Buat Peluncur"
3. Jika pilihan "Buat Peluncur" tidak berfungsi lakukan langkah instalasi berikut:
masuk ke terminal, lalu ketik: sudo apt-get install alacarte gnome-panel [Enter], tunggu sampai selesai.
4. Setelah instalasi selesai, ulangi klik kanan di desktop dan pilih "Buat Peluncur" sehingga muncul dialog box berikut:

5. Pilih Tipe "Aplikasi"
6. Beri Nama: (sesuai nama aplikasi yang akan dibuatkan link-nya didesktop)
7. Perintah: (klik tombol Cari untuk mencari nama aplikasi yang akan dipasang link-nya)
8. Beri Deskripsi seperlunya.
9. Klik OK
10. Link sudah ada di desktop
11. Klik link tersebut untuk menjalankan
12. Jika aplikasi tidak muncul, ulangi langklah 5 dengan memilih Tipe sebagai "Aplikasi pada Terminal". lanjutkan langkah 6 - 11.

Memasang MMV (Molegro Molecular Viewer) versi 2.2.0 di BlankOn

Molegro Molecular Viewer

Molegro Molecular Viewer is a free cross-platform application for visualization of molecules and Molegro Virtual Docker results.

Molegro Molecular Viewer is able to visualize most common molecular file formats (PDB, Mol2, SDF) as well as docking results from Molegro Virtual Docker.

The main user interface

Features at a glance

Free!
Cross-platform: Windows, Linux, and Mac OS X is supported.
Share and view results from Molegro Virtual Docker docking runs.
Imports and exports PDB, SDF, Mol2, and MVDML files.
Built-in raytracer for high-quality images.
Automatic preparation of molecules.
Molecular surface and backbone visualization.
Labels, sequence viewer and biomolecule generator.
Cropping of molecules and clipping planes.
Structural protein alignment.
Support for KNIME workflows.

Langkah pemasangan MMV:

1. Download MMV di link berikut: http://www.molegro.com/mmv-download.php. Untuk versi linux 32 bit link download-nya adalah http://www.daimi.au.dk/~molegro/MolecularViewer/MMV_2_2_0.tar.gz.
2. Setelah selesai didownload, masuk ke folder tempat file MMV tersimpan menggunakan terminal.
3. Ekstrak di terminal dengan ketik: tar -xvf MMV_2_2_0.tar.gz
4. Selesai ekstrak masuk ke folder bin dari MMV, ketik: cd Molegro/MMV/bin/ [Enter]
5. Untuk menjalankan MMV cukup ketik: ./mmv [Enter]

Minggu, 27 November 2011

Ringkasan Command Line

Panduan Perintah Dasar Linux

Linux terinspirasi oleh sistem operasi Unix yang pertama kali muncul pada tahun 1969, dan terus digunakan dan dikembangkan sejak itu. Banyak dari konvensi desain untuk Unix juga terdapat pada Linux, dan bagian penting untuk memahami dasar-dasar dari sistem Linux.

Orientasi utama dari Unix adalah penggunaan antarmuka baris perintah, dan warisan ini ikut terbawa ke Linux. Jadi antarmuka pengguna berbasis grafik dengan jendela, ikon dan menunya dibangun di atas dasar antarmuka baris perintah. Lagipula, hal ini berarti bahwa sistem berkas Linux tersusun agar dapat dengan mudah dikelola dan diakses melalui baris perintah.

Sumber Belajar Perintah Dasar

Pertama – halaman manual perintah.
- man <perintah> : menampilkan semua informasi tentang perintah.
- <perintah> help : menampilkan opsi yang tersedia dari sebuah perintah.
Kedua – Buku dan Internet.

Perintah Penanganan File

mkdir - membuat direktori.

sintaks :
```
mkdir [OPTION] DIRECTORY...
```
contoh :
```
$ mkdir data
```

ls - menampilkan isi dari direktori.

sintaks :
```
ls [OPTION]... [FILE]...
```
contoh :
```
$ ls -ls
```

cd - berpindah direktori.

sintaks :
```
cd [DIRECTORY]
```
contoh :
```
$ cd data
```

pwd - menampilkan tempat direktori yang sedang dikerjakan.

sintaks :
```
$ pwd
```

cp - mengcopy file dan direktori.

sintaks :
```
cp [OPTION]... SOURCE DEST
```

contoh :

$ cp sample.txt sample_copy.txt

$ cp sample_copy.txt target_dir

mv - memindahkan atau merubah nama file.

sintaks :
```
mv [OPTION]... SOURCE DEST
```

contoh :

$ mv source.txt target_dir

$ mv old.txt new.txt

rm - menghapus file atau direktori.

sintaks :
```
rm [OPTION]... FILE...
```
contoh :
```
$ rm file1.txt , rm rf some_dir
```

find - mencari file dalam sebuah direktori.

sintaks :
```
find [OPTION] [path] [pattern]
```
contoh :
```
$ find file1.txt, find name file1.txt
```

touch - Update waktu akses dan modifikasi setiap BERKAS ke waktu sekarang. Argumen FILE yang tidak ada menjadi ada kosong.

