[med-svn] [smrtanalysis] 01/02: Imported Upstream version 2.3.0

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch master
in repository smrtanalysis.

commit ce85675f1b6d14bb4d42e35afd9d4f51d2ded675
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Sun Jun 7 01:47:12 2015 -0700

    Imported Upstream version 2.3.0
---
 .gitmodules                                    |  3 +++
 README.md                                      | 35 ++++++++++++++++++++++++++
 add_on_scripts/finetune_distributed/README.txt | 17 +++++++++++++
 3 files changed, 55 insertions(+)

diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..0ab21d6
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,3 @@
+[submodule "docs"]
+	path = docs
+	url = https://github.com/PacificBiosciences/SMRT-Analysis.wiki.git
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..9366638
--- /dev/null
+++ b/README.md
@@ -0,0 +1,35 @@
+## Overview
+
+SMRT<sup><small>®</small></sup> Analysis is a powerful, open-source bioinformatics software suite available for analysis of DNA sequencing data from [Pacific Biosciences](http://www.pacificbiosciences.com)’ SMRT technology.
+
+Users can choose from a variety of analysis protocols that utilize PacBio<sup><small>®</small></sup> and third-party tools. Analysis protocols include _de novo_ genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.
+
+The browser-based SMRT Portal GUI offers push-button analysis, allowing the user to create, submit, and monitor analysis jobs. The underlying algorithms can be accessed on the command-line for pipeline development with SMRT Pipe, utilizing LIMS-friendly APIs and a large collection of utilities for working with PacBio bas.h5 files and other common file formats. SMRT View is an application for graphical visualization of processed and annotated sequence data, including kinetics data unique  [...]
+
+SMRT Analysis can run in single, distributed, or mixed modes. An Amazon Web Service (AWS) cloud-based implementation is available.
+
+
+## Getting Support
+
+[__PacBio Developer's Network Website__](http://pacbiodevnet.com)
+
+Visit PacBio DevNet for the most up-to-date downloads, documentation and more.
+
+
+[__PacBio Customer Portal__](http://www.pacbioportal.com)
+
+Support for PacBio customers is available through the  Customer Portal.
+
+
+[__SMRT Analysis GitHub wiki__](https://github.com/PacificBiosciences/SMRT-Analysis/wiki)
+
+For customers of PacBio [Sequencing Providers](http://www.pacificbiosciences.com/support/sequencing_provider/).
+
+
+
+
+[![githalytics.com alpha](https://cruel-carlota.pagodabox.com/104b77caac44b82e52bce19ad64c9c0b "githalytics.com")](http://githalytics.com/github.com/PacificBiosciences)
+
+
+
+[![githalytics.com alpha](https://cruel-carlota.pagodabox.com/28728759ba8fe51b8c1c0e6b39f6e339 "githalytics.com")](http://githalytics.com/PacificBiosciences/SMRT-Analysis)
diff --git a/add_on_scripts/finetune_distributed/README.txt b/add_on_scripts/finetune_distributed/README.txt
new file mode 100644
index 0000000..25813c3
--- /dev/null
+++ b/add_on_scripts/finetune_distributed/README.txt
@@ -0,0 +1,17 @@
+AUTHOR
+
+Tamas Vince
+
+DATE OF INITIAL COMMIT
+
+???
+
+PURPOSE
+
+This script allows SMRT Analysis to use more threads when running Consensus jobs in distributed mode.  Other non-multi-threaded jobs can still be run using a few cores if NPROC = 1.
+
+USAGE
+
+???
+
+

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/smrtanalysis.git