From: Peter Amstutz Date: Mon, 4 Aug 2014 15:28:28 +0000 (-0400) Subject: Fixed "Tutorial align using bwa mem and SortSam" template. Tweaked X-Git-Tag: 1.1.0~2376^2~1 X-Git-Url: https://git.arvados.org/arvados.git/commitdiff_plain/66525e1578a6247f902cd4c215494600302bf857?ds=sidebyside Fixed "Tutorial align using bwa mem and SortSam" template. Tweaked instructions for creating and editing template. Fixed docker image in template provided on "writing a crunch script". --- diff --git a/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid b/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid index dcce375439..c2be9e281a 100644 --- a/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid +++ b/doc/_includes/_tutorial_bwa_sortsam_pipeline.liquid @@ -1,65 +1,65 @@ { - "name": "Tutorial align using bwa mem and SortSam", - "components": { - "bwa-mem": { - "script": "run-command", - "script_version": "master", - "repository": "arvados", - "script_parameters": { - "command": [ - "bwa", - "mem", - "-t", - "$(node.cores)", - "-R", - "@RG\\tID:group_id\\tPL:illumina\\tSM:sample_id", - "$(glob $(dir $(reference_collection))/*.fasta)", - "$(glob $(dir $(sample))/*_1.fastq)", - "$(glob $(dir $(sample))/*_2.fastq)" - ], - "reference_collection": { - "required": true, - "dataclass": "Collection" + "name": "Tutorial align using bwa mem and SortSam", + "components": { + "bwa-mem": { + "script": "run-command", + "script_version": "master", + "repository": "arvados", + "script_parameters": { + "command": [ + "bwa", + "mem", + "-t", + "$(node.cores)", + "-R", + "@RG\\tID:group_id\\tPL:illumina\\tSM:sample_id", + "$(glob $(dir $(reference_collection))/*.fasta)", + "$(glob $(dir $(sample))/*_1.fastq)", + "$(glob $(dir $(sample))/*_2.fastq)" + ], + "reference_collection": { + "required": true, + "dataclass": "Collection" + }, + "sample": { + "required": true, + "dataclass": "Collection" + }, + "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam" + }, + "runtime_constraints": { + "docker_image": "arvados/jobs-java-bwa-samtools" + } }, - "sample": { - "required": true, - "dataclass": "Collection" - }, - "stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam" - }, - "runtime_constraints": { - "docker_image": "arvados/jobs-java-bwa-samtools" - } - } - }, - "SortSam": { - "script": "run-command", - "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2", - "repository": "arvados", - "script_parameters": { - "command": [ - "java", - "-Xmx4g", - "-Djava.io.tmpdir=$(tmpdir)", - "-jar", - "$(dir $(picard))/SortSam.jar", - "CREATE_INDEX=True", - "SORT_ORDER=coordinate", - "VALIDATION_STRINGENCY=LENIENT", - "INPUT=$(glob $(dir $(input))/*.sam)", - "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam" - ], - "input": { - "output_of": "bwa-mem" - }, - "picard": { - "required": true, - "dataclass": "Collection", - "default": "88447c464574ad7f79e551070043f9a9+1970" + "SortSam": { + "script": "run-command", + "script_version": "847459b3c257aba65df3e0cbf6777f7148542af2", + "repository": "arvados", + "script_parameters": { + "command": [ + "java", + "-Xmx4g", + "-Djava.io.tmpdir=$(tmpdir)", + "-jar", + "$(dir $(picard))/SortSam.jar", + "CREATE_INDEX=True", + "SORT_ORDER=coordinate", + "VALIDATION_STRINGENCY=LENIENT", + "INPUT=$(glob $(dir $(input))/*.sam)", + "OUTPUT=$(basename $(glob $(dir $(input))/*.sam)).sort.bam" + ], + "input": { + "output_of": "bwa-mem" + }, + "picard": { + "required": true, + "dataclass": "Collection", + "default": "88447c464574ad7f79e551070043f9a9+1970" + } + }, + "runtime_constraints": { + "docker_image": "arvados/jobs-java-bwa-samtools" + } } - }, - "runtime_constraints": { - "docker_image": "arvados/jobs-java-bwa-samtools" - } } -} \ No newline at end of file +} diff --git a/doc/user/tutorials/running-external-program.html.textile.liquid b/doc/user/tutorials/running-external-program.html.textile.liquid index 6a91cca902..36c7e9889d 100644 --- a/doc/user/tutorials/running-external-program.html.textile.liquid +++ b/doc/user/tutorials/running-external-program.html.textile.liquid @@ -8,7 +8,7 @@ This tutorial demonstrates how to construct a two stage pipeline template that u {% include 'tutorial_expectations' %} -Use the following command to create a new empty template using @arv pipeline_template create@, then open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@) using @arv edit@. +Use the following command to create a new empty template using @arv pipeline_template create@: 
~$ arv edit $(arv --format=uuid pipeline_template create --pipeline-template '{}') name components
@@ -16,7 +16,7 @@ Use the following command to create a new empty template using @arv pipeline_tem * @--format=uuid@ option prints out just the unique identifier for the new template, instead of the entire template record (default) -Next, in the text editor opened by @arv edit@ replace the empty fields with the following content: +This will open the template record in an interactive text editor (as specified by $EDITOR or $VISUAL, otherwise defaults to @nano@) using @arv edit@. Now add the following content: {% code 'tutorial_bwa_sortsam_pipeline' as javascript %} @@ -43,6 +43,6 @@ When using @run-command@, the tool should write its output to the current workin h2. Running your pipeline -Your new pipeline template should appear at the top of the Workbench "pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page. You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html +Your new pipeline template should appear at the top of the Workbench "pipeline templates":https://{{ site.arvados_workbench_host }}/pipeline_templates page. You can run your pipeline "using Workbench":tutorial-pipeline-workbench.html or the "command line.":{{site.baseurl}}/user/topics/running-pipeline-command-line.html Test data is available in the "Arvados Tutorial":https://{{ site.arvados_workbench_host }}/projects/qr1hi-j7d0g-u7zg1qdaowykd8d project. For more information and examples for writing pipelines, see the "pipeline template reference":{{site.baseurl}}/api/schema/PipelineTemplate.html diff --git a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid index aac7dbd507..9c3242fd2a 100644 --- a/doc/user/tutorials/tutorial-firstscript.html.textile.liquid +++ b/doc/user/tutorials/tutorial-firstscript.html.textile.liquid @@ -115,7 +115,7 @@ Next, create a file that contains the pipeline definition: "script_version":"master", "output_is_persistent":true, "runtime_constraints":{ - "docker_image":"arvados/jobs" + "docker_image":"arvados/jobs-java-bwa-samtools" } } }