[ARVADOS] updated: 2c7150729fcf1521d831b38c6aab016818b6b66a
git at public.curoverse.com
git at public.curoverse.com
Tue Jan 21 17:03:55 EST 2014
Summary of changes:
doc/_config.yml | 2 +
doc/_includes/navbar_left.html | 2 +-
doc/_includes/navbar_top.html | 1 +
doc/_includes/run-md5sum.py | 35 ++
doc/_layouts/default.html | 7 +-
doc/css/bootstrap.css | 4 +-
doc/images/glyphicons-halflings-white.png | Bin 0 -> 8777 bytes
doc/images/glyphicons-halflings.png | Bin 0 -> 12799 bytes
doc/index.html | 7 +-
doc/mkpydoc.sh | 5 +
doc/sdk/index.textile | 12 +
.../python}/crunch-utility-libraries.textile | 48 +-
doc/sdk/python/python.textile | 10 +
.../reference => sdk/python}/sdk-python.textile | 10 +-
doc/user/reference/sdk-cli.textile | 4 +-
.../tutorials/running-external-program.textile | 65 +++
doc/user/tutorials/tutorial-firstscript.textile | 2 +-
.../tutorial-gatk-variantfiltration.textile | 5 +-
doc/user/tutorials/tutorial-job-debug.textile | 2 +-
doc/user/tutorials/tutorial-job1.textile | 2 +-
doc/user/tutorials/tutorial-keep.textile | 2 +-
doc/user/tutorials/tutorial-new-pipeline.textile | 2 +-
doc/user/tutorials/tutorial-parallel.textile | 4 +-
doc/user/tutorials/tutorial-trait-search.textile | 4 +-
sdk/python/arvados/__init__.py | 606 +-------------------
sdk/python/arvados/collection.py | 215 +++++++
sdk/python/arvados/keep.py | 251 ++++++++
sdk/python/arvados/stream.py | 225 ++++++++
28 files changed, 884 insertions(+), 648 deletions(-)
create mode 100644 doc/_includes/run-md5sum.py
create mode 100644 doc/images/glyphicons-halflings-white.png
create mode 100644 doc/images/glyphicons-halflings.png
create mode 100755 doc/mkpydoc.sh
create mode 100644 doc/sdk/index.textile
rename doc/{user/reference => sdk/python}/crunch-utility-libraries.textile (91%)
create mode 100644 doc/sdk/python/python.textile
rename doc/{user/reference => sdk/python}/sdk-python.textile (95%)
create mode 100644 doc/user/tutorials/running-external-program.textile
create mode 100644 sdk/python/arvados/collection.py
create mode 100644 sdk/python/arvados/keep.py
create mode 100644 sdk/python/arvados/stream.py
via 2c7150729fcf1521d831b38c6aab016818b6b66a (commit)
via 746f932006d9921e27f5100fcbadb86933c5234f (commit)
via ae03931ec5d885c4faa677aebc4645272a625a12 (commit)
via e30f2cc5c876a3efc62f619654971f8200210576 (commit)
via 900b251f2dec14fba09e5e7a859cd67933946e56 (commit)
via 843ff49bf3d4585a31d525df3b4dfe4891314da7 (commit)
via 18e4d66b6fc65bc7dc486b3ff144cce92af5df8c (commit)
via 9e31035da243334912a5dc6143a65ac7df389c69 (commit)
via 12c9306193a1ec1a427e0ffda3f317a5f9ae091a (commit)
via f34faaa3ee1e9fc6780b6bcdd19ee1d21d410be0 (commit)
via 2e4fc5b7ec286d2beee8f93262dd70e481d161e2 (commit)
via e73f2804198ccd6d44e38312f3d4385dbd9b13ae (commit)
via dd20d6a93d7ec92e477b3d957da8f984cfbfdff9 (commit)
via 86ec3f61b905b2887cf7158ac97a4b817492ebad (commit)
from 26745c3d05f3a49902ac892297f76d0bfb92a272 (commit)
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commit 2c7150729fcf1521d831b38c6aab016818b6b66a
Merge: 746f932 900b251
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Jan 21 17:04:11 2014 -0500
Merge branch '1868-tutorial-running-binary-progs'
commit 746f932006d9921e27f5100fcbadb86933c5234f
Merge: ae03931 e30f2cc
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Jan 21 17:03:38 2014 -0500
Merge branch '1911-python-sdk-pydoc'
commit ae03931ec5d885c4faa677aebc4645272a625a12
Merge: 843ff49 26745c3
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Jan 21 17:03:00 2014 -0500
Merge branch 'master' of git.clinicalfuture.com:arvados
commit 843ff49bf3d4585a31d525df3b4dfe4891314da7
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date: Tue Jan 21 16:35:37 2014 -0500
Removed "Tutorial:" from titles since that was an artifact from before we had improved the navbar. Also fixed typo in tutorial-trait-search.
diff --git a/doc/user/tutorials/tutorial-firstscript.textile b/doc/user/tutorials/tutorial-firstscript.textile
index 4917cf9..b582eef 100644
--- a/doc/user/tutorials/tutorial-firstscript.textile
+++ b/doc/user/tutorials/tutorial-firstscript.textile
@@ -6,7 +6,7 @@ title: "Writing a Crunch script"
navorder: 13
---
-h1. Tutorial: Writing a Crunch script
+h1. Writing a Crunch script
In this tutorial, we will write the "hash" script demonstrated in the first tutorial.
diff --git a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
index 8163bd3..779761a 100644
--- a/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
+++ b/doc/user/tutorials/tutorial-gatk-variantfiltration.textile
@@ -6,7 +6,7 @@ title: "Using GATK with Arvados"
navorder: 16
---
-h1. Tutorial: Using GATK with Arvados
+h1. Using GATK with Arvados
This tutorials demonstrates how to use the Genome Analysis Toolkit (GATK) with Arvados. In this example we will install GATK and then create a VariantFiltration job to assign pass/fail scores to variants in a VCF file.
