X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/68287acb04a459bb6d9410dd619c5b3b00631a15..e333aa8b481c3347a3543eb108a622dfef5b30b6:/doc/user/tutorials/running-external-program.html.textile.liquid diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid index accc47c3d8..90dc1970a7 100644 --- a/doc/user/tutorials/running-external-program.html.textile.liquid +++ b/doc/user/tutorials/running-external-program.html.textile.liquid @@ -24,7 +24,7 @@ This will open the template record in an interactive text editor (as specified b * @"repository"@, @"script_version"@, and @"script"@ indicate that we intend to use the external @"run-command"@ tool wrapper that is part of the Arvados. These parameters are described in more detail in "Writing a script":tutorial-firstscript.html. * @"runtime_constraints"@ describes runtime resource requirements for the component. ** @"docker_image"@ specifies the "Docker":https://www.docker.com/ runtime environment in which to run the job. The Docker image @"bcosc/arv-base-java"@ supplied here has the Java runtime environment, bwa, and samtools installed. -** @"arvados_sdk_version"@ specifies a version of the Arvados SDK to load alongside the job's script. The example uses 'master'. If you would like to use a specific version of the sdk, you can find it in the "Arvados Python sdk repository":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*. +** @"arvados_sdk_version"@ specifies a version of the Arvados SDK to load alongside the job's script. The example uses 'master'. If you would like to use a specific version of the sdk, you can find it in the "Arvados Python sdk repository":https://dev.arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*. * @"script_parameters"@ describes the component parameters. ** @"command"@ is the actual command line to invoke the @bwa@ and then @SortSam@. The notation @$()@ denotes macro substitution commands evaluated by the run-command tool wrapper. ** @"task.stdout"@ indicates that the output of this command should be captured to a file. @@ -42,7 +42,7 @@ When using @run-command@, the tool should write its output to the current workin See the "run-command reference":{{site.baseurl}}/user/topics/run-command.html for more information about using @run-command@. *Note:* When trying to get job reproducibility without re-computation, you need to set these parameters to their specific hashes. Using a version such as master in @"arvados_sdk_version"@ will grab the latest version hash, which will allow Arvados to re-compute your job if the sdk gets updated. -* @"arvados_sdk_version"@ : The latest version can be found on the "Arvados Python sdk repository":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*. +* @"arvados_sdk_version"@ : The latest version can be found on the "Arvados Python sdk repository":https://dev.arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*. * @"script_version"@ : The current version of your script in your git repository can be found by using the following command: @@ -68,7 +68,7 @@ Arvados allows users to re-use jobs that have the same inputs in order to save c Note: Job reuse can only happen if all input collections do not change. -* @"arvados_sdk_version"@ : The arvados_sdk_version parameter is used to download the specific version of the Arvados sdk into the docker image. The latest version can be found in the "Arvados Python sdk repository":https://arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*. Make sure you set this to the same version as the previous run that you are trying to reuse. +* @"arvados_sdk_version"@ : The arvados_sdk_version parameter is used to download the specific version of the Arvados sdk into the docker image. The latest version can be found in the "Arvados Python sdk repository":https://dev.arvados.org/projects/arvados/repository/revisions/master/show/sdk/python under *Latest revisions*. Make sure you set this to the same version as the previous run that you are trying to reuse. * @"script_version"@ : The script_version is the commit hash of the git branch that the crunch script resides in. This information can be found in your git repository by using the following command: