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HUSAR Bioinformatics Lab :: Documentation | |||||
Another important feature of UNIX is the hierarchical structure of the file system. Generally there are several thousand files and directories stored on a UNIX computer. In order to provide a reasonable way of accessing them, the storage medium is logically structured in a tree like manner (see page 2 for an example). All UNIX systems start with the root directory at the top level, and from there multiple subdirectories branch which again contain either files or other subdirectories.
A file can be specified by its name (filename) and its location in the directory tree (the pathname). Filenames can be up to 256 characters and may contain letters or digits (it is also possible, but not advisable to use characters with a special meaning under UNIX e.g.: $,*,/). Filenames do not require a certain structure (like "filename. extension"), hence they might for example contain multiple dots. Names can be lower or upper case or a mixture of both, but beware, UNIX is strictly case sensitive, which applies for both command names and filenames. As a rule, always use lower case letters for a UNIX command or program.
Pathnames can be stated either as absolute or relative pathnames. An absolute pathname always leads from the root directory (abbreviated with "/") down the hierarchical directory tree to the target directory. All directory names on the way down have to be included and each element must be separated by a slash (/). Example of an absolute path to the directory workshop: /lfs/people/work03/workshop.
A relative pathname begins at the current working directory (i.e. no leading slash) and then follows the path through the directory structure to the target. Example for a relative path designation starting at people: work03/workshop.
There are two directories which are especially important for a user.:
Convex Exemplar SPP-1000 Series (genius) login: work01 (type in your user-id) password: (type in your password) |
Your password will not be echoed on the screen.
After your login you are prompted for the terminal type which the GENIUS computer will use. If you find vt100 in parentheses you can accept this default value by just pressing the RETURN key. Otherwise type vt100 and press RETURN.
Welcome to Convex Exemplar SPP-Ux Operating System
(Other messages about new mail etc. might appear here.)
TERM = (network) vt100
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You will then see the main menu system of the GENIUS computer:
0101010101010101010101010101010101010101010101010101010101010101010100101
@
@
@ * * * Welcome ---------- @
@ * * to the Biocomputing Unit / / @
@ * E D R * at the / GENIUSnet / @
@ * * German Cancer Research Center / / @
@ * * * Heidelberg ----------- @
@ @
0101010101010101010101010101010101010101010101010101010101010101010100101
Some programs require the X Window System. If you have an X-Server
connected to the Internet you can choose 'Enable X-Programs'.
X-Programs are disabled.
h Sequence Analysis (Husar 4.0)
o OMIM (call GDB from the Menu System)
t Text Menu System (Lynx)
x Enable X-Programs
s Unix Shell
e Exit
Enter your choice:
|
To enter the Unix Shell you have to write 's':
Type "exit" to leave shell
> |
Now you see a prompt sign. This is the UNIX system prompt if you are running the c- shell as the command interpreter (default) and indicates that the UNIX system is now ready to accept your commands.
As long as you see the ">"-sign you can launch any UNIX command by simply typing: command name [parameters] [filenames]
Parameters: - modify the way a command works
- are often single letters prefixed by a dash
Filennames: - specify files to be used
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It is possible to write several commands on one command line, by separating each command with a semicolon: e.g. command1 ; command2; command3. If a command does not fit on one line it can be continued on the next line by placing a backslash (\) at the end of the first line.
You CANNOT use the command "logout" at the HUSAR or UNIX prompt because
you first have to return to your login shell.
> exit (to return to the main menu, see above) |
After typing "e" you will now leave the GENIUS computer.
> passwd |
Changing password for work01
Old password: (The system asks you for your old password to verify
that you are authorized to change the password.)
New password: (type in the new password, it will not be echoed)
Retype new password: (retype the new password to verify its correct spelling)
|
The following rules apply to passwords:
If you have not changed your password in the last 12 weeks you will get the following
message during your login:
Your password has not been changed in 12 week(s)
Choose a new one!
Old password (Type in the old password and then choose a new one
to complete the login.)
|
> pwd /lfs/people/work01 |
> cd workshop > > pwd /lfs/people/work01/workshop |
If you want to change to a directory which is not directly beneath your cwd you must include a path in your cd command using either absolute or relative pathnames (s. above). For this purpose you can use a number of abbreviations:
~ = the home directory |
The command cd (alone, without any additions) will always bring you directly back to the home directory - irrespective of the current position in the directory tree. Therefore cd is equivalent to cd ~.
Examples:
> cd ../../.. (change to the root directory, using relative pathname ".."
to indicate parent directories)
>
> pwd
/ (pwd shows that the cwd is root = /)
> cd (change back to the home directory)
>
> pwd
/lfs/people/work01
|
If your cwd is ~/workshop and you wanted to change to the directory ~/project you could choose among different possibilities:
> cd /lfs/people/work03/project (cd with absolute pathnames) > cd ../project (cd with relative pathnames) > cd ~/project (cd with the home directory in the pathname) |
mkdir [pathname][directory name] (Make Directory)
> mkdir project (creates the directory project beneath the home directory) > > cd project > > pwd /lfs/people/work03/project |
To remove a directory use the command: rmdir [pathname][directory name] (Remove Directory). However two requirements must be met before a directory can be deleted:
> cd .. > rmdir project |
> ls a.map baum3 genius.txt test.fasta workshop a.seq emnew.strings mail.kurs test.mail baum2 gchbba6.fasta mbox test.map |
A central feature of UNIX is the usage of command line parameters which extend or modify simple commands. Using parameters makes UNIX very powerful (and sometimes rather cryptic). Very often UNIX commands have a large number of possible parameters (ls has about 20) however only a few are frequently used. Some of the important parameters for the ls command are:
-l = lists content in long format -a = lists all directory entries. |
Without this option files which have a dot (.) in the first position of their filename (the so called "hidden" files) are not listed
-t = sorts all entries according to the last change of a file (default is an alphabetical
order)
-F = shows the type of a file: directories are marked with a slash (/) executables with
an asterisk (*)
|
> ls -l
total 109
-rw-rw-r-- 1 work01 6568 Oct 31 16:07 a.map
-rw-rw-r-- 1 work01 1072 Oct 31 16:07 a.seq
-rw-rw-r-- 1 work01 539 Oct 31 16:07 baum2
-rw-rw-r-- 1 work01 539 Oct 31 16:07 baum3
-rw-rw-r-- 1 work01 200 Oct 31 16:07 emnew.strings
-rw-rw-r-- 1 work01 48609 Oct 31 16:07 gchbba6.fasta
-rw-rw-r-- 1 work01 921 Oct 31 16:07 genius.txt
-rw-rw-r-- 1 work01 363 Oct 31 16:07 mail.kurs
-rw-rw-r-- 1 work01 348 Oct 31 16:08 mbox
-rw-rw-r-- 1 work01 39973 Oct 31 16:08 test.fasta
-rw-rw-r-- 1 work01 358 Oct 31 16:08 test.mail
-rw-rw-r-- 1 work01 3379 Oct 31 16:08 test.map
drwxrwxr-x 2 work01 512 Oct 31 16:08 workshop
---------- - ------ ----- ------ ----- -----------
(1) (2) (3) (4) (5) (6) (7)
|
This long listing shows considerably more information than the standard "ls" command. The output can be grouped into different fields: (e.g. for the first entry "a.map"):
(1): File type (-) and permissions (rw-rw-r--)
(2): Number of names linked to the file (1)
(3): Name of owner of the file (work01)
(4): Size of file in bytes (6568)
(5): Date the file was last modified (Oct 31)
(6): Time the file was last modified (16:08)
(7): Filename or directory name (a.map)
total 109 is the number of disk blocks used by the files in the directory.
