newfile

bioinf
chr22_with_ERCC92.gtf
Desktop
Documents
Downloads
examples.desktop
get-docker.sh
miniconda3
Music
Pictures
project
Public
share
srr
SRR6213653_1.fastq.gz.partial
SRR949627_1.fastq.gz.partial
Templates
temt.txt
test2.sh
tutorial
Videos
Sat Oct 23 11:45:03 +08 2021
ls: cannot access 'xxxx': No such file or directory

# hanchochang @ ubuntu in ~/share on git:master x [17:51:04] 
$ cd ../mynewrepo 

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [17:51:24] 
$ git status
On branch master

No commits yet

nothing to commit (create/copy files and use "git add" to track)

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [17:51:50] 
$ touch README

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:52:10] 
$ git add README

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:52:24] 
$ git status
On branch master

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

	new file:   README


# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:52:49] 
$ touch newfile

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:54:54] 
$ git status
On branch master

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

	new file:   README

Untracked files:
  (use "git add <file>..." to include in what will be committed)

	newfile


# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:55:03] 
$ cd  

# hanchochang @ ubuntu in ~ [17:56:08] 
$ cat temt.txt >> mynewrepo/newfile 

# hanchochang @ ubuntu in ~ [17:56:24] 
$ cd mynewrepo 

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:56:31] 
$ cat newfile 
bioinf
chr22_with_ERCC92.gtf
Desktop
Documents
Downloads
examples.desktop
get-docker.sh
miniconda3
Music
Pictures
project
Public
share
srr
SRR6213653_1.fastq.gz.partial
SRR949627_1.fastq.gz.partial
Templates
temt.txt
test2.sh
tutorial
Videos
Sat Oct 23 11:45:03 +08 2021
ls: cannot access 'xxxx': No such file or directory

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:56:37] 
$ git add newfile

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:56:57] 
$ git status
On branch master

No commits yet

Changes to be committed:
  (use "git rm --cached <file>..." to unstage)

	new file:   README
	new file:   newfile


# hanchochang @ ubuntu in ~/mynewrepo on git:master x [17:57:02] 
$ git commit -m "My first commit"
[master (root-commit) f67c5d6] My first commit
 2 files changed, 23 insertions(+)
 create mode 100644 README
 create mode 100644 newfile

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [17:58:02] 
$ git commit
On branch master
nothing to commit, working tree clean

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [17:58:52] C:1
$ git status
On branch master
nothing to commit, working tree clean

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [18:00:05] 
$ echo "Lockdown Learning Special: Introduction to Git" > README

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [18:02:42] 
$ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   README

no changes added to commit (use "git add" and/or "git commit -a")

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [18:02:53] 
$ git commit -m "Changed README"
On branch master
Changes not staged for commit:
	modified:   README

no changes added to commit

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [18:05:48] C:1
$ git commit -a -m "Changed README"
[master 6483b2b] Changed README
 1 file changed, 1 insertion(+)

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [18:06:21] 
$ git diff

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [18:06:51] 
$ git diff

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [19:01:43] 
$ echo "This is a README file for a test project" >> README

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:02:40] 
$ git diff                                                 

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:03:12] 
$ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

	modified:   README

no changes added to commit (use "git add" and/or "git commit -a")

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:12:49] 
$ git commit -a -m "A Second change to README"
[master 87819f9] A Second change to README
 1 file changed, 1 insertion(+)

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [19:13:31] 
$ git diff

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [19:13:53] 
$ git log

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [19:14:56] 
$ mkdir data

# hanchochang @ ubuntu in ~/mynewrepo on git:master o [19:46:21] 
$ echo 'data' > .gitignore

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:46:53] 
$ cp ~/chr22_with_ERCC92.gtf data/

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:47:32] 
$ ls
data  newfile  README

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:47:35] 
$ git status
On branch master
Untracked files:
  (use "git add <file>..." to include in what will be committed)

	.gitignore

nothing added to commit but untracked files present (use "git add" to track)

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:47:51] 
$ git status
On branch master
Untracked files:
  (use "git add <file>..." to include in what will be committed)

	.gitignore

nothing added to commit but untracked files present (use "git add" to track)

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:49:19] 
$ cat .gitignore 
data

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:50:35] 
$ git commit -a -m "Committing .gitignore"
On branch master
Untracked files:
	.gitignore

nothing added to commit but untracked files present

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:53:49] C:1
$ echo "A destructive change" > README

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:55:28] 
$ git commit -a -m "oops"
[master 6286598] oops
 1 file changed, 1 insertion(+), 2 deletions(-)

