bash on ridgeside (simcenter)

Simcenter default shell is not bash. So, calling bash should use 'bash' not sh

Free unix shell online

https://www.tutorialspoint.com/unix_terminal_online.php

tar backup byte laptop

lapphy-pc1:~ hqin$ cat backup.byte.sh 

date

 echo "Back up Byte laptop  now"

 time perl /Users/hqin/perl/backup4.pl /Volumes/bear/byte > /tmp/_backup.hqin.txt 

date

lapphy-pc1:~ hqin$ sh backup.byte.sh 

Wed Jan 20 20:23:37 EST 2016

Back up Byte laptop  now

defined(%hash) is deprecated at /Users/hqin/lib/perl/Util.pm line 610.

(Maybe you should just omit the defined()?)

du: Library/Saved Application State/com.adobe.flashplayer.installmanager.savedState: Permission denied

tar: wdijk-112507/trash: Couldn't visit directory: Permission denied

tar: wdijk-112507/doc: Couldn't visit directory: Permission denied

tar: day2.tab: could not open file: Permission denied

tar: day3.tab: could not open file: Permission denied

tar: day4.tab: could not open file: Permission denied

tar: Error exit delayed from previous errors.

tar: Google: Cannot stat: No such file or directory

tar: Error exit delayed from previous errors.

real 82m9.817s

user 0m9.009s

sys 5m13.683s

Wed Jan 20 21:45:47 EST 2016

Unix shell tutorial

http://www.tutorialspoint.com/unix/unix-loop-control.htm

Useful Unix / Linux shell commands

 cat tmp.txt | sed s/CREATE/DROP/


 who | cut -c1-8 | sort | uniq | nl
 cat /usr/local/apache2/logs/access_log | grep 128\.135 | cut -c1-16 | uniq     
 ps -ef | grep nohup | cut -c53-57 | sort | uniq | nl 

 /sbin/shutdown -r now ?
 lsof

 /etc/rc.local  # system startup configuration

 grep CREATE ensembl_mart_16_1.sql | sed s/CREATE/DROP/ | sed s/\(/\;/ > $HOME/trim_mart.sql

ls enc.* | sed "s/^/\"/" | sed "s/$/\"\,/"

Bio386 day 2, unix shell, computer basics

Let students worked on unix shell.
Apple computer basics

ls,
pwd
cd
man
ls -a -l

Students are not aware of proper posture to use computers.

Todo: Computers in room 277 use OS 10.6.8. They need to be updated.

audio recording at
http://youtu.be/brHu46IL1zc

git, 2011scengs, shell operations, aborted and then GitHub piecemeal fashion.

I had trouble to push the large data using Gui version. So, I tried to use the shell commands. 


git config --global user.name "hongqin"

biolaptop17:2011scengs hongqin$ sudo curl -s -O \
  http://github-media-downloads.s3.amazonaws.com/osx/git-credential-osxkeychain

biolaptop17:bin hongqin$ ll git-credential-osxkeychain 
-rw-r--r--  1 root  wheel    15K Mar  6 11:11 git-credential-osxkeychain

sudo chmod u+x git-credential-osxkeychain

biolaptop17:bin hongqin$ sudo git config --global credential.helper osxkeychain

biolaptop17:2011scengs hongqin$ pwd
/Users/hongqin/github/2011scengs

$ git add src/*

$ git commit -m "src"

biolaptop17:2011scengs hongqin$ git remote add origin https://github.com/hongqin/2011scengs.git

fatal: remote origin already exists.

git push --force origin master
#fatal error

I deleted the .git directory. Re-cloned Gibhut directory, and then move small-sized folders into the github project. Synch with Github Gui worked this time. 

It turns out that Gibhub limize files size to 100M. How did I uploaded 1.6G tarfile into the Bacillus coat repository? 

Check Github show that 2011scengs was not updated.