X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/a0ee198f06282e0e5fb6325bb4de852d08546eaf..e0a1fc70f919741a8ad840dc40cfcc87f2751722:/doc/user/tutorials/tutorial-submit-job.html.textile.liquid diff --git a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid index 3d58fad97f..a6edc7dd0a 100644 --- a/doc/user/tutorials/tutorial-submit-job.html.textile.liquid +++ b/doc/user/tutorials/tutorial-submit-job.html.textile.liquid @@ -11,7 +11,9 @@ This tutorial demonstrates how to create a pipeline to run your crunch script on This tutorial uses @$USER@ to denote your username. Replace @$USER@ with your user name in all the following examples. -h2. Setting up Git +Also, this tutorial uses the @tutorial@ arvados repository created in "Adding a new arvados repository":add-new-repository.html as the example repository. + +h2. Clone arvados repository All Crunch scripts are managed through the Git revision control system. Before you start using Git, you should do some basic configuration (you only need to do this the first time): @@ -20,21 +22,28 @@ All Crunch scripts are managed through the Git revision control system. Before ~$ git config --global user.email $USER@example.com -On the Arvados Workbench, click on the dropdown menu icon in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Manage account* to go to the account management page. - -On the *Manage account* page, you will see *Repositories* panel. In this panel, you should see a repository with your user name listed in the *name* column. Next to *name* is the column *URL*. Copy the *URL* value associated with your repository. This should look like git@git.{{ site.arvados_api_host }}:$USER/$USER.git. +On the Arvados Workbench, click on the dropdown menu icon in the upper right corner of the top navigation menu to access the user settings menu, and click on the menu item *Repositories*. In the *Repositories* page, you should see the @$USER/tutorial@ repository listed in the *name* column. Next to *name* is the column *URL*. Copy the *URL* value associated with your repository. This should look like https://git.{{ site.arvados_api_host }}/$USER/tutorial.git. Alternatively, you can use git@git.{{ site.arvados_api_host }}:$USER/tutorial.git Next, on the Arvados virtual machine, clone your Git repository: 
~$ cd $HOME # (or wherever you want to install)
-~$ git clone git@git.{{ site.arvados_api_host }}:$USER/$USER.git
-Cloning into '$USER'...
+~$ git clone https://git.{{ site.arvados_api_host }}/$USER/tutorial.git +Cloning into 'tutorial'... -This will create a Git repository in the directory called @$USER@ in your home directory. Say yes when prompted to continue with connection. +This will create a Git repository in the directory called @tutorial@ in your home directory. Say yes when prompted to continue with connection. Ignore any warning that you are cloning an empty repository. +*Note:* If you are prompted for username and password when you try to git clone using this command, you may first need to update your git configuration. Execute the following commands to update your git configuration. + + +
+~$ git config 'credential.https://git.{{ site.arvados_api_host }}/.username' none
+~$ git config 'credential.https://git.{{ site.arvados_api_host }}/.helper' '!cred(){ cat >/dev/null; if [ "$1" = get ]; then echo password=$ARVADOS_API_TOKEN; fi; };cred'
+
+ + {% include 'notebox_begin' %} For more information about using Git, try @@ -45,7 +54,7 @@ or *"search Google for Git tutorials":http://google.com/#q=git+tutorial*. h2. Creating a Crunch script -Start by entering the @$USER@ directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory: +Start by entering the @tutorial@ directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory: 
~$ cd $USER
@@ -55,7 +64,7 @@ Start by entering the @$USER@ directory created by @git clone@.  Next create a s
 
 Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory.
 
-notextile. 
~/$USER/crunch_scripts$ nano hash.py

+notextile. 
~/tutorial/crunch_scripts$ nano hash.py

 
 Add the following code to compute the MD5 hash of each file in a collection (if you already completed "Writing a Crunch script":tutorial-firstscript.html you can just copy the @hash.py@ file you created previously.)
 
@@ -63,16 +72,16 @@ Add the following code to compute the MD5 hash of each file in a collection (if
 
 Make the file executable:
 
-notextile. 
~/$USER/crunch_scripts$ chmod +x hash.py

+notextile. 
~/tutorial/crunch_scripts$ chmod +x hash.py

 
 Next, add the file to the staging area.  This tells @git@ that the file should be included on the next commit.
 
-notextile. 
~/$USER/crunch_scripts$ git add hash.py

+notextile. 
~/tutorial/crunch_scripts$ git add hash.py

 
 Next, commit your changes.  All staged changes are recorded into the local git repository:
 
 
-
~/$USER/crunch_scripts$ git commit -m"my first script"
+
~/tutorial/crunch_scripts$ git commit -m"my first script"
 [master (root-commit) 27fd88b] my first script
  1 file changed, 45 insertions(+)
  create mode 100755 crunch_scripts/hash.py

@@ -81,12 +90,12 @@ Next, commit your changes.  All staged changes are recorded into the local git r
 Finally, upload your changes to the Arvados server:
 
 
-
~/$USER/crunch_scripts$ git push origin master
+
~/tutorial/crunch_scripts$ git push origin master
 Counting objects: 4, done.
 Compressing objects: 100% (2/2), done.
 Writing objects: 100% (4/4), 682 bytes, done.
 Total 4 (delta 0), reused 0 (delta 0)
-To git@git.qr1hi.arvadosapi.com:$USER/$USER.git
+To git@git.qr1hi.arvadosapi.com:$USER/tutorial.git
  * [new branch]      master -> master

 
 
@@ -102,7 +111,7 @@ In the editor, enter the following template:
 
  {% code 'tutorial_submit_job' as javascript %} 
 
-* @"repository"@ is the name of a git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench in the *Manage account* page using the   top navigation menu icon.
+* @"repository"@ is the name of a git repository to search for the script version.  You can access a list of available git repositories on the Arvados Workbench in the *Repositories* page using the   top navigation menu icon.
 * @"script_version"@ specifies the version of the script that you wish to run.  This can be in the form of an explicit Git revision hash, a tag, or a branch (in which case it will use the HEAD of the specified branch).  Arvados logs the script version that was used in the run, enabling you to go back and re-run any past job with the guarantee that the exact same code will be used as was used in the previous run.
 * @"script"@ specifies the filename of the script to run.  Crunch expects to find this in the @crunch_scripts/@ subdirectory of the Git repository.
 * @"runtime_constraints"@ describes the runtime environment required to run the job.  These are described in the "job record schema":{{site.baseurl}}/api/schema/Job.html