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:55:56] 
$ git log

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:56:12] 
$ git diff

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:57:00] 
$ git log 

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:57:59] 
$ git reset --hard 87819f90990f44e7aabedfa791eeff37110eed26
HEAD is now at 87819f9 A Second change to README

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:58:18] 
$ cat README 
Lockdown Learning Special: Introduction to Git
This is a README file for a test project

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [19:58:31] 
$ git remote add origin https://github.com/pathscientist/git-test.git

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:16:42] 
$ ls
data  newfile  README

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:16:48] 
$ cd

# hanchochang @ ubuntu in ~ [20:16:55] 
$ git remote add origin https://github.com/pathscientist/git-test.git
fatal: not a git repository (or any of the parent directories): .git

# hanchochang @ ubuntu in ~ [20:17:01] C:128
$ cd mynewrepo 

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:20:24] 
$ git remote add origin https://github.com/pathscientist/git-test.git
fatal: remote origin already exists.

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:20:31] C:128
$ git push origin master
Username for 'https://github.com': pathscientist
Password for 'https://pathscientist@github.com': 
remote: Support for password authentication was removed on August 13, 2021. Please use a personal access token instead.
remote: Please see https://github.blog/2020-12-15-token-authentication-requirements-for-git-operations/ for more information.
fatal: Authentication failed for 'https://github.com/pathscientist/git-test.git/'

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:21:15] C:128
$ git push origin master
Username for 'https://github.com': ^C

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:23:32] C:130
$ git remote add origin https://github.com/pathscientist/git-test.git
fatal: remote origin already exists.

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:24:31] C:128
$ git push -u origin main

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:26:32] C:1
$ git config -l

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:28:59] 
$ git pull -v
There is no tracking information for the current branch.
Please specify which branch you want to merge with.
See git-pull(1) for details.

    git pull <remote> <branch>

If you wish to set tracking information for this branch you can do so with:

    git branch --set-upstream-to=origin/<branch> master


# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:29:35] C:1
$ git config --global --unset credential.helper

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:34:04] C:5
$ git pull                                     
There is no tracking information for the current branch.
Please specify which branch you want to merge with.
See git-pull(1) for details.

    git pull <remote> <branch>

If you wish to set tracking information for this branch you can do so with:

    git branch --set-upstream-to=origin/<branch> master


# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:36:35] C:1
$ git push origin master                                             
fatal: unable to access 'https://github.com/pathscientist/git-test.git/': gnutls_handshake() failed: Error in the pull function.

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:37:06] C:128
$ git push -u origin main
error: src refspec main does not match any.
error: failed to push some refs to 'https://github.com/pathscientist/git-test.git'

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:38:10] C:1
$ cd

# hanchochang @ ubuntu in ~ [20:41:30] 
$ git --version 
git version 2.17.1

# hanchochang @ ubuntu in ~ [20:41:36] 
$ sudo apt-get install git
[sudo] password for hanchochang: 
Reading package lists... Done
Building dependency tree       
Reading state information... Done
git is already the newest version (1:2.17.1-1ubuntu0.9).
The following packages were automatically installed and are no longer required:
  efibootmgr libfwup1
Use 'sudo apt autoremove' to remove them.
0 upgraded, 0 newly installed, 0 to remove and 110 not upgraded.

# hanchochang @ ubuntu in ~ [20:42:09] 
$ cd mynewrepo 

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:44:06] 
$ git remote add origin git@github.com:pathscientist/git-test.git
fatal: remote origin already exists.

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:44:26] C:128
$ git push -u origin master
Username for 'https://github.com': ^C

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:45:00] C:130
$ git push -u origin master
fatal: unable to access 'https://github.com/pathscientist/git-test.git/': gnutls_handshake() failed: Error in the pull function.

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:45:23] C:128
$ git push -u origin master
fatal: unable to access 'https://github.com/pathscientist/git-test.git/': Failed to connect to github.com port 443: Connection refused

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:45:49] C:128
$ git push -u origin master
fatal: unable to access 'https://github.com/pathscientist/git-test.git/': Failed to connect to github.com port 443: Connection refused

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:47:43] C:128
$ git push -u origin master
fatal: unable to access 'https://github.com/pathscientist/git-test.git/': gnutls_handshake() failed: Error in the pull function.

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:48:07] C:128
$ git push -u origin master
^C

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:48:41] C:130
$ git push origin master                                      
fatal: unable to access 'https://github.com/pathscientist/git-test.git/': Failed to connect to github.com port 443: Connection refused

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:49:14] C:128
$ git remote add origin git@github.com:pathscientist/mynewrepo.git
fatal: remote origin already exists.