sintaks:
```
touch [OPTION]... FILE...
```
contoh :
```
$ touch done
```

file - menentukan jenis file.

sintaks:
```
file [OPTION...] [FILE...]
```
contoh :
```
$ file ubuntu-desktop.pdf
```

locate - menemukan atau mencari file.

sintaks :
```
locate [OPTION]... FILE...
```
contoh :
```
$ locate file1.txt
```

whereis - locate the binary, source, and manual page files for a command.

sintaks :

whereis [-bmsu] [-BMS directory...  -f] filename...

contoh :
```
$ whereis ssh
```

Pola

Pola adalah ungkapan yang menggambarkan satu set string yang digunakan untuk memberikan gambaran ringkas dari sebuah himpunan, tanpa harus daftar semua elemen. contoh : ab*cd cocok apa pun yang dimulai dengan ab dan diakhiri dengan cd dll.

$ ls *.txt

artinya mencetak semua file yang berekstensi .txt (file teks)

Pemrosesan Teks

cat - menggabungkan file dan cetak pada keluaran standar.

sintaks :
```
cat [OPTION] [FILE]...
```

contoh :

$ cat avatar.avi.001 avatar.avi.002 > avatar.avi

$ cat readme.txt

echo - menampilkan baris teks.

sintaks :
```
echo [OPTION] [string] ...
```
contoh :
```
$ echo I love Indonesia
```
```
$ echo $HOME
```

grep - mencetak baris yang cocok dengan pola.

sintaks :
```
grep [OPTION] PATTERN [FILE]...
```
contoh :
```
$ grep i apple sample.txt
```

wc - mencetak jumlah baris, kata, dan byte di file.

sintaks :
```
wc [OPTION]... [FILE]...
```
contoh :
```
$ wc file1.txt
```

sort - mengurutkan file teks baris.

sintaks :
```
sort [OPTION]... [FILE]...
```
contoh :
```
$ sort file1.txt
```

md5sum - compute and check MD5 message digest.

sintaks :
```
md5sum [OPTION]... [FILE]...
```

contoh :

$ md5sum LinuxMint-5-Fluxbox.iso > md5sums

$ md5sum -c md5sums

Linux File Permissions

3 jenis file permission – read, write, execute 10 bit format dari perintah 'ls -l' 1 2 3 4 5 6 7 8 9 10 file type owner group others contoh : drwxrwr owner berarti memiliki semua tiga hak akses, group mempunyai izin membaca dan menulis, others hanya mempunyai izin membaca. read - 4, write - 2, execute - 1 contoh :

rwxrwr   = 764

Sistem Administrasi

chmod - mengubah hak akses file.

sintaks :
```
chmod [OPTION] [MODE] [FILE]
```
contoh :
```
$ chmod 744 calculate.sh
```

chown - mengubah pemilik file dan group.

sintaks :

chown [OPTION]... OWNER[:[GROUP]] FILE...

contoh :
```
$ chown ugos myfile.txt
```

su - mengubah user ID atau menjadi super-user.

sintaks :
```
su [OPTION] [LOGIN]
```
contoh :
```
$ su ugos
```
```
$ su
```

passwd - update token otentikasi pengguna.

sintaks :
```
passwd [options] [LOGIN]
```
contoh :
```
$ passwd ugos
```

who - menunjukkan siapa yang login.

sintaks :
```
who [OPTION]
```
contoh :
```
$ who
```

Managemen Proses

ps - laporan snapshot dari proses saat ini.

sintaks :
```
ps [OPTION]
```
contoh :
```
$ ps ax
```

kill - untuk membunuh proses (menggunakan mekanisme sinyal).

sintaks :
```
kill [OPTION] pid
```
contoh :
```
$ kill 9 2275
```

lsusb - daftar perangkat USB.

sintaks :
```
$ lsusb
```

jobs - menampilkan nama dan id latar belakang pekerjaan.

sintaks :
```
$ jobs
```

top - tampilan tugas Linux.

sintaks :

top -hv | -bcisSH -d delay -n iterations [-u user | -U user] -p pid [,pid ...]

contoh :
```
$ top
```

clear - menghapus layar terminal.

sintaks :
```
$ clear
```

free - menampilkan jumlah memori yang bebas dan digunakan dalam sistem.

sintaks :

free [-b | -k | -m | -g] [-o] [-s delay ] [-t] [-V]

contoh :
```
$ free -m
```

Arsip

tar - ke arsip file.

sintaks :
```
tar [OPTION] DEST SOURCE
```

contoh :

$ tar cvf original.tar original/

$ tar -cpvf original.tar.gz original/

$ tar xvf original.tar

$ tar xjvf original.tar.bz2

bzip2 - kompresor blok-menyortir file.

sintaks :
```
bzip2 [OPTION] FILE...
```

contoh :

$ bzip2 original.mp3

$ bzip2 -d original.mp3.bz2

zip - paket dan kompres (arsip) file.

sintaks :
```
zip [OPTION] DEST SOURCE
```
contoh :
```
$ zip -r original.zip original/
```

rar - arsip file dengan kompresi.

sintaks :

rar <command> [-<switch 1> -<switch N>] archive [files...]