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Details to (1): the first character indicates the type of file in the listing: Example:
- = regular file (standard) d = directory l = symbolic link |
The next nine characters form 3 sets of 3 permission flags:
the first triplet stands for the permissions of the user, the second for the group and
the third for all other users on the machine.
r = read permission, w = write permission (also to delete a file) x = execute permission (e.g. to run a program) |
It is also possible to combine multiple parameters on the command line, e.g. the parameter "l" for a "long" listing and the parameter "t" to list files sorted according to to last change of a file, so a new created or changed file will be listed first.
> ls -lt -rw-rw-r-- 1 work01 348 Oct 31 16:08 mbox -rw-rw-r-- 1 work01 39973 Oct 31 16:08 test.fasta -rw-rw-r-- 1 work01 6568 Oct 31 16:07 a.map -rw-rw-r-- 1 work01 1072 Oct 31 16:07 a.seq -rw-rw-r-- 1 work01 539 Oct 31 16:07 baum2 -rw-rw-r-- 1 work01 539 Oct 31 16:07 baum3 -rw-rw-r-- 1 work01 200 Oct 30 16:07 emnew.strings -rw-rw-r-- 1 work01 48609 Oct 30 16:07 gchbba6.fasta -rw-rw-r-- 1 work01 921 Oct 25 16:07 genius.txt -rw-rw-r-- 1 work01 363 Oct 25 16:07 mail.kurs |
To make an exact copy of an already existing file use the command:
cp [pathname][source-filename] [pathname][target-filename] (copy)
This creates a new file ("target") as a duplicate of the "source" or overwrites a target file if this file already exists.
Examples:
> cp a.map a.map.2 A copy of the file a.map called a.map.2 is created in
the same directory.
> cp a.map project The cwd is home, out of this directory the file a.map is
copied to the directory project
> cp a.map project/b.map The cwd is home, the file a.map is copied to the directory
project and renamed to b.map
> cd project (change the cwd to project)>
> cp ../a.seq .
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The cwd is now project. Copy a file (a.seq) from the parent directory (indicated by the two dots) to the current directory (indicated by one dot). If you mention a filename for the target you do not need to state the current (target) directory.
> cp ../a.seq a.2.seq |
To copy all files of a directory to a second directory at once, use:
cpall [pathname][source-directory name] [pathname][target-directory name]
Example:
> cpall ~/workshop . |
This copies all files and subdirectories from workshop to the cwd "project".
This command also copies subdirectories and their contents
To copy only files and no subdirectories with one command to a second directory use wildcards (metacharacters). UNIX wildcards are:
a) the asterisk (*): it stands for any number of alphanumeric characters (and also for
NO characters at all). As soon as the c-shell finds a wildcard it will expand this
wildcard and substitute it with all possible characters.
b) the question mark (?): it matches a single character (but always one character -
not null)
c) the square brackets ([]): any characters which are enclosed in these brackets will
be used, it is also possible to state a range of characters, e.g. [a-z] would use any
character between "a" and "z".
Examples:
> cp ~/test.* . (copies all files which start with "test." in the home
directory to the cwd)
> cp ~/test?.seq . (copies the files "test1.seq", " test2.seq",
"test3.seq" etc. to the cwd, the "?" is
substituted by the figures 1,2,3)
> cp ~/test[abc] . (this copy command matches all files which start
with "test" and end with "a", "b" or "c").
> cp ~/test[1-8] . (this copy command matches all files which start
with "test" and end with one of the figures from
1 to 8)
|
Metacharacters can be used with all UNIX commands.
To rename or move a file use the command:
mv [pathname][source-filename] [pathname][target-filename] (move)
Examples:
> cd (go back to the home directory) > mv a.seq b.seq (the file "a.seq" will be renamed to "b.seq") > mv mbox project/mbox.2 |
The file mbox will be deleted in the home directory and a copy of it will be simultaneously created in the directory project under the name "mbox.2".
