X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/715869b9a22e22ac68a7dbefa96f27150017f75d..41c7c826a7e4c3a074a6ab5a719bf4c88e9a0e28:/doc/user/tutorials/tutorial-firstscript.html.textile.liquid diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid index 2422bb2814..4c49d19355 100644 --- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid +++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid @@ -10,9 +10,9 @@ h1. Writing a Crunch script In this tutorial, we will write the "hash" script demonstrated in the first tutorial. -*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.basedoc}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.basedoc}}/user/getting_started/check-environment.html* +*This tutorial assumes that you are "logged into an Arvados VM instance":{{site.baseurl}}/user/getting_started/ssh-access.html#login, and have a "working environment.":{{site.baseurl}}/user/getting_started/check-environment.html* -This tutorial uses _you_ to denote your username. Replace _you_ with your user name in all the following examples. +This tutorial uses *@you@* to denote your username. Replace *@you@* with your user name in all the following examples. h2. Setting up Git @@ -21,20 +21,20 @@ As discussed in the previous tutorial, all Crunch scripts are managed through th First, you should do some basic configuration for git (you only need to do this the first time): -
$ git config --global user.name "Your Name"
-$ git config --global user.email you@example.com
+
~$ git config --global user.name "Your Name"
+~$ git config --global user.email you@example.com
 -On the Arvados Workbench, navigate to _Access %(rarr)→% Repositories._ You should see two repositories, one named "arvados" (under the *name* column) and a second with your user name. Next to *name* is the column *push_url*. Copy the *push_url* cell associated with your repository. This should look like git@git.{{ site.arvados_api_host }}:you.git. +On the Arvados Workbench, navigate to _Compute %(rarr)→% Code repositories._ You should see two repositories, one named "arvados" (under the *name* column) and a second with your user name. Next to *name* is the column *push_url*. Copy the *push_url* cell associated with your repository. This should look like git@git.{{ site.arvados_api_host }}:you.git. Next, on the Arvados virtual machine, clone your git repository: -
$ git clone git@git.{{ site.arvados_api_host }}:you.git
-Cloning into 'you'...
+
~$ git clone git@git.{{ site.arvados_api_host }}:you.git
+Cloning into 'you'...
 -This will create an git checkout in the directory called @you@. +This will create an git checkout in the directory called *@you@*. {% include 'notebox_begin' %} For more information about using @git@, try @@ -46,17 +46,17 @@ or "click here to search Google for git tutorials":http://google.com/#q=git+t h2. Creating a Crunch script -Start by entering the @you@ directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory: +Start by entering the *@you@* directory created by @git clone@. Next create a subdirectory called @crunch_scripts@ and change to that directory: -
$ cd you
-$ mkdir crunch_scripts
-$ cd crunch_scripts
+
~$ cd you
+~/you$ mkdir crunch_scripts
+~/you$ cd crunch_scripts
 Next, using @nano@ or your favorite Unix text editor, create a new file called @hash.py@ in the @crunch_scripts@ directory. -notextile. 
$ nano hash.py
+notextile. 
~/you/crunch_scripts$ nano hash.py
Add the following code to compute the md5 hash of each file in a collection: @@ -64,16 +64,16 @@ Add the following code to compute the md5 hash of each file in a collection: Make the file executable: -notextile. 
$ chmod +x hash.py
+notextile. 
~/you/crunch_scripts$ chmod +x hash.py
Next, add the file to @git@ staging. This tells @git@ that the file should be included on the next commit. -notextile. 
$ git add hash.py
+notextile. 
~/you/crunch_scripts$ git add hash.py
Next, commit your changes to git. All staged changes are recorded into the local @git@ repository: -
$ git commit -m"my first script"
+
~/you/crunch_scripts$ git commit -m"my first script"
 [master (root-commit) 27fd88b] my first script
  1 file changed, 33 insertions(+)
  create mode 100755 crunch_scripts/hash.py

@@ -82,7 +82,7 @@ Next, commit your changes to git.  All staged changes are recorded into the loca
 Finally, upload your changes to the Arvados server:
 
 
-
$ git push origin master
+
~/you/crunch_scripts$ git push origin master
 Counting objects: 4, done.
 Compressing objects: 100% (2/2), done.
 Writing objects: 100% (4/4), 682 bytes, done.
@@ -94,7 +94,7 @@ To git@git.qr1hi.arvadosapi.com:you.git
 You should now be able to run your script using Crunch, similar to how we did it in the "first tutorial.":tutorial-job1.html  The field @"script_version"@ should be @you:master@ to tell Crunch to run the script at the head of the "master" git branch, which you just uploaded.
 
 
-
$ cat >the_job <<EOF
+
~/you/crunch_scripts$ cat >~/the_job <<EOF
 {
  "script": "hash.py",
  "script_version": "you:master",
@@ -104,19 +104,19 @@ You should now be able to run your script using Crunch, similar to how we did it
  }
 }
 EOF
-$ arv -h job create --job "$(cat the_job)"
+~/you/crunch_scripts$ arv job create --job "$(cat ~/the_job)"
 {
  ...
  "uuid":"qr1hi-xxxxx-xxxxxxxxxxxxxxx"
  ...
 }
-$ arv -h job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx
+~/you/crunch_scripts$ arv job get --uuid qr1hi-xxxxx-xxxxxxxxxxxxxxx
 {
  ...
  "output":"880b55fb4470b148a447ff38cacdd952+54",
  ...
 }
-$ arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt
+~/you/crunch_scripts$ arv keep get 880b55fb4470b148a447ff38cacdd952+54/md5sum.txt
 44b8ae3fde7a8a88d2f7ebd237625b4f var-GS000016015-ASM.tsv.bz2