contoh :
```
$ rar original.rar original
```

unzip - daftar, test dan ekstrak file yang dikompresi dalam sebuah ZIP archive.

sintaks :

unzip [-Z] [-opts[modifiers]] file[.zip] [list] [-x xlist] [-d exdir]

contoh :
```
$ unzip original.zip
```

unrar - daftar, test dan ekstrak file yang dikompresi dalam sebuah RAR archive.

sintaks :

unrar <command> -<switch 1> -<switch N> <archive> <files...> <@listfiles...> <path_to_extract>

contoh :
```
$ unrar -x original.rar
```

7z - Sebuah pengarsipan file dengan rasio kompresi tertinggi.

sintaks :

7z <command> [<switches>...] <archive_name> [<file_names>...] [<@listfiles...>]

contoh :
```
$ 7z e original.7z
```

Jaringan

ssh - SSH client (remote login program) "ssh adalah program untuk login ke mesin remote dan untuk mengeksekusi perintah pada mesin remote".

sintaks :
```
ssh [options] [user]@hostname
```
contoh :
```
$ ssh -l guest 10.105.11.20
```

scp - secure copy (copy file program remote) "scp salinan file antara host pada jaringan".

sintaks :

scp [options] [[user]@host1:file1] [[user]@host2:file2]

contoh :
```
$ scp file1.txt guest@ip_address:~/ 
```

ifconfig - mengkonfigurasi perangkat jaringan.

sintaks :

ifconfig [-a] [-v] [-s] <interface> [[<AF>] <address>]

contoh :
```
$ ifconfig
```

iwconfig - mengkonfigurasi perangkat jaringan nirkabel.

sintaks :
```
iwconfig [interface]
```
contoh :
```
$ iwconfig
```

wget - Downloader non-interaktif jaringan.

sintaks :
```
wget [option]... [URL]...
```

contoh :

$ wget -c http://repo.ugm.ac.id/iso/ubuntu/10.04/ubuntu-10.04-netbook-i386.iso

netstat - Cetak koneksi jaringan, tabel routing, statistik interface, koneksi masquerade, dan keanggotaan multicast.

sintaks :
```
netstat [-vWeenNcCF] [<Af>] -r
```
contoh :
```
$ netstat
```

mtr - tool diagnostik jaringan.

sintaks :

mtr [-hvrwctglspniu46] [--help] [--version] [--report]

contoh :
```
$ mtr google.co.id
```

iftop - menampilkan penggunaan bandwidth pada sebuah perangkat ethernet oleh host.

sintaks :

iftop -h | [-nNpbBP] [-i interface] [-f filter code] [-F net/mask]

contoh :
```
# iftop -i eth0
```

File Systems

fdisk - partisi manipulator.

sintaks :
```
fdisk [options] <disk>
```
contoh :
```
# fdisk l
```

mount - mount file system.

sintaks :
```
mount t type device dir
```
contoh :
```
# mount /dev/sda5 /media/target
```

umount - unmount file system.

sintaks :
```
umount [OPTIONS] dir | device...
```
contoh :
```
# umount /media/target
```

du - estimasi sintaks kapasitas file.

sintaks :
```
du [OPTION]... [FILE]...
```
contoh :
```
$ du -h
```

df - diskfile, laporan sintaks kapasitas hardisk.

sintaks :
```
df [OPTION]... [FILE]...
```
contoh :
```
$ df -h
```

eject - eject removable media

sintaks :
```
eject [OPTION]
```
contoh :
```
$ eject
```
```
$ eject -t
```

Editor perintah

nano - Nano, editor lainnya, yang bebas disempurnakan Pico clone.

sintaks:
```
nano [OPTIONS] [[+LINE,COLUMN] FILE]..
```
contoh :
```
$ nano readme.txt
```

pico - sebuah program editor teks yang ditingkatkan.

sintaks:
```
pico [OPTIONS] [[+LINE,COLUMN] FILE]..
```
contoh :
```
$ pico readme.txt
```

vi - program text editor.

sintaks :
```
vi [OPTION] [file]...
```
contoh :
```
$  vi hello.c
```

vim - Vi Improved, program text editor.

sintaks :
```
vim [OPTION] [file]...
```
contoh :
```
$  vim hello.c
```

Perintah Advanced

reboot - reboot sistem.

sintaks :
```
reboot [OPTION]
```
contoh :
```
# reboot
```

halt - shutdown komputer.

sintaks :
```
# halt
```

shutdown - shutdown komputer.

sintaks :
```
shutdown [OPTION]
```
contoh :
```
# shutdown -h now
```

sed - stream editor untuk penyaringan dan mengubah teks.

sintaks :
```
sed [OPTION] [inputfile]...
```
contoh :
```
$ sed 's/love/hate/g' loveletter.txt 
```

awk - pola scanning dan pengolahan bahasa.

contoh :

$ awk F: '{ print $1 }' sample_awk.txt

watch - menjalankan program secara berkala, menunjukkan output fullscreen.

sintaks :
```
watch [OPTION] <command>
```
contoh :
```
$ watch lsusb
```

alias - membuat alias dari sebuah perintah.