> cd project (change from the home directory to the directory
"project")
> mv ../mail.kurs . (deletes "mail.kurs" in the home directory and
creates a copy in the cwd)
|
To delete a file use the command: rm [pathname][filename] (remove)
Example:
> cd (change back to the home directory)
> rm project/mail.kurs (deletes the file "mail.kurs" in the directory project)
> rm * (this will delete all files in the current directory)
|
To avoid that files are deleted unintentionally while using wildcards add the
parameter
"-i" (for interactive) to the command line:
> rm -i * rm: remove a.map? n rm: remove a.seq? y rm: remove baum2? rm: remove emnew.strings? ... |
You are then asked for each file which matches the wildcard expression whether this file should be deleted or not. If you press RETURN after the question mark this will be interpreted as "no" (the same as typing "n") and the file will be kept. If you press "y" the file will be deleted.
There are a couple of commands to view the content of a text file:
cat [pathname][filename]: this command is not very handy since it does not stop the
screen output after each screen page.
more [pathname][filename]: stops screen output after each screen page, continue by
pressing the space bar
less [pathname][filename]: This is the recommended command to look at the content
of a file.
Example:
> less test.fasta |
You have several possibilities to move through this file:
Action: Press the key: Forward one page: blank Backward one page: b Forward one line: RETURN Backward one line: y Go to line number n [n]g top of file: g end of file: G Quit the less program: q |
A file editor enables the creation of files, e.g. for preparing a mail message, for writing a poster or a batch file (this is a file containing a list of UNIX commands). The following editors are available on the GENIUS computer:
- vi [pathname][filename], this is the standard editor on most UNIX systems
- emacs
- pico
- textedit, textedit is not as powerful as the other editors (i.e. this editor is not
very well suited for handling large files), however, it is very easy to use textedit and it
is most convenient for small files like batch files. Textedit is only available in the
HUSAR environment; it is not one of the general purpose UNIX editors.
|
Because "vi" is standard on most UNIX systems we will give a short introduction here. Start "vi" with e.g.:
> vi test.fasta |
If the file mentioned on the command line already exists, it will automatically be loaded in the editor, otherwise a new file with this name will be created. Inside "vi" two general modes are available:
a) the command mode: in this mode the cursor is moved, text is deleted or character patterns are substituted and file related commands like saving the text in a file are launched. Immediately after starting the "vi" the command mode is activated. b) the insert mode: in this mode text is either entered or overwritten.
- To change from insert mode to command mode press the "Escape"-key.
- To enter the insert mode you can use one of the following commands:
i = insert text in front of the current cursor position
I = insert text at the beginning of the current line
a = insert text after the current cursor position
A = insert text at the end of the current line
o = a blank line is inserted after the current line
O = a blank line is inserted in front of the current line
|
- Available commands in the command mode:
To move in the text:
(use the cursor keys to move up one line, left one chararcter etc.)
- ^ : begin of the current line
- $ : end of the current line
- Control-F : forward one page
- control-B : backward one page
- control-D : forward half a page
- Control-U :backward half a page
- [n]G : go to line number [n]
- G : go to the last line of the file
|
To edit the text:
- x : deletes the current character
- [n]dd : deletes n lines (the current line if n = 0)
- D : deletes the rest of the current line
- J : merges the current and the following line
- p : inserts the content of the buffer (e.g. after a deletion)
after the current cursor position
- P : insert the buffer content before the current cursor
position
|
To search in the text:
/ pattern (Return) : starting from the current cursor position this
searches for "pattern"
:a,b s/pat1/pat2 /g : substitutes "pat1" with "pat2" only for the first
occurrence of pat1 unless "/g" is specified. The
substitution starts at line "a" and ends at line "b".
Abbreviations: $ stands for the last line of the file,
> stands for the whole file
|
Example:
:>s/old/new/g (substitutes "old" with "new" for all occurrences of
"old" in the whole file)
:20,$ s/old//g (substitutes "old" with blank - deletes "old" from line
20 to the end of the file)
|
File commands:
- :r [filename] :inserts the specified filename at the current cursor
position
- :q :terminates the editor, if the buffer was not changed
- :q! :terminates the editor even if the buffer was changed
- :wq :terminates the editor , the old version of the file is
overwritten by the buffer content.
