[ARVADOS] updated: 66525e1578a6247f902cd4c215494600302bf857
git at public.curoverse.com
git at public.curoverse.com
Mon Aug 4 11:28:31 EDT 2014
Summary of changes:
.../_tutorial_bwa_sortsam_pipeline.liquid | 122 ++++++++++-----------
.../running-external-program.html.textile.liquid | 6 +-
.../tutorial-firstscript.html.textile.liquid | 2 +-
3 files changed, 65 insertions(+), 65 deletions(-)
via 66525e1578a6247f902cd4c215494600302bf857 (commit)
from d6d7788c4e6b1d3da88833329b326fd7a3891503 (commit)
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commit 66525e1578a6247f902cd4c215494600302bf857
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Mon Aug 4 11:28:28 2014 -0400
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 dcce375..c2be9e2 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 6a91cca..36c7e98 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 $VISUAL, otherwise defaults to @nano@) using @arv edit at .
+Use the following command to create a new empty template using @arv pipeline_template create@:
<notextile>
<pre><code>~$ <span class="userinput">arv edit $(arv --format=uuid pipeline_template create --pipeline-template '{}') name components </span></code></pre>
@@ -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 at . Now add the following content:
<notextile>{% code 'tutorial_bwa_sortsam_pipeline' as javascript %}</notextile>
@@ -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 aac7dbd..9c3242f 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"
}
}
}
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