[ARVADOS] updated: bdd309b073b6e836b78de28e82da89baba66a2a9
git at public.curoverse.com
git at public.curoverse.com
Wed Oct 8 15:00:48 EDT 2014
Summary of changes:
crunch_scripts/run-command | 5 +-
doc/_includes/_run_command_foreach_example.liquid | 61 ++++++++++++++---------
doc/_includes/_run_command_simple_example.liquid | 51 ++++++++++---------
doc/user/topics/run-command.html.textile.liquid | 10 ++++
4 files changed, 79 insertions(+), 48 deletions(-)
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via e74cd2fb8d2863e3c40febd5b71a24a1bf945ec5 (commit)
via 50de1d57245ed33b7f0a563eef9da73f16e0ca6c (commit)
from ba18dc96b40c463b921b04f7c8a66de447101927 (commit)
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commit bdd309b073b6e836b78de28e82da89baba66a2a9
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Oct 8 15:00:42 2014 -0400
Updated examples.
diff --git a/doc/_includes/_run_command_foreach_example.liquid b/doc/_includes/_run_command_foreach_example.liquid
index 828499f..d5643e6 100644
--- a/doc/_includes/_run_command_foreach_example.liquid
+++ b/doc/_includes/_run_command_foreach_example.liquid
@@ -15,25 +15,10 @@
{
"foreach": "read_pair",
"command": "$(read_pair)"
- },
- "$(glob $(dir $(sample))/*_1.fastq)",
- "$(glob $(dir $(sample))/*_2.fastq)"
+ }
],
"task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
"task.foreach": ["sample_subdir", "read_pair"],
- "reference_collection": "2463fa9efeb75e099685528b3b9071e0+438",
- "samples": "df45f4be79668b6d3d974e24f78e766f+149",
- "sample_subdir": "$(dir $(samples))",
- "read_pair": {
- "group": "sample_subdir",
- "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
- }
- }
- }
- }
-}
-
-
"reference_collection": {
"required": true,
"dataclass": "Collection"
@@ -42,3 +27,14 @@
"required": true,
"dataclass": "Collection"
}
+ "sample_subdir": "$(dir $(samples))",
+ "read_pair": {
+ "value": {
+ "group": "sample_subdir",
+ "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
+ }
+ }
+ }
+ }
+ }
+}
diff --git a/doc/user/topics/run-command.html.textile.liquid b/doc/user/topics/run-command.html.textile.liquid
index 078f4a3..dc4bc1f 100644
--- a/doc/user/topics/run-command.html.textile.liquid
+++ b/doc/user/topics/run-command.html.textile.liquid
@@ -214,3 +214,13 @@ This evaluates to the commands:
["echo", "bob", "carol"]
["echo", "bob", "dave"]
</pre>
+
+h1. Examples
+
+The following is a single task pipeline using run-command to run the bwa alignment tool to align a single paired-end read fastq sample. The input to this pipeline is the reference genome and a collection consisting of two fastq files for the read pair.
+
+<notextile>{% code 'run_command_simple_example' as javascript %}</notextile>
+
+The following is a concurrent task pipeline using run-command to run the bwa alignment tool to align a set of fastq reads over multiple sample. The input to this pipeline is the reference genome and a collection consisting subdirectories for each sample, with each subdirectory containing pairs of fastq files for each set of reads.
+
+<notextile>{% code 'run_command_foreach_example' as javascript %}</notextile>
commit e74cd2fb8d2863e3c40febd5b71a24a1bf945ec5
Merge: 50de1d5 ba18dc9
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Oct 8 14:50:12 2014 -0400
Merge branch '4042-run-command-MxN' of git.curoverse.com:arvados into 4042-run-command-MxN
# Please enter a commit message to explain why this merge is necessary,
# especially if it merges an updated upstream into a topic branch.
#
# Lines starting with '#' will be ignored, and an empty message aborts
# the commit.
commit 50de1d57245ed33b7f0a563eef9da73f16e0ca6c
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Wed Oct 8 14:49:54 2014 -0400
4042: Update documentation samples. Small fix to dry-run to allow supplying custom TASK_KEEPMOUNT.
diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 837e267..f46148e 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -56,8 +56,9 @@ else:
jobp = json.loads(args.job_parameters)
os.environ['JOB_UUID'] = 'zzzzz-8i9sb-1234567890abcde'
os.environ['TASK_UUID'] = 'zzzzz-ot0gb-1234567890abcde'
- os.environ['CRUNCH_SRC'] = '/tmp/crunch-src'
- os.environ['TASK_KEEPMOUNT'] = '/keep'
+ os.environ['CRUNCH_SRC'] = '/tmp/crunche-src'
+ if 'TASK_KEEPMOUNT' not in os.environ:
+ os.environ['TASK_KEEPMOUNT'] = '/keep'
links = []
diff --git a/doc/_includes/_run_command_foreach_example.liquid b/doc/_includes/_run_command_foreach_example.liquid
index dfa14c9..828499f 100644
--- a/doc/_includes/_run_command_foreach_example.liquid
+++ b/doc/_includes/_run_command_foreach_example.liquid
@@ -1,25 +1,44 @@
-"bwa-mem": {
- "script": "run-command",
- "script_version": "master",
- "repository": "arvados",
- "script_parameters": {
- "command": [
- "bwa",
- "mem",
- "-t",
- "$(node.cores)",
- "$(glob $(dir $(reference_collection))/*.fasta)",
- "$(glob $(dir $(sample))/*_1.fastq)",
- "$(glob $(dir $(sample))/*_2.fastq)"
- ],
- "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
- "reference_collection": {
- "required": true,
- "dataclass": "Collection"
- },
- "samples": {
- "required": true,
- "dataclass": "Collection"
- },
+{
+ "name":"run-command example pipeline",
+ "components":{
+ "bwa-mem": {
+ "script": "run-command",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "bwa",
+ "mem",
+ "-t",
+ "$(node.cores)",
+ "$(glob $(dir $(reference_collection))/*.fasta)",
+ {
+ "foreach": "read_pair",
+ "command": "$(read_pair)"
+ },
+ "$(glob $(dir $(sample))/*_1.fastq)",
+ "$(glob $(dir $(sample))/*_2.fastq)"
+ ],
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
+ "task.foreach": ["sample_subdir", "read_pair"],
+ "reference_collection": "2463fa9efeb75e099685528b3b9071e0+438",
+ "samples": "df45f4be79668b6d3d974e24f78e766f+149",
+ "sample_subdir": "$(dir $(samples))",
+ "read_pair": {
+ "group": "sample_subdir",
+ "regex": "(.*)_[12]\\.fastq(\\.gz)?$"
+ }
+ }
+ }
}
}
+
+
+ "reference_collection": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "sample": {
+ "required": true,
+ "dataclass": "Collection"
+ }
diff --git a/doc/_includes/_run_command_simple_example.liquid b/doc/_includes/_run_command_simple_example.liquid
index dfa14c9..abd0071 100644
--- a/doc/_includes/_run_command_simple_example.liquid
+++ b/doc/_includes/_run_command_simple_example.liquid
@@ -1,25 +1,30 @@
-"bwa-mem": {
- "script": "run-command",
- "script_version": "master",
- "repository": "arvados",
- "script_parameters": {
- "command": [
- "bwa",
- "mem",
- "-t",
- "$(node.cores)",
- "$(glob $(dir $(reference_collection))/*.fasta)",
- "$(glob $(dir $(sample))/*_1.fastq)",
- "$(glob $(dir $(sample))/*_2.fastq)"
- ],
- "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam"
- "reference_collection": {
- "required": true,
- "dataclass": "Collection"
- },
- "samples": {
- "required": true,
- "dataclass": "Collection"
- },
+{
+ "name":"run-command example pipeline",
+ "components":{
+ "bwa-mem": {
+ "script": "run-command",
+ "script_version": "master",
+ "repository": "arvados",
+ "script_parameters": {
+ "command": [
+ "bwa",
+ "mem",
+ "-t",
+ "$(node.cores)",
+ "$(glob $(dir $(reference_collection))/*.fasta)",
+ "$(glob $(dir $(sample))/*_1.fastq)",
+ "$(glob $(dir $(sample))/*_2.fastq)"
+ ],
+ "task.stdout": "$(basename $(glob $(dir $(sample))/*_1.fastq)).sam",
+ "reference_collection": {
+ "required": true,
+ "dataclass": "Collection"
+ },
+ "sample": {
+ "required": true,
+ "dataclass": "Collection"
+ }
+ }
+ }
}
}
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