- :x :same as wq, but the file is only overwritten if changes
were made
- :w [filename] :the content of the buffer is stored. If a filename is given
the buffer will be stored under this name
|
To use a control sequence press the CONTROL key ("Strg"-key on a German keyboard) together with the respective character:
- Control-s :freezes the screen output.
- Control-q :unfreezes the screen output (this will show you the
subsequent pages)
- Control-c :program interrupt. ("in case of emergency"). This terminates
most of the UNIX commands (with a few exceptions like "less")
or programs if you face any problems, or if you started the
program with the wrong para-meters, etc. You do not have to
wait until a program or command is completed, no results will
be, however, produced upon terminating a program/command with
control-c.
- Control-d :End of file character in UNIX. You can use control-d to
terminate your UNIX session (if you are in your login shell),
or to send your e-mail (if you use the program "mail" for
e-mail).
- Control-z :Stops a running job but does not interrupt (kill) it. With
the command "bg" you can then start this job again and let it
run in the background, with the command "fg" you start it
again in the foreground.
|
To get information about your available disk space use: quota -v
> quota -v Disk quotas for work01 (uid 8527): Filesystem usage quota limit timeleft files quota limit timeleft /lfs/people 616 4000 5000 0 0 0 |
Usage tells you how much disk space has already been used by this user-id (all figures are in KB i.e. 616 = 616000 Byte). Quota is the amount of disk space which is regularly available. You might pass over this value up to the value which is spezified in limit. However you are only allowed to exceed your quota for a certain amount of time (about one week). As soon as quota is overstepped timeleft will show you the amount of days which are left to clean the disk space which exceeds quota. During the login you will be notified if quota is exceeded.
Process control:
All commands which you launch on the GENIUS computer can be regarded as a process. However, for each command/program a shell (the command interpreter) is started, giving rise to an additional process also. Since a user usually has multiple processes running simultaneously, it is sometimes necessary to get information about these processes, especially if access to one of these processes is no more longer possible (e.g., after interruption of the communication line). To see all own processes use: ps
> ps
PID TT STAT TIME COMMAND
2624 qb R 0:00 (ps)
10470 qb I 0:00 -csh[dok419]
10538 qb I 0:00 /bin/csh /usr/local/husar/uwgcg/com/.husar.csh
10545 qb S 0:03 -sh
|
PID stands for process identification number.
TT for the terminal identifier,
STAT for the state of the process (e.g. R = running, I = idle, S = stopped)
TIME for the cpu-time used
COMMAND for the command which is run by the process.
> ps -l F UID PID PPID CP PRINI SZ RSS WCHAN STAT TT TIME COMMAND 9 337 2768 10545 11 1.3e+02 0 5152 308 ........ (ps) 8002 337 10470 10467 0 1.3e+02 0 116 ........ -csh[d 209 337 10538 10470 0 1.3e+02 0 108 ........ /bin/c 209 337 10545 10538 3 1.3e+02 0 156 ........ -sh |
If you use ps with the parameter -l you get a long listing of your processes. This is especially important if you have to remove one of the processes. In some cases it is even necessary also to remove the parent process (the shell which is running the respective process). To identify the parent process look at the process you want to remove and search the PPID (parent process identification).
To remove a process use the command: kill [PID]
Example:
Remove the ps process (assuming that it would still be running)
> kill 2768 |
This will remove the process with the PID 2768 (10545 is the PPID of the ps
command). The ps command will then be killed.
If a process fails to terminate this way use the parameter: -9, this parameter forces a
process to terminate in any case:
> kill -9 2768 |
The "history" facility memorises the commands you issue and thus provides a means for reissuing previous commands. "History" allows you to repeat and modify the last 20 commands by using the "arrow" keys (cursor keys). To move backward or forward through these commands , press the "up-arrow" or"down-arrow" key, respectively.