sintaks:
```
alias [name[=value] ... ]
```
contoh :
```
$ alias dir='ls -l'
```

screen - layar manajer dengan emulasi terminal VT100/ANSI.

sintaks :
```
screen [-opts] [cmd [args]]
```
contoh :
```
$ screen -S ugos
```

lshw - list hardware.

sintaks :
```
lshw [-format] [-options ...]
```
contoh :
```
$ lshw -C network
```

dmidecode - DMI table decoder

sintaks :
```
dmidecode [OPTIONS]
```
contoh :
```
# dmidecode --type memory
```

uptime - menampilkan berapa lama sistem telah berjalan.

sintaks :
```
$ uptime
```

split - membagi file menjadi potongan-potongan.

sintaks :
```
split [OPTION]... [INPUT [PREFIX]]
```
contoh :
```
$ split -b 200MB avatar.avi avatar.avi.
```

espeak - Sebuah perangkat lunak multi-lingual speech synthesizer.

sintaks :
```
espeak [options] [<words>]
```
contoh :
```
$ espeak -s 80 "Linux"
```

aplay - command-line perekam suara dan pemutar untuk driver soundcard ALSA.

sintaks :
```
aplay [OPTION]... [FILE]...
```
contoh :
```
$ aplay -l
```
```
$ aplay donw.wav
```

arecord - command-line perekam suara untuk driver soundcard ALSA.

sintaks :
```
arecord [OPTION]... [FILE]...
```

contoh :

$ arecord -f cd -t raw | lame -x -r – out.mp3

lsb_release - cetak distribusi informasi spesifik.

sintaks :
```
lsb_release [options]
```
contoh :
```
$ lsb_release -a
```

cal - menampilkan sebuah kalender.

sintaks :
```
cal [-hjy] [[month] year]
```
contoh :
```
$ cal 4 2011
```

date - mencetak atau mengatur tanggal dan waktu sistem.

sintaks :
```
date [OPTION]... [+FORMAT]
```

contoh :

# date 041520152011

artinya Apr 15 8:15 2011

history - menampilkan perintah-perintah yang sudah digunakan.

sintaks :
```
$ history
```

bc - bahasa kalkulator.

sintaks :

bc [ -hlwsqv ] [long-options] [  file ... ]

contoh :
```
$ bc
```

Sabtu, 26 November 2011

Command Tar

How do I list files inside compressed tar ball (gzip’d tar’d) archive?

Tar command provides the option to list files inside compressed tar ball. However mtools includes command called lz which gunzips and shows a listing of a gzip’d tar’d archive without extracting files.

For example, display listing of file called backup.tar.gz type command:

$ lz backup.tar.gz

As you see lz provides a listing of a gzip’d tar’d archive, that is a tar archive compressed with the gzip command. It is not strictly necessary on Debian GNU/Linux (or other Linux/BSD/Solaris oses), because the GNU tar(1) program provides the same capability with the command:

$ tar -tzf backup.tar.gz

How To Extract a Single File / Directory from Tarball Archive

Question. How do I extract a single file or directory form a tarball under UNIX / Linux shell prompt? How do I restore a single file from /dev/st0 tape device?

Answer. tar command allows to extract a single file or directory using the following format. It works under UNIX, Linux, and BSD operating systems.

tar xvf /dev/st0 filename

tar xvf /dev/st0 directory-name

tar xvf mytar.ball.tar filename

tar -zxvf mytar.ball.tar.gz directory-name

Extract file to /tmp directory

tar -zxvf mytar.ball.tar.gz -C /tmp filename

tar -zxvf mytar.ball.tar.gz -C /tmp dir-name

Read tar man page for more information:

man tar

Tar Extract a Single File(s) From a Large Tarball

Question. I’m new to Linux. Over few days I found lots software distributed as .tar.gz file. How do I install tar.gz files under Linux?

Answer. tar.gz also known as tarball, an archive format for electronic data and software. Most Linux tarball contains a source code for software. If you are new to Linux I recommend using apt-get, rpm and yum command to install all binary packages.

Tarballs are a group of files in one file. Tarball files have the extension .tar.gz, .tgz or .tar.bz2. Most open source software use tarballs to distribute programs/source codes.

# 1: Uncompress tarball

To uncompress them, execute the following command(s) depending on the extension:

$ tar zxf file.tar.gz

$ tar zxf file.tgz

$ tar jxf file.tar.bz2

$ tar jxf file.tbz2

Now change directory

$ ls

$ cd path-to-software/

# 2: Build and install software

Generally you need to type 3 commands as follows for building and compiling software:

# ./configure

# make

# make install

Where,

./configure will configure the software to ensure your system has the necessary functionality and libraries to successfully compile the package
make will compile all the source files into executable binaries.
Finally, make install will install the binaries and any supporting files into the appropriate locations.

# 3: Read INSTALL / README file

Each tarball comes with installation and build instructions. Open INSTALL or README file for more information:
$ vi INSTALL

Tar Extract a Single File(s) From a Large Tarball

Q. I’ve couple of large tarballs such as www.tar and images.tar. Is it possible to extract a single file or a list of files from a large tarball such as images.tar instead of extracting the entire tarball? How do I extract specific files under Linux / UNIX operating systems?