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:52:01] C:128
$ git push origin master                                          
Username for 'https://github.com': pathscientist
Password for 'https://pathscientist@github.com': 
remote: Support for password authentication was removed on August 13, 2021. Please use a personal access token instead.
remote: Please see https://github.blog/2020-12-15-token-authentication-requirements-for-git-operations/ for more information.
fatal: Authentication failed for 'https://github.com/pathscientist/git-test.git/'

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:52:31] C:128
$ git push origin master
Username for 'https://github.com': pathscientist
Password for 'https://pathscientist@github.com': 
remote: Support for password authentication was removed on August 13, 2021. Please use a personal access token instead.
remote: Please see https://github.blog/2020-12-15-token-authentication-requirements-for-git-operations/ for more information.
fatal: Authentication failed for 'https://github.com/pathscientist/git-test.git/'

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:53:14] C:128
$ 

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:53:27] C:130
$ git push origin master
Username for 'https://github.com': pathscientist
Password for 'https://pathscientist@github.com': 
Counting objects: 10, done.
Delta compression using up to 4 threads.
Compressing objects: 100% (8/8), done.
Writing objects: 100% (10/10), 1.09 KiB | 223.00 KiB/s, done.
Total 10 (delta 0), reused 0 (delta 0)
remote: This repository moved. Please use the new location:
remote:   https://github.com/pathscientist/mynewrepo.git
To https://github.com/pathscientist/git-test.git
 * [new branch]      master -> master

# hanchochang @ ubuntu in ~/mynewrepo on git:master x [20:58:14] 
$ cd

# hanchochang @ ubuntu in ~ [20:58:28] 
$ cat git_tokens
cat: git_tokens: No such file or directory

# hanchochang @ ubuntu in ~ [20:58:58] C:1
$ touch git_tokens

# hanchochang @ ubuntu in ~ [20:59:48] 
$ echo "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" > git_tokens 

# hanchochang @ ubuntu in ~ [21:00:02] 
$ ll
total 514M
-rw-rw-r--  1 hanchochang hanchochang  104 Oct 23 11:51 1
drwxr-xr-x  6 hanchochang hanchochang 4.0K Apr 12  2020 bioinf
drwxrwxr-x  3 hanchochang hanchochang 4.0K Oct 23 17:47 Bioinformatics-Resources
-rw-r--r--  1 hanchochang hanchochang  30M Oct 24  2018 chr22_with_ERCC92.gtf
drwxr-xr-x  2 hanchochang hanchochang 4.0K Feb 16  2020 Desktop
drwxr-xr-x  2 hanchochang hanchochang 4.0K Feb 16  2020 Documents
drwxr-xr-x  4 hanchochang hanchochang 4.0K Feb 16  2020 Downloads
-rw-r--r--  1 hanchochang hanchochang 8.8K Feb 16  2020 examples.desktop
-rw-r--r--  1 hanchochang hanchochang  15K Jun 16 02:32 get-docker.sh
-rw-rw-r--  1 hanchochang hanchochang   41 Oct 23 21:00 git_tokens
drwxr-xr-x 20 hanchochang hanchochang 4.0K Jul 15 19:47 miniconda3
drwxr-xr-x  2 hanchochang hanchochang 4.0K Feb 16  2020 Music
drwxrwxr-x  4 hanchochang hanchochang 4.0K Oct 23 19:58 mynewrepo
drwxr-xr-x  2 hanchochang hanchochang 4.0K Feb 16  2020 Pictures
drwxr-xr-x  3 hanchochang hanchochang 4.0K Apr 11  2020 project
drwxr-xr-x  2 hanchochang hanchochang 4.0K Feb 16  2020 Public
drwxr-xr-x  9 hanchochang hanchochang 4.0K Oct 23 17:50 share
-rw-r--r--  1 hanchochang hanchochang   11 Apr 11  2020 srr
-rw-r--r--  1 hanchochang hanchochang 108M Apr 11  2020 SRR6213653_1.fastq.gz.partial
-rw-r--r--  1 hanchochang hanchochang 377M Apr 11  2020 SRR949627_1.fastq.gz.partial
drwxr-xr-x  2 hanchochang hanchochang 4.0K Feb 16  2020 Templates
-rw-rw-r--  1 hanchochang hanchochang  323 Oct 23 11:52 temt.txt
-rwxr--r--  1 hanchochang hanchochang   33 Jul 12 01:06 test2.sh
drwxr-xr-x  3 hanchochang hanchochang 4.0K Jun 30 02:23 tutorial
drwxr-xr-x  2 hanchochang hanchochang 4.0K Feb 16  2020 Videos