An alias allows the renaming or abbreviating of a command. If you have for example a long command sequence you can set an alias for this sequence and use a single letter to start it. Use the command: alias [aliasname] [command]
> alias h husar |
If you now type in "h" the command "husar" will be launched. You can also set an alias for a combination of commands. You have to enclose, however, the list of commands in forward single quotes (').
> alias lm 'ls -al | more' |
If you type in "lm", a long listing of all files in a directory will be shown, the output
stops after each screen page.
An alias is only active during the current terminal session, after logout it will be
deleted. To establish a permanent alias you have to add the alias definition to your
".cshrc"-file. This file is one of the "hidden" files in your home directory.
If you need further information about a certain UNIX command you can call the online help with the command: man [command name]
> man ls
ls(1)
NAME (gives the command name and a short description)
ls, lf, ll, lr - list contents of directory
SYNOPSIS (an exact explanation on how to call the command)
ls [ -acdfghilqrstu1ACHLFR ] name ...
lf [ -acdfghilqrstu1ACHLR ] name ...
ll [ -acdfghiqrstu1ACHLFR ] name ...
lr [ -acdfghilqrstu1ACHLF ] name ...
DESCRIPTION (General description of the command and parameters)
For each directory argument, ls lists the contents of the
directory; for each file argument, ls repeats its name and
.................
|
You can browse through the online help using all "less" commands e.g. "q" to quit
the help program, space bar to move one page forward etc.
Another online help is info. Info also gives a description of UNIX commands,
however info is menu driven and instead of entering an already known command
name you choose a certain topic (e.g. looking at file contents).
Electronic mail offers you an easy way to send and receive messages around the
world. Before you can communicate with another user you must know his or her
user-id, which is the name with which a user logs into the system. If the person you
wish to communicate with is on another computer system, then you will also need to
know the network address of his or her computer system (nodename).
There are three commands on the Genius computer to handle mail. One is the "elm"
command, which is automatically used, if you choose the second menu point
"Electronic-Mail" of the submenu 'UNIX'. The problem in using ??elm?? is, that you
have to use one of the UNIX file editors (usually "vi"). If you are familiar with vi, "elm"
is very easy to use with its self-describing menu system. Otherwise the command
"mailx" is easier to use or the third one "pine", which uses an editor
named "pico". Both are described in the following section.
I. Working with "mailx":
Sending mail. To send mail to user "work01" for example, type
> mailx work01 (if the user work01 is in the same computer system) |
If the user is on another computer system, you must specify the address of the receiver:
> mailx work01@genius.embnet.dkfz-heidelberg.de (work01 is the username and genius.embnet.dkfz-heidelberg.de is the nodename of the GENIUS computer at the DKFZ, where the GENIUSnet users are working on) |
Reading mail.
1.) If you call mailx without arguments, it checks whether new mail has arrived and prints out a one line header for each message available. The current message is initially the first message (numbered 1).
> mailx |
File commands:
p read the current message
|
II. Working with Pine
Another possibility is to use Pine. Pine was originally conceived in 1989 as a simple, easy-to-use mailer for the administrative staff at the University of Washington in Seattle. The goal was to provide a simple mailer that naive users could use without fear of making mistakes. At that time, there was no such Unix mailer commercially or freely available, but Elm seemed closest to the goal, so they started modifying it. The name "Pine" originally stood for "Pine Is Nearly Elm"; today "Pine Is No-longer Elm" is more appropriate. Pine and Pico, the editor used by Pine; are now available on the GENIUSnet. Just start by typing pine (or pico) to start the e-mail program (or the editor), respectively:
> pine
Pine 3.91 MAIN MENU Folder: Inbox 0 Messages
? HELP - Get help using Pine
C COMPOSE MESSAGE - Compose and send a message
I FOLDER INDEX - View messages in current folder
L FOLDER LIST - Select a folder to view
A ADDRESS BOOK - Update address book
S SETUP - Configure or update Pine
Q QUIT - Exit the Pine program
Copyright 1989-1994. PINE is a trademark of the University of Washington.