A. GNU tar can be used to extract a single or more files from a tarball. To extract specific archive members, give their exact member names as arguments, as printed by -t option.

Extracting Specific Files

Extract a file called etc/default/sysstat from config.tar.gz tarball:

$ tar -ztvf config.tar.gz

$ tar -zxvf config.tar.gz etc/default/sysstat

$ tar -xvf {tarball.tar} {path/to/file}

Some people prefers following syntax:
tar --extract --file={tarball.tar} {file}
Extract a directory called css from cbz.tar:
$ tar --extract --file=cbz.tar css

Wildcard based extracting

You can also extract those files that match a specific globbing pattern (wildcards). For example, to extract from cbz.tar all files that begin with pic, no matter their directory prefix, you could type:
$ tar -xf cbz.tar --wildcards --no-anchored 'pic*'
To extract all php files, enter:
$ tar -xf cbz.tar --wildcards --no-anchored '*.php'

Where,

-x: instructs tar to extract files.
-f: specifies filename / tarball name.
-v: Verbose (show progress while extracting files).
-j : filter archive through bzip2, use to decompress .bz2 files.
-z: filter archive through gzip, use to decompress .gz files.
–wildcards: instructs tar to treat command line arguments as globbing patterns.
–no-anchored: informs it that the patterns apply to member names after any / delimiter.

Command Line Basics: Tar

Written by Bradford

This website caters to both advanced and novice users. So in addition to articles like fixing Modsecparse.pl cronjob errors I also need to hit the basics. One command that many webmasters know, have used in the past, but forget how to use is the tar command. How does one “untar” a file? What if it has been compressed with gzip or bzip2? Don’t some of you wish that you had a site where you could reference an easy to understand reference to these compression formats? Well, look no further! You could bookmark this particular post, but why bother when you can just bookmark the site as a whole and reference this later on in the Webmaster Wiki? Linux commands (done via command line or SSH) will be linked directly from the main page of the wiki and resides here. A guide to the Tar command can then be reached from there. So here are the basics that will help you extract those tar files you often download from places like Sourceforge:

What Is A Tarball?

A tarball is an archive of files and/or directories. If a tarball is gzip’d or bz2′d, then it has been compressed.

“Untar” A File

If you are dealing with a tarball (example.tar) file, you can extract the files from it using:

tar xvf example.tar

If the tarball has been gzipped(example.tar.gz), you can extract the files from it using:

tar xvfz example.tar.gz

If the tarball has been gzipped(example.tgz), you can extract the files from it using:

tar xzvf example.tgz

If the tarball has been compressed with bzip2(example.tar.bz2), then you will need to have bzip2 installed. ( Most servers will have this, but if yours does not, visit http://www.bzip.org/ ) If all is well and bzip2 is installed, you can extract the files from it using:

tar yxf example.tar.bz2

Sometimes you only want to extract certain directories from the tarball. An example of doing so would be:

tar xvzf example.tar.gz */DIRECTORY_YOU_WANT_REPLACES_THIS_TEXT/*

List The Contents

If you would like to see what is inside a tarball, you can use the command:

tar tvf example.tar

If you would like to see what is inside a gzip’d tarball, you can use the command:

tar tzf example.tar.gz

Tar It Up!

If you would like to tarball some files, you can do so by using the command:

tar cvf filename.tar files/directories

If you would like to tarball some files AND compress them (with gzip), you can do so by using the command:

tar cfz blah.tar.gz files/directories

man tar

The man page for the tar command:

NAME
       tar - The GNU version of the tar archiving utility

SYNOPSIS
       tar  [options]

       Operations:
       [-]A --catenate --concatenate
       [-]c --create
       [-]d --diff --compare
       [-]r --append
       [-]t --list
       [-]u --update
       [-]x --extract --get
       --delete

       Common Options:
       -C, --directory DIR
       -f, --file F
       -j, --bzip2
       -p, --preserve-permissions
       -v, --verbose
       -z, --gzip

