[med-svn] [kineticstools] 01/01: Install manpages and examples
Afif Elghraoui
afif-guest at moszumanska.debian.org
Wed Dec 9 10:02:29 UTC 2015
This is an automated email from the git hooks/post-receive script.
afif-guest pushed a commit to branch master
in repository kineticstools.
commit 36c4f37754d7b59cc02e2658abb7aa26d402df62
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Wed Dec 9 01:26:37 2015 -0800
Install manpages and examples
---
debian/control | 1 +
debian/examples | 1 +
debian/manpages | 1 +
debian/patches/man-pages.patch | 79 +++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
debian/rules | 12 +++++--
debian/summarizeModifications.1 | 13 +++++++
7 files changed, 105 insertions(+), 3 deletions(-)
diff --git a/debian/control b/debian/control
index 6c0e729..9a00a40 100644
--- a/debian/control
+++ b/debian/control
@@ -9,6 +9,7 @@ Build-Depends:
dh-python,
python-all,
python-setuptools,
+ python-docutils,
python-pbcore (>= 1.2.2),
python-pbcommand (>= 0.2.0),
python-numpy (>= 1.6.0),
diff --git a/debian/examples b/debian/examples
new file mode 100644
index 0000000..bbbe1df
--- /dev/null
+++ b/debian/examples
@@ -0,0 +1 @@
+doc/regional_detection_manual.rst
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..fe31762
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/summarizeModifications.1
diff --git a/debian/patches/man-pages.patch b/debian/patches/man-pages.patch
new file mode 100644
index 0000000..fb0722b
--- /dev/null
+++ b/debian/patches/man-pages.patch
@@ -0,0 +1,79 @@
+Description: Format RST documentation into input for rst2man
+Author: Afif Elghraoui <afif at ghraoui.name>
+Forwarded: not-needed
+Last-Update: 2015-12-09
+--- kineticstools.orig/doc/manual.rst
++++ kineticstools/doc/manual.rst
+@@ -1,23 +1,22 @@
++==========
++ipdSummary
++==========
+
++------------------------------------------------------
++Detect DNA base-modifications from kinetic signatures.
++------------------------------------------------------
+
++:Date: December 2015
++:Manual section: 1
+
+-========
+-Overview
+-========
++
++DESCRIPTION
++===========
+
+ kineticsTool loads IPDs observed at each position in the genome, and compares those IPDs to value expected for unmodified DNA, and outputs the result of this statistical test.
+ The expected IPD value for unmodified DNA can come from either an *in-silico control* or an *amplified control*. The in silico control is trained by PacBio and shipped with the package. It predicts predicts the IPD using the local sequence context around the current position.
+ An amplified control dataset is generated by sequencing unmodified DNA with the same sequence as the test sample. An amplified control sample is usually generated by whole-genome amplification of the original sample.
+
+-
+-Dependencies
+-------------
+-kineticsTools depends on:
+- * pbcore (http://github.com/PacificBiosciences/pbcore)
+- * h5py
+- * numpy
+- * scipy
+-
+ Modification Detection
+ ----------------------
+ The basic mode of kineticsTools does an independent comparison of IPDs at each position on the genome, for each strand, and emits various statistics to CSV and GFF (after applying a significance filter).
+@@ -28,8 +27,11 @@
+ * Different modifications occuring on the same base can be distinguished (for example m5C and m4C)
+ * The signal from one modification is combined into one statistic, improving sensitivity, removing extra peaks, and correctly centering the call
+
++OPTIONS
++=======
++
++Please call this program with **--help** to see the available options.
+
+-=========
+ Algorithm
+ =========
+
+@@ -55,7 +57,6 @@
+ -------------------
+ We test the hypothesis that IPDs observed at a particular locus in the sample have a longer means than IPDs observed at the same locus in unmodified DNA. If we have generated a Whole Genome Amplified dataset, which removes DNA modifications, we use a case-control, two-sample t-test. This tool also provides a pre-calibrated 'synthetic control' model which predicts the unmodified IPD, given a 12 base sequence context. In the synthetic control case we use a one-sample t-test, with an adj [...]
+
+-======
+ Inputs
+ ======
+
+@@ -69,7 +70,6 @@
+
+ The tool requires the reference sequence used to perform alignments. Currently this must be supplied via the path to a SMRTportal reference repository entry.
+
+-=======
+ Outputs
+ =======
+
+@@ -178,3 +178,8 @@
+ meanCoverage Mean coverage of detected instances
+ objectiveScore Objective score of this motif in the motif finder algorithm
+ ================== ===========
++
++SEE ALSO
++========
++
++**summarizeModifications**\ (1)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..16baf4a
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+man-pages.patch
diff --git a/debian/rules b/debian/rules
index 60801da..4d69305 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,14 +1,20 @@
#!/usr/bin/make -f
#DH_VERBOSE = 1
-#include /usr/share/dpkg/default.mk
+include /usr/share/dpkg/default.mk
export PYBUILD_NAME=kineticstools
+INSTDIR = $(CURDIR)/debian/$(DEB_SOURCE)
+BINDIR = $(INSTDIR)/usr/bin
+MANDIR = $(INSTDIR)/usr/share/man/
+
%:
LC_ALL=C.UTF-8 dh $@ --with python2 --buildsystem=pybuild
override_dh_auto_install:
dh_auto_install
- mkdir -p debian/kineticstools/usr/bin
- mv debian/python-kineticstools/usr/bin/* debian/kineticstools/usr/bin
+ mkdir -p $(BINDIR)
+ mv debian/python-kineticstools/usr/bin/* $(BINDIR)
+ mkdir -p $(MANDIR)/man1
+ rst2man doc/manual.rst > $(MANDIR)/man1/ipdSummary.1
diff --git a/debian/summarizeModifications.1 b/debian/summarizeModifications.1
new file mode 100644
index 0000000..7cd0446
--- /dev/null
+++ b/debian/summarizeModifications.1
@@ -0,0 +1,13 @@
+.TH SUMMARIZEMODIFICATIONS 1 "December 2015"
+.SH NAME
+summarizeModifications \- Summarize kinetic DNA modifications.
+.SH DESCRIPTION
+This program is part of the kineticsTools module from the
+Pacific Biosciences SMRT Analysis suite.
+.SH OPTIONS
+A summary of options is available from the program's help menu.
+.TP
+.B \-h, \-\-help
+Show summary of options.
+.SH SEE ALSO
+.BR ipdSummary (1)
--
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