[Folder ?INBOX? opened with 0 messages]
? Help P PrevCmd R RelNotes
O Other CMDS L [List Fldrs] N Next Cmd K KBLock
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Now you are in the main menu of Pine. To write an email just type c:
PINE 3.91 COMPOSE MESSAGE Folder: INBOX 0 Messages To : Genome@DKFZ-Heidelberg.de Cc : Attchmnt : Subject : Problem with HUSAR ------------Message Text ---------- Dear User Support, I forgot my password .. |
If you want to read your received messages just type i and you will get a list of the mails in your mailbox. By scrolling the curser up and down you can choose the mail you would like to read.
Network News can be compared to bulletin boards. It provides a way for groups of people to discuss ideas. Different boards are devoted to specific topics and anyone can put a message on it. Network News articles are circulated among sites. At such sites news articles are stored centrally where they may be read by the users. After a period of time the expired articles are removed from the newsgroup. In order to access Network News, type tin.
> tin 3 61 bionet.general General BIOSCI discussion. 4 11 bionet.genome.arabidopsis Information about the Arabidopsi 5 13 bionet.jobs Scientific Job opportunities. 6 1 bionet.journals.contents Contents of biology journal publ 7 1 bionet.molbio.ageing Discussions of cellular and orga 8 bionet.molbio.bio-matrix Computer applications to biologi 9 bionet.molbio.embldatabank Info about the EMBL Nucleic acid 10 15 bionet.molbio.evolution How genes and proteins have evol 11 bionet.molbio.genbank Info about the GenBank Nucleic a 12 138 bionet.molbio.genbank.updates Hot off the presses! (Moderated) 13 bionet.molbio.gene-linkage Discussions about genetic linkag 14 3 bionet.molbio.genome-program Discussion of Human Genome Proje 15 133 bionet.molbio.methds-reagnts Requests for information and lab 16 41 bionet.molbio.proteins Research on proteins and protein |
Once you are in Network News you can proceed by using the CURSOR to go up to the desired newsgroup and then by pressing RETURN. You then come to the newsgroup articles. Here is an example of some articles that we found under the newsgroup bionet.molbio.methds-reagnts:
1 + Basic Info Chris Boyd
2 + Western Blotting Current Problem David Ward Rusnak
3 + 3 Plate Readers Paul Herron
4 + 3 license for TAQ Tracy Aquilla
5 + 2 shooting yourself in the foot.... Tracy Aquilla
6 + 2 microsomes in IVT Michael Coady
7 + 5 Q: Properties of Phospho-cellulose Dima Klenchin
8 + Cyanobacterial RNA Edgar Valencia
9 + Nonisotopic Labels, Suggestions? Joan Boyce
10 + Ni-NTA Spin kit ....HELP Mike Rogers
11 + New Company Formed - Looking for People Glenn Diamond
12 + DNasing RNA samples jms93
13 + Qiagen PN Buffer???? Mary P. Remington
14 + direct PCR from E.coli jms93
15 + Help! RNA isolation from Guinea Pig Liver jms93
16 + Wanted: Articles about your Career Experience Dr.Heasley
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If you find something that looks of interest to you, then you can call the article up in the same way as was done to call up a newsgroup. We have choosen to read the article "Qiagen PN Buffer???"
Mon, 06 May 1996 13:33:06 bionet.molbio.methds-reagnts Thread 13 of 85 Lines 3 Qiagen PN Buffer??? No responses mremingt@umabnet.ab.umd.edu Mary P. Remington at University of Maryland One of Qiagens protocols calls for the use of this buffer. I have no Qiagen Buffer called "PN Buffer". Is this a misprint? Can PE Buffer be used instead? Thanks, Mary |
Computer files can be transferred between your local computer and the Genius computer. One of the most popular file transfer programs is kermit. You can use kermit, for instance, if you are connected via a public data network like Datex-P. If you use the Internet computer network to log on to the Genius computer, you have to use ftp to transfer files.