       All Options:
       [  --atime-preserve  ]  [ -b, --blocking-factor N ]
       [ -B, --read-full-records ] [ --backup BACKUP-TYPE ]
       [ --block-compress ] [ -C, --directory DIR ] [ --check-links ]
       [ --checkpoint ] [ -f, --file [HOSTNAME:]F  ]
       [  -F,  --info-script  F  --new-volume-script  F  ]
       [  --force-local   ] [ --format FORMAT ]
       [ -g, --listed-incremental F ] [ -G, --incremental ]
       [ --group GROUP ] [ -h, --dereference ] [ --help ]
       [ -i,  --ignore-zeros  ]  [  --ignore-case  ]
       [ --ignore-failed-read  ]  [ --index-file FILE ] [ -j, --bzip2 ]
       [ -k, --keep-old-files ] [ -K, --starting-file F ]
       [ --keep-newer-files ] [ -l, --one-file-system ]
       [ -L, --tape-length N ] [ -m, --touch, --modification-time ]
       [  -M, --multi-volume  ]  [  --mode  PERMISSIONS  ]
       [ -N, --after-date DATE, --newer DATE ] [ --newer-mtime DATE ]
       [ --no-anchored ] [ --no-ignore-case ] [ --no-recursion ]
       [ --no-same-permissions ] [ --no-wildcards ]
       [  --no-wildcards-match-slash  ] [ --null     ] [ --numeric-owner ]
       [ -o, --old-archive, --portability, --no-same-owner ]
       [ -O, --to-stdout ] [ --occurrence NUM ] [ --overwrite ]
       [ --overwrite-dir ] [ --owner USER ]
       [ -p, --same-permissions, --pre-serve-permissions  ]
       [  -P,  --absolute-names  ]  [  --pax-option  KEYWORD-LIST ]
       [ --posix ] [ --preserve ] [ -R, --block-number ]
       [ --record-size SIZE ] [ --recursion ] [ --recursive-unlink ]
       [ --remove-files ]  [  --rmt-command CMD  ]
       [  --rsh-command  CMD  ] [ -s, --same-order, --preserve-order ]
       [ -S, --sparse ] [ --same-owner ] [ --show-defaults ]
       [ --show-omitted-dirs ]
    [ --strip-components NUMBER, --strip-path NUMBER (1) ]
       [ --suffix SUFFIX ] [ -T, --files-from  F ] [ --totals   ]
    [ -U, --unlink-first ] [ --use-compress-program PROG ] [ --utc ]
    [ -v, --verbose ] [ -V, --label NAME ] [ --version  ] [ --volno-file F ]
       [ -w, --interactive, --confirmation ] [  -W,  --verify  ]
    [ --wildcards  ] [  --wildcards-match-slash  ]  [  --exclude PATTERN ]
       [ -X, --exclude-from FILE ] [ -Z, --compress, --uncompress ]
       [ -z, --gzip, --gunzip, --ungzip ] [ -[0-7][lmh] ]

       (1) tar-1.14 uses --strip-path, tar-1.14.90+ uses --strip-components

DESCRIPTION
       This manual page documents the GNU version of tar, an archiving program
    designed to store and extract files from an archive  file  known  as  a
    tarfile.  A tarfile may be made on a tape drive, however, it is also
    common to write a tarfile to a normal file.  The first argument to tar
    must be one of the options Acdrtux, followed by any optional functions.
    The final arguments to tar are the names of the files or directories
    which should be archived.  The use of a directory name always implies
    that the subdirectories below should be included in the archive.

EXAMPLES
       tar -xvf foo.tar
              verbosely extract foo.tar

       tar -xzf foo.tar.gz
              extract gzipped foo.tar.gz

       tar -cjf foo.tar.bz2 bar/
              create bzipped tar archive of the directory bar called foo.tar.bz2

       tar -xjf foo.tar.bz2 -C bar/
              extract bzipped foo.tar.bz2 after changing directory to bar

       tar -xzf foo.tar.gz blah.txt
              extract the file blah.txt from foo.tar.bz2

FUNCTION LETTERS
       One of the following options must be used:

       -A, --catenate, --concatenate
              append tar files to an archive

       -c, --create
              create a new archive

       -d, --diff, --compare
              find differences between archive and file system

       -r, --append
              append files to the end of an archive

       -t, --list
              list the contents of an archive

       -u, --update
              only append files that are newer than the existing in archive

       -x, --extract, --get
              extract files from an archive

       --delete
              delete from the archive (not for use on mag tapes!)

COMMON OPTIONS
       -C, --directory DIR
              change to directory DIR

       -f, --file [HOSTNAME:]F
              use archive file or device F (default "-", meaning stdin/stdout)

       -j, --bzip2
              filter archive through bzip2, use to decompress .bz2 files

       -p, --preserve-permissions
              extract all protection information

       -v, --verbose
              verbosely list files processed

       -z, --gzip, --ungzip
              filter the archive through gzip

ALL OPTIONS
       --atime-preserve
              donât change access times on dumped files

       -b, --blocking-factor N
              block size of Nx512 bytes (default N=20)

       -B, --read-full-blocks
              reblock as we read (for reading 4.2BSD pipes)

       --backup BACKUP-TYPE
              backup files instead of deleting them using BACKUP-TYPE simple or numbered
       --block-compress
              block the output of compression program for tapes

       -C, --directory DIR
              change to directory DIR

       --check-links
              warn if number of hard links to the file on the filesystem mismatch the
     number of links recorded in the archive

       --checkpoint
              print directory names while reading the archive

       -f, --file [HOSTNAME:]F
              use archive file or device F (default "-", meaning stdin/stdout)

       -F, --info-script F --new-volume-script F
              run script at end of each tape (implies --multi-volume)

       --force-local
              archive file is local even if has a colon

       --format FORMAT
              selects output archive format
              v7 - Unix V7
              oldgnu - GNU tar <=1.12
              gnu - GNU tar 1.13
              ustar - POSIX.1-1988
              posix - POSIX.1-2001

       -g, --listed-incremental F
              create/list/extract new GNU-format incremental backup

       -G, --incremental
              create/list/extract old GNU-format incremental backup

       -h, --dereference
              donât dump symlinks; dump the files they point to

       --help like this manpage, but not as cool

       -i, --ignore-zeros
              ignore blocks of zeros in archive (normally mean EOF)