@@ -204,8 +204,7 @@ Tue Dec 17 19:04:12 2013 qr1hi-8i9sb-n9k7qyp7bs5b9d4 4867 log manifest is 1e77a
Once the job completes, the output can be found in hu34D5B9-exome-filtered.vcf:
-<notextile>
-$ <span class="userinput">arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91</span>
+<notextile><pre><code>$ <span class="userinput">arv keep ls bedd6ff56b3ae9f90d873b1fcb72f9a3+91</span>
hu34D5B9-exome-filtered.vcf
</code></pre>
</notextile>
diff --git a/doc/user/tutorials/tutorial-job-debug.textile b/doc/user/tutorials/tutorial-job-debug.textile
index 24364f0..6be687c 100644
--- a/doc/user/tutorials/tutorial-job-debug.textile
+++ b/doc/user/tutorials/tutorial-job-debug.textile
@@ -6,7 +6,7 @@ title: "Debugging a Crunch script"
navorder: 14
---
-h1. Tutorial: Debugging a Crunch script
+h1. Debugging a Crunch script
To test changes to a script by running a job, the change must be pushed into @git@, the job queued asynchronously, and the actual execution may be run on any compute server. As a result, debugging a script can be difficult and time consuming. This tutorial demonstrates using @arv-crunch-job@ to run your job in your local VM. This avoids the job queue and allows you to execute the script from your uncomitted git tree.
diff --git a/doc/user/tutorials/tutorial-job1.textile b/doc/user/tutorials/tutorial-job1.textile
index 982eb75..53d2342 100644
--- a/doc/user/tutorials/tutorial-job1.textile
+++ b/doc/user/tutorials/tutorial-job1.textile
@@ -6,7 +6,7 @@ title: "Running a Crunch job"
navorder: 12
---
-h1. Tutorial: Running a crunch job
+h1. Running a crunch job
This tutorial introduces the concepts and use of the Crunch job system using the @arv@ command line tool and Arvados Workbench.
diff --git a/doc/user/tutorials/tutorial-keep.textile b/doc/user/tutorials/tutorial-keep.textile
index 9922b04..6683498 100644
--- a/doc/user/tutorials/tutorial-keep.textile
+++ b/doc/user/tutorials/tutorial-keep.textile
@@ -6,7 +6,7 @@ title: "Storing and Retrieving data using Arvados Keep"
navorder: 11
---
-h1. Tutorial: Storing and Retrieving data using Arvados Keep
+h1. Storing and Retrieving data using Arvados Keep
This tutorial introduces you to the Arvados file storage system.
diff --git a/doc/user/tutorials/tutorial-new-pipeline.textile b/doc/user/tutorials/tutorial-new-pipeline.textile
index 7a9ecfb..101d6ac 100644
--- a/doc/user/tutorials/tutorial-new-pipeline.textile
+++ b/doc/user/tutorials/tutorial-new-pipeline.textile
@@ -6,7 +6,7 @@ title: "Constructing a Crunch pipeline"
navorder: 15
---
-h1. Tutorial: Constructing a Crunch pipeline
+h1. Constructing a Crunch pipeline
A pipeline in Arvados is a collection of crunch scripts, in which the output from one script may be used as the input to another script.
diff --git a/doc/user/tutorials/tutorial-parallel.textile b/doc/user/tutorials/tutorial-parallel.textile
index b76d1a5..f17178f 100644
--- a/doc/user/tutorials/tutorial-parallel.textile
+++ b/doc/user/tutorials/tutorial-parallel.textile
@@ -6,7 +6,7 @@ title: "Parallel Crunch tasks"
navorder: 15
---
-h1. Tutorial: Parallel Crunch tasks
+h1. Parallel Crunch tasks
In the tutorial "writing a crunch script,":tutorial-firstscript.html our script used a "for" loop to compute the md5 hashes for each file in sequence. This approach, while simple, is not able to take advantage of the compute cluster with multiple nodes and cores to speed up computation by running tasks in parallel. This tutorial will demonstrate how to create parallel Crunch tasks.
diff --git a/doc/user/tutorials/tutorial-trait-search.textile b/doc/user/tutorials/tutorial-trait-search.textile
index 9ea4cb6..d7fe50b 100644
--- a/doc/user/tutorials/tutorial-trait-search.textile
+++ b/doc/user/tutorials/tutorial-trait-search.textile
@@ -6,13 +6,13 @@ title: "Querying the Metadata Database"
navorder: 16
---
-h1. Tutorial: Querying the Metadata Database
+h1. Querying the Metadata Database
This tutorial introduces the Arvados Metadata Database. The Metadata Database stores information about files in Keep. This example will use the Python SDK to find public WGS (Whole Genome Sequencing) data for people who have reported a certain medical condition.
*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*
-In tutorial example, three angle brackets (>>>) will be used to denote code to enter at the Python prompt.
+In the tutorial examples, three angle brackets (>>>) will be used to denote code to enter at the interactive Python prompt.
Start by running Python.
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