If you want to transfer files with kermit, you have to start a second kermit program on the Genius computer. Both kermits (the one on your local machine and the one on the Genius) will manage the file transfer.
> kermit |
Then you will see the "C-Kermit>" prompt of the "Genius kermit".
Sending files from the Genius computer to your local computer:
To send a file use the command send:
C-Kermit> send a.map (sending the file a.map) |
Then you have to return to the PC kermit by pressing "Alt-X". You will see the prompt
Kermit-MS>
To receive the file, type
Kermit-MS> receive (receiving the file a.map) |
A status screen will show you the progress of the file transfer. When the file has been completely transferred, your PC will beep and you will return to the Kermit-MS> prompt. With
Kermit-MS> c (connect) |
you will return to the Genius computer and with
C-Kermit> q (quit) |
you will exit the kermit program on the Genius computer.
Receiving files from your local computer to the Genius Computer:
In this case you have to use "send" and "receive" in the opposite way. Type
C-Kermit> receive |
on the Genius computer, then switch to your local computer with "Alt-X". Afterwards, give a send command:
Kermit-MS> send klon1.seq (sending the file klon1.seq) |
The status screen will be displayed again.
File transfer over Internet is initiated from your local computer using the ftp program. The specific syntax of ftp commands varies from implementation to implementation, if the commands described here do not correspond to your version, please consult your local system manager.
To initiate a connection to the Genius computer from your local machine, enter
>ftp genius.embnet.dkfz-heidelberg.de |
You will usually see a lot of messages. Then you are asked to enter your user-name and your password:
... username: work01 331 Password required for work01. password: work01 230 User work01 logged in. ftp> |
Now you will see the ftp> prompt, if you are succesfully logged in.
Sending a file from a local computer to the Genius:
ftp> put klon1.seq |
Receiving a file from the Genius computer to your local computer command:
ftp> get a.map |
Changing the current working directory
After your login on the Genius your are in your home directory. But in the most cases this is not the correct directory for the file transfer. You can change your current working directory with the command
ftp> cd project |
Now you are in the directory "project". It is also possible to change the directory on your local computer. With
ftp> lcd biomol |
you have changed to the directory "biomol". (The command "lcd" means "local change directory").
Listing your files on the Genius
If you want to list your files in the current working directory on the Genius computer you can type either
ftp> dir or ftp> ls |
With ls only the filenames are listed while the command dir gives you more information about the files like type, permissions, size of the file, name of the owner etc. With
ftp> quit |
you can exit the ftp program and return to your local machine.
pwd print working directory
ls [directory] lists the files in the directory
ls -l [directory] lists the files in long format
ls -t [directory] lists the files sorted by time
ls -lt [directory] lists the files in long format but sorted by time
mkdir project makes the project directory
rmdir project removes the project directory if it is empty
cd project changes to the directory project
cd go back to your login directory
cp file1 file2 copy file1 to the new file2
cp file(s) directory copy file(s) to the directory
mv file1 file2 rename file1 to be file2
mv file(s) directory move file(s) to the directory
rm file(s) delete the file(s)
rm -i file(s) delete the file(s) with query
pico remark.txt edit the file remark.txt with the pico editor
vi remark.txt edit the file remark.txt with the vi editor
more seq1.map types out the file seq1.map on the screen
less seq1.map types out the file seq1.map on the screen
man ls online help for the UNIX command ls
quota -v displays information about the available disk
space
passwd sets a new password
mailx [user address] an easy mailing program
pine a menu-guided mailing program using pico editor
elm another menu-guided mailing program using vi
editor
ftp [address] transfers file(s) over internet with ftp
kermit transfers file(s) with kermit
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