[med-svn] [pbgenomicconsensus] 01/11: Update patches
Afif Elghraoui
afif-guest at moszumanska.debian.org
Fri Feb 12 09:03:49 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository pbgenomicconsensus.
commit 12f1c8deb1e0319d71aea0b453890c8da36bffb6
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Feb 11 23:32:16 2016 -0800
Update patches
---
debian/patches/manpages.patch | 77 +++++++++++++++----------------------------
debian/patches/python-scripts | 13 ++++----
2 files changed, 33 insertions(+), 57 deletions(-)
diff --git a/debian/patches/manpages.patch b/debian/patches/manpages.patch
index 6e9d1c1..8e86641 100644
--- a/debian/patches/manpages.patch
+++ b/debian/patches/manpages.patch
@@ -4,7 +4,7 @@ Description: Turn upstream file format documentation into a manpage
http://docutils.sourceforge.net/sandbox/manpage-writer/rst2man.txt
Author: Afif Elghraoui <afif at ghraoui.name>
Forwarded: not-needed
-Last-Update: 2015-10-06
+Last-Update: 2016-02-11
--- pbgenomicconsensus.orig/doc/VariantsGffSpecification.rst
+++ pbgenomicconsensus/doc/VariantsGffSpecification.rst
@@ -1,6 +1,20 @@
@@ -52,7 +52,7 @@ Last-Update: 2015-10-06
We can currently translate `variants.gff` files to these formats, but
--- pbgenomicconsensus.orig/doc/HowToQuiver.rst
+++ pbgenomicconsensus/doc/HowToQuiver.rst
-@@ -1,51 +1,23 @@
+@@ -1,51 +1,22 @@
+======
+quiver
+======
@@ -65,8 +65,7 @@ Last-Update: 2015-10-06
-Quiver is bundled in SMRTanalysis version 1.4 and later. The easiest
-way to get Quiver is to install the most recent version of SMRTanalysis.
-+:Date: October 2015
-+:Version: 1.0.0
++:Date: February 2016
+:Manual section: 1
-If you want to install Quiver as a standalone package from the latest
@@ -115,29 +114,12 @@ Last-Update: 2015-10-06
Data file requirements
----------------------
-@@ -65,65 +37,16 @@
- If you are using an older version than SMRTportal/SMRTanalysis 1.3.3,
+@@ -66,45 +37,11 @@
please upgrade.
-+OPTIONS
-+=======
--Automatic installation instructions
-------------------------------------
--If your system meets the installation requirements, you can perform an
--automatic installation of the PacBio software for Quiver by
--executing::
--
-- $ curl -L http://git.io/JR7TnQ | bash
--
--
--Manual installation instructions
----------------------------------
--If your SWIG or BOOST installations are in non-standard locations or
--you encounter a problem with the automatic installation script, you
--can follow these steps to install Quiver manually.
--
--
+-Installation instructions
+--------------------------
-
-Step 1: Set up your Python environment
-``````````````````````````````````````
@@ -150,20 +132,14 @@ Last-Update: 2015-10-06
-and activate the virtualenv using ::
-
- $ source ~/VE-QUIVER/bin/activate
-+See the help menu: **quiver --help**
-
--There are some additional Python libraries required (NumPy and h5py),
--which can be installed via ::
--
-- $ pip install numpy==1.6.1
-- $ pip install h5py==2.0.1
-
-
-Step 2: Install PacBio libraries
-````````````````````````````````
-To install the PacBio software, execute ::
-
-- $ pip install git+https://github.com/PacificBiosciences/pbcore
+- $ pip install pbcore
+-
- $ git clone https://github.com/PacificBiosciences/ConsensusCore
- $ cd ConsensusCore; python setup.py install --swig=$SWIG --boost=$BOOST
- $ pip install git+https://github.com/PacificBiosciences/GenomicConsensus
@@ -187,10 +163,21 @@ Last-Update: 2015-10-06
+--------------
For example, ::
- $ quiver -j8 aligned_reads.cmp.h5 \
-@@ -141,8 +64,8 @@
- will be suboptimal.
+ $ quiver -j8 aligned_reads.bam \
+@@ -120,8 +57,8 @@
+ QV metrics required for optimal Quiver accuracy. The command will still work,
+ but it will give a warning that its accuracy will be suboptimal.
+
+-Step 3.5: Run Quiver on Multiple Input Files
+-````````````````````````````````````````````
++Run Quiver on Multiple Input Files
++----------------------------------
+ Multiple alignment files in a FOFN (File of File Names) can be quivered against
+ a single reference (`GenomicConsensus` >= 1.1.0).
+@@ -140,22 +77,18 @@
+ Quiver can also be used with DataSet XML files. See pbcore for details on
+ generating new DataSet XML files for your alignment files.
-Step 4: Highly-accurate assembly consensus
-``````````````````````````````````````````
@@ -199,18 +186,7 @@ Last-Update: 2015-10-06
Quiver enables consensus accuracies on genome assemblies at accuracies
approaching or even exceeding Q60 (one error per million bases). If
you use the HGAP assembly protocol in SMRTportal 2.0 or later, Quiver
-@@ -158,21 +81,18 @@
- assembly.
-
-
--Known issues
--------------
-+BUGS
-+====
-+
- There is a bug in the `multiprocessing` module in Python 2.7.2 and
- lower that causes the interpreter to crash during shutdown. Use
- Python 2.7.3 or newer.
+ runs automatically as the final "assembly polishing" step.
-Resources
@@ -221,11 +197,12 @@ Last-Update: 2015-10-06
-recommend reading the supplementary material of our 2013 *Nature
-Methods* `HGAP paper`_
-
+-
+-.. _`FAQ document`: https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/QuiverFAQ.rst
+-.. _`HGAP paper`: http://www.nature.com/nmeth/journal/v10/n6/full/nmeth.2474.html
+SEE ALSO
+========
-
--.. _`FAQ document`: https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/QuiverFAQ.rst
--.. _`HGAP paper`:
++
+**quiver-faq**\ (7)
+**plurality**\ (1)
+**variantCaller.py**\ (1)
diff --git a/debian/patches/python-scripts b/debian/patches/python-scripts
index 2fd0975..47c01e3 100644
--- a/debian/patches/python-scripts
+++ b/debian/patches/python-scripts
@@ -3,18 +3,17 @@ Description: Don't install scripts with distutils
for setuptools to know about it.
Author: Afif Elghraoui <afif at ghraoui.name>
Forwarded: not-needed
-Last-Update: 2015-09-14
+Last-Update: 2016-02-11
--- pbgenomicconsensus.orig/setup.py
+++ pbgenomicconsensus/setup.py
-@@ -15,13 +15,6 @@
+@@ -15,12 +15,6 @@
author='Pacific Biosciences',
author_email='devnet at pacificbiosciences.com',
license=open('LICENSES').read(),
-- scripts = ['bin/variantCaller.py',
-- 'bin/summarizeConsensus.py',
-- 'bin/gffToVcf.py',
-- 'bin/gffToBed.py',
-- 'bin/makePbi.py',
+- scripts = ['bin/variantCaller',
+- 'bin/summarizeConsensus',
+- 'bin/gffToVcf',
+- 'bin/gffToBed',
- 'bin/plurality',
- 'bin/quiver'],
packages = find_packages(),
--
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