[med-svn] [pbgenomicconsensus] 01/01: Patch more of the upstream documentation to format as manpages
Afif Elghraoui
afif-guest at moszumanska.debian.org
Thu Oct 8 08:04:15 UTC 2015
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afif-guest pushed a commit to branch master
in repository pbgenomicconsensus.
commit b72f05e57aabcb886f3289d5245a3ec8c6ad0ef5
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Thu Oct 8 01:03:46 2015 -0700
Patch more of the upstream documentation to format as manpages
---
debian/patches/manpages.patch | 228 ++++++++++++++++++++++++++++++++++++++++++
debian/rules | 4 +-
2 files changed, 231 insertions(+), 1 deletion(-)
diff --git a/debian/patches/manpages.patch b/debian/patches/manpages.patch
index 0898f29..a075582 100644
--- a/debian/patches/manpages.patch
+++ b/debian/patches/manpages.patch
@@ -50,3 +50,231 @@ Last-Update: 2015-10-06
The VCF and BED standards describe variant-call specific file formats.
We can currently translate `variants.gff` files to these formats, but
+--- pbgenomicconsensus.orig/doc/HowToQuiver.rst
++++ pbgenomicconsensus/doc/HowToQuiver.rst
+@@ -1,51 +1,23 @@
++======
++quiver
++======
+
+-How to install and use Quiver
+-=============================
++--------------------------------------------------------------
++genomic consensus caller designed for Pacific Biosciences data
++--------------------------------------------------------------
+
+-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
++:Manual section: 1
+
+-If you want to install Quiver as a standalone package from the latest
+-bleeding-edge code, follow the instructions below.
+
+-*Note: please install this software on an isolated machine that does
+-not have SMRTanalysis installed. Older versions of SMRTanalysis
+-pollute the ``PYTHONPATH``, which has the undesirable effect of
+-overriding ``virtualenv``-installed modules.*
++DESCRIPTION
++===========
+
+-Background
+-----------
+ **Quiver** is an algorithm for calling highly accurate consensus from
+ multiple PacBio reads, using a pair-HMM exploiting both the basecalls
+ and QV metrics to infer the true underlying DNA sequence.
+
+-Quiver is available through the ``quiver`` script from the
+-``GenomicConsensus`` package. To use Quiver, the following PacBio
+-software is required.
+-
+-- ``GenomicConsensus``, containing ``quiver``
+-- ``ConsensusCore``, a C++ library containing the core computational
+- routines for Quiver
+-- ``pbcore``, a package providing access to PacBio data files
+-
+-
+-Required libraries and tools
+-----------------------------
+-To install the PacBio software, the following are required:
+-
+-- Boost >= 1.4.7 (standard C++ libraries)
+-- SWIG >= 2.0.7 (library wrapper generator)
+-- Python 2.7.3
+-- virtualenv (builds isolated Python environments)
+-
+-If you are within PacBio, these requirements are already installed
+-within the cluster environment.
+-
+-Otherwise, you will need to install them yourself. The automatic
+-installation script requires that the ``swig`` executable is in your
+-UNIX ``$PATH`` and that your boost installation can be found under
+-``/usr/include`` or ``/usr/local``.
+-
+
+ Data file requirements
+ ----------------------
+@@ -65,65 +37,16 @@
+ If you are using an older version than SMRTportal/SMRTanalysis 1.3.3,
+ 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.
+-
+-
+-
+-Step 1: Set up your Python environment
+-``````````````````````````````````````
+-I recommend using a Python *virtualenv* to isolate your sandbox.
+-
+-To set up a new virtualenv, do ::
+-
+- $ cd; virtualenv -p python2.7 --no-site-packages VE-QUIVER
+-
+-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
+- $ 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
+-
+-where you replace ``$SWIG`` with the path to your ``swig`` executable
+-and ``$BOOST`` with the path to your boost install (the top level
+-directory). (Note that if SWIG is in your ``$PATH`` and boost is in
+-``/usr/local`` or ``/usr/include/``, you do not need to specify these
+-flags on the command line---``setup.py`` will find them).
+-
+-
+-Step 3: Run Quiver
+-``````````````````
+-Those who wish to call consensus on a resequencing job can simply use
+-the ``quiver`` script that has been installed in your
+-virtualenv (from `GenomicConsensus`).
++EXAMPLES
++========
+
++Running Quiver
++--------------
+ For example, ::
+
+ $ quiver -j8 aligned_reads.cmp.h5 \
+@@ -141,8 +64,8 @@
+ will be suboptimal.
+
+
+-Step 4: Highly-accurate assembly consensus
+-``````````````````````````````````````````
++Highly-accurate assembly consensus
++----------------------------------
+ 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.
+
+
+-Resources
+----------
+-Here is an `FAQ document`_ to address common issues.
+-
+-For a technical summary of some of the details of how Quiver works, I
+-recommend reading the supplementary material of our 2013 *Nature
+-Methods* `HGAP paper`_
+-
++SEE ALSO
++========
+
+-.. _`FAQ document`: https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/QuiverFAQ.rst
+-.. _`HGAP paper`:
++**quiver-faq**\ (7)
++**plurality**\ (1)
++**variantCaller.py**\ (1)
++**pbgff**\ (5)
+--- pbgenomicconsensus.orig/doc/QuiverFAQ.rst
++++ pbgenomicconsensus/doc/QuiverFAQ.rst
+@@ -1,5 +1,17 @@
+-Quiver FAQ
+ ==========
++quiver-faq
++==========
++
++------------------------------------------------------------------------
++frequently asked questions regarding the quiver genomic consensus caller
++------------------------------------------------------------------------
++
++:Date: October 2015
++:Version: 1.0.0
++:Manual section: 7
++
++QUESTIONS
++=========
+
+ What are EviCons? GenomicConsensus? Quiver? Plurality?
+ ------------------------------------------------------------
+@@ -67,14 +79,6 @@
+ The name **Quiver** reflects a consensus-calling algorithm that is
+ `QV-aware`.
+
+-How do I run Quiver?
+---------------------
+-
+-For general instructions on installing and running, see the
+-HowToQuiver_ document.
+-
+-
+-
+ What does Quiver put in its output files?
+ -----------------------------------------
+ There are three output files from Quiver:
+@@ -372,5 +376,10 @@
+ calls.
+
+
++SEE ALSO
++========
+
+-.. _HowToQuiver: https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/HowToQuiver.rst
++**quiver**\ (1)
++**plurality**\ (1)
++**variantCaller.py**\ (1)
++**pbgff**\ (5)
diff --git a/debian/rules b/debian/rules
index 9bb6a3c..69022c2 100755
--- a/debian/rules
+++ b/debian/rules
@@ -13,8 +13,10 @@ MANDIR=$(CURDIR)/debian/$(DEB_SOURCE)/usr/share/man/
override_dh_auto_build:
dh_auto_build
- mkdir -p $(MANDIR)/man5
+ mkdir -p $(MANDIR)/man5 $(MANDIR)/man1 $(MANDIR)/man7
rst2man doc/VariantsGffSpecification.rst > $(MANDIR)/man5/pbgff.5
+ rst2man doc/HowToQuiver.rst > $(MANDIR)/man1/quiver.1
+ rst2man doc/QuiverFAQ.rst > $(MANDIR)/man7/quiver-faq.7
override_dh_install:
dh_install
--
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