       --ignore-case
              ignore case when excluding files

       --ignore-failed-read
              donât exit with non-zero status on unreadable files

       --index-file FILE
              send verbose output to FILE instead of stdout

       -j, --bzip2
              filter archive through bzip2, use to decompress .bz2 files

       -k, --keep-old-files
              keep existing files; donât overwrite them from archive

       -K, --starting-file F
              begin at file F in the archive

       --keep-newer-files
              do not overwrite files which are newer than the archive

       -l, --one-file-system
              stay in local file system when creating an archive

       -L, --tape-length N
              change tapes after writing N*1024 bytes

       -m, --touch, --modification-time
              donât extract file modified time

       -M, --multi-volume
              create/list/extract multi-volume archive

       --mode PERMISSIONS
              apply PERMISSIONS while adding files (see chmod(1))

       -N, --after-date DATE, --newer DATE
              only store files newer than DATE

       --newer-mtime DATE
              like --newer, but with a DATE
       --no-anchored
              match any subsequenceof the nameâs components with --exclude

       --no-ignore-case
              use case-sensitive matching with --exclude

       --no-recursion
              donât recurse into directories

       --no-same-permissions
              apply userâs umask when extracting files instead of recorded permissions

       --no-wildcards
              donât use wildcards with --exclude

       --no-wildcards-match-slash
              wildcards do not match slashes (/) with --exclude

       --null --files-from reads null-terminated names, disable --directory

       --numeric-owner
              always use numbers for user/group names

       -o, --old-archive, --portability
              like --format=v7; -o exhibits this behavior when creating an
     archive (deprecated behavior)

       -o, --no-same-owner
              do not attempt to restore ownership when extracting; -o exhibits
     this behavior when extracting an archive

       -O, --to-stdout
              extract files to standard output

       --occurrence NUM
              process only NUM occurrences of each named file; used with --delete,
     --diff, --extract, or --list

       --overwrite
              overwrite existing files and directory metadata when extracting

       --overwrite-dir
              overwrite directory metadata when extracting

       --owner USER
              change owner of extraced files to USER

       -p, --same-permissions, --preserve-permissions
              extract all protection information

       -P, --absolute-names
              donât strip leading â/âs from file names

       --pax-option KEYWORD-LIST
              used only with POSIX.1-2001 archives to modify the way tar handles
     extended header keywords

       --posix
              like --format=posix

       --preserve
              like --preserve-permissions --same-order

       -R, --record-number
              show record number within archive with each message

       --record-size SIZE
              use SIZE bytes per record when accessing archives

       --recursion
              recurse into directories

       --recursive-unlink
              remove existing directories before extracting directories of the
     same name

       --remove-files
              remove files after adding them to the archive

       --rmt-command CMD
              use CMD instead of the default /usr/sbin/rmt

       --rsh-command CMD
              use remote CMD instead of rsh(1)

       -s, --same-order, --preserve-order
              list of names to extract is sorted to match archive

       -S, --sparse
              handle sparse files efficiently
       --same-owner
              create extracted files with the same ownership

       --show-defaults
              display the default options used by tar

       --show-omitted-dirs
              print directories tar skips while operating on an archive

       --strip-components NUMBER, --strip-path NUMBER
              strip NUMBER of leading components from file names before extraction

              (1) tar-1.14 uses --strip-path, tar-1.14.90+ uses --strip-components

       --suffix SUFFIX
              use SUFFIX instead of default â~â when backing up files

       -T, --files-from F
              get names to extract or create from file F

       --totals
              print total bytes written with --create

       -U, --unlink-first
              remove existing files before extracting files of the same name

       --use-compress-program PROG
              access the archive through PROG which is generally a compression
     program

       --utc  display file modification dates in UTC

       -v, --verbose
              verbosely list files processed

       -V, --label NAME
              create archive with volume name NAME

       --version
              print tar program version number

       --volno-file F
              keep track of which volume of a multi-volume archive its working
     in FILE; used with --multi-volume 

       -w, --interactive, --confirmation
              ask for confirmation for every action

       -W, --verify
              attempt to verify the archive after writing it

       --wildcards
              use wildcards with --exclude

       --wildcards-match-slash
              wildcards match slashes (/) with --exclude

       --exclude PATTERN
              exclude files based upon PATTERN

       -X, --exclude-from FILE
              exclude files listed in FILE

       -Z, --compress, --uncompress
              filter the archive through compress

       -z, --gzip, --gunzip, --ungzip
              filter the archive through gzip

       --use-compress-program PROG
              filter the archive through PROG (which must accept -d)

       -[0-7][lmh]
              specify drive and density

BUGS
       The  GNU  folks,  in general, abhor man pages, and create info documents
    instead.  The maintainer of tar falls into this category.  Thus this man
    page may not be complete, nor current, and was included in the Red Hat CVS
    tree because  man  is  a  great  tool   .   This man page was first taken
    from Debian Linux and has since been lovingly updated here.

REPORTING BUGS
       Please report bugs via https://bugzilla.redhat.com

SEE ALSO
       The full documentation for tar is maintained as a Texinfo manual.  If
    the info and tar programs are properly installed at your site, the command

              info tar

       should give you access to the complete manual.

AUTHORS
       Debian Linux http://www.debian.org/
       Mike Frysinger 

GNU                                                      Oct 2004                                                   TAR(1)

The Full Tar Manual

See The Wiki for the full manual.

Finishing Statements

That concludes today’s tidbit of command line reference! I hope that you found this useful. If you would like to see any further information added, you can do so by editing the Wiki right here.

Jumat, 25 November 2011

Memasang VMD dari File Binary

Salah satu aplikasi kimia yang sering dipakai sebagai viewer dalam komputasi adalah software VMD.

"VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting"

Untuk memasang VMD dalam Blankon/Ubuntu/Linux perlu dilakukan langkah-langkah berikut:

1. Download source code VMD dari website-nya yaitu http://www.ks.uiuc.edu/Research/vmd/vmd-1.9/files/final/vmd-1.9.bin.LINUX.opengl.tar.gz

2. Masuk ke terminal dengan klik Aplikasi --> Aksesoris --> Terminal atau tekan "Ctrl+Alt+T"

3. Masuk ke direktori tempat download file VMD

4. Ekstrak file tersebut dengan ketik: tar -xvf vmd-1.9.bin.LINUX.opengl.tar.gz

5. Masuk ke folder hasil ekstrak file VMD, ketik cd vmd-1.9

6. Baca file README dengan ketik: gedit README

Perhatikan bagian akhir file: Quick Installation Instructions

7. Perhatikan langkah-langkah instalasi berikut:

Quick Installation Instructions

-------------------------------------------------

Detailed instructions for compiling VMD from source code

can be found in the programmer's guide.

The Windows version of VMD is distributed as a self-extracting

archive, and should be entirely self explanatory.

The native MacOS X version of VMD is packaged as a disk image and is

extracted by opening the disk image, and dragging the "VMD" application

contained inside into an appropriate directory.

For quick installation of the binary distribution for Unix do the following:

1) Uncompress and untar the distribution into a working directory.

In this working directory, there are several subdirectories such

as bin, src, doc, data, as well as this README and a configure script.

Change to this working directory after the unpacking is complete.

2) Edit the file 'configure'; change the values for

the $install_library_dir and $install_bin_dir to a directory in

which vmd data files and executables should be installed, be sure

that you installing into a clean target directory and not overwriting

an existing version of VMD (which would otherwise give problems):

$install_bin_dir is the location of the startup script 'vmd'.

It should be located in the path of users interested in running VMD.

$install_library_dir is the location of all other VMD files.

This included the binary and helper scripts. It should not be

in the path.

3) A Makefile must be generated based on these configuration variables

by running "./configure".

4) After configuration is complete, cd to the src directory,

and type "make install". This will install VMD in the two

directories listed above. Note that running "make install"

twice will print error messages because you are attempting to

overwrite some read-only files. Similarly, if you have incorrectly

specified the target installation directories or attempt to overwrite

an existing VMD installation, you will get error messages.

5) When installed, type 'vmd' to start (make sure the

$install_bin_dir directory is in your path).

8. Baca file "configure", perhatikan bagian awalnya:

#!/usr/bin/env perl

# Usage: configure [ optionlist ] (See full option description down below)

# Perl 5.x must be in your path, and /usr/bin/env must exist in order

# for this to work correctly.

##############################################################################

# User modifiable installation parameters, can be overridden by env variables

##############################################################################

# Name of shell script used to start program; this is the name used by users

$install_name = "vmd";

# Directory where VMD startup script is installed, should be in users' paths.

$install_bin_dir="/usr/local/bin";

# Directory where VMD files and executables are installed

$install_library_dir="/usr/local/lib/$install_name";

# optionally override hard-coded defaults above with environment variables

if ($ENV{VMDINSTALLNAME}) {

$install_name = $ENV{VMDINSTALLNAME}

}

if ($ENV{VMDINSTALLBINDIR}) {

$install_bin_dir = $ENV{VMDINSTALLBINDIR}

}

if ($ENV{VMDINSTALLLIBRARYDIR}) {

$install_library_dir = $ENV{VMDINSTALLLIBRARYDIR}

}

9. Okay, sekarang masuk ke folder vmd-1.9

10.ketik: ./configure

11. masuk ke folder "src" dengan ketik: cd src

12. ketik: make install

13. Biarkan sampai instalasi selesai

14. untuk menjalankan software VMD ketik: vmd [Enter]

15. Selamat berlatih!

KIMUX: Paket Aplikasi Kimia - Linux

Kimux 1.01 hydrogen adalah rilis perdana paket aplikasi kimia linux yang merupakan remastering distro Ubuntu 11.04. Kimux ini dibuat untuk membantu para pengguna pemula linux yang tidak ingin direpotkan dengan instalasi linux dan aplikasi kimia yang begitu banyak. Hanya dengan instalasi Kimux maka akan diperoleh paket linux beserta aplikasi kimia yang tinggal pakai. Pengembangan sekarang ini sudah sampai edisi Kimux 1.02 hydrogen yang merupakan perbaikan dan penambahan aplikasi dari edisi sebelumnya.