[med-svn] [express] 01/01: rename to berkeley-express
Michael Crusoe
misterc-guest at moszumanska.debian.org
Sat Aug 22 00:55:25 UTC 2015
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository express.
commit 4af36da8c79025fd67841222b8185c04e30ed0f6
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Fri Aug 21 17:22:30 2015 -0700
rename to berkeley-express
relax boost builddep
fix upstream's spelling
---
...-doc.doc-base => berkeley-express-doc.doc-base} | 2 +-
...{express-doc.docs => berkeley-express-doc.docs} | 0
debian/{express.1 => berkeley-express.1} | 2 +-
debian/{express.dirs => berkeley-express.dirs} | 0
debian/{express.docs => berkeley-express.docs} | 0
debian/berkeley-express.install | 1 +
debian/berkeley-express.links | 1 +
debian/berkeley-express.manpages | 1 +
debian/changelog | 6 +++
debian/control | 60 ++++++++++++++++++----
debian/express.install | 1 -
debian/express.manpages | 1 -
debian/patches/fix-bamtools-path | 20 ++++++++
debian/patches/series | 1 +
debian/patches/spelling-fixes | 37 +++++++++++++
debian/rules | 2 +-
16 files changed, 120 insertions(+), 15 deletions(-)
diff --git a/debian/express-doc.doc-base b/debian/berkeley-express-doc.doc-base
similarity index 95%
rename from debian/express-doc.doc-base
rename to debian/berkeley-express-doc.doc-base
index 94bd7d0..0d160cb 100644
--- a/debian/express-doc.doc-base
+++ b/debian/berkeley-express-doc.doc-base
@@ -20,4 +20,4 @@ Abstract: Streaming quantification for high-throughput sequencing
Section: Science/Biology
Format: pdf
-Files: /usr/share/doc/express-doc/express-doc.pdf
+Files: /usr/share/doc/berkeley-express-doc/express-doc.pdf
diff --git a/debian/express-doc.docs b/debian/berkeley-express-doc.docs
similarity index 100%
rename from debian/express-doc.docs
rename to debian/berkeley-express-doc.docs
diff --git a/debian/express.1 b/debian/berkeley-express.1
similarity index 97%
rename from debian/express.1
rename to debian/berkeley-express.1
index 1365658..7cf658b 100644
--- a/debian/express.1
+++ b/debian/berkeley-express.1
@@ -1,6 +1,6 @@
.TH EXPRESS "1" "February 2015" "express 1.5.1" "User Commands"
.SH NAME
-express \- Streaming quantification for high-throughput sequencing
+berkeley-express \- Streaming quantification for high-throughput sequencing
.SH DESCRIPTION
File Usage: express [options] <target_seqs.fa> <hits.(sam/bam)>
Piped Usage: bowtie [options] \fB\-S\fR <index> <reads.fq> | express [options] <target_seqs.fa>
diff --git a/debian/express.dirs b/debian/berkeley-express.dirs
similarity index 100%
rename from debian/express.dirs
rename to debian/berkeley-express.dirs
diff --git a/debian/express.docs b/debian/berkeley-express.docs
similarity index 100%
rename from debian/express.docs
rename to debian/berkeley-express.docs
diff --git a/debian/berkeley-express.install b/debian/berkeley-express.install
new file mode 100644
index 0000000..057df0c
--- /dev/null
+++ b/debian/berkeley-express.install
@@ -0,0 +1 @@
+usr/bin/express usr/lib/debian-med/bin/
diff --git a/debian/berkeley-express.links b/debian/berkeley-express.links
new file mode 100644
index 0000000..414702a
--- /dev/null
+++ b/debian/berkeley-express.links
@@ -0,0 +1 @@
+usr/lib/debian-med/bin/express usr/bin/berkeley-express
diff --git a/debian/berkeley-express.manpages b/debian/berkeley-express.manpages
new file mode 100644
index 0000000..b3453c7
--- /dev/null
+++ b/debian/berkeley-express.manpages
@@ -0,0 +1 @@
+debian/berkeley-express.1
diff --git a/debian/changelog b/debian/changelog
index fdd9b83..677581c 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+berkeley-express (1.5.1-3) UNRELEASED; urgency=low
+
+ * Renamed to berkeley-express.
+
+ -- Michael R. Crusoe <crusoe at ucdavis.edu> Fri, 21 Aug 2015 17:18:15 -0700
+
express (1.5.1-2) unstable; urgency=low
* Adding omitted install instruction for executable.
diff --git a/debian/control b/debian/control
index fa91112..75d43d3 100644
--- a/debian/control
+++ b/debian/control
@@ -1,16 +1,16 @@
-Source: express
+Source: berkeley-express
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Michael R. Crusoe <mcrusoe at msu.edu>
+Uploaders: Michael R. Crusoe <crusoe at ucdavis.edu>
Section: science
Priority: optional
Build-Depends: debhelper (>= 9),
- libboost-thread1.54-dev,
- libboost-system1.54-dev,
- libboost-filesystem1.54-dev,
- libboost-program-options1.54-dev,
- libboost-date-time1.54-dev,
+ libboost-thread-dev,
+ libboost-system-dev,
+ libboost-filesystem-dev,
+ libboost-program-options-dev,
+ libboost-date-time-dev,
libbamtools-dev,
- libboost1.54-tools-dev,
+ libboost-tools-dev,
libgoogle-perftools-dev [amd64 arm64 armel armhf i386 powerpc ppc64el],
cmake,
zlib1g-dev
@@ -19,7 +19,7 @@ Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/express.git
Vcs-Git: git://anonscm.debian.org/debian-med/express.git
Homepage: http://bio.math.berkeley.edu/eXpress/index.html
-Package: express
+Package: berkeley-express
Architecture: any
Depends: ${shlibs:Depends},
${misc:Depends}
@@ -64,10 +64,50 @@ Description: Streaming quantification for high-throughput sequencing
useful in any analysis where reads multi-map to sequences that differ in
abundance.
-Package: express-doc
+Package: berkeley-express-doc
Architecture: all
Section: doc
Depends: ${misc:Depends}
Description: Documentation for RNA-Seq tool eXpress
This package provides a PDF with the documentation for eXpress.
+ .
+ eXpress is a streaming tool for quantifying the abundances of a set of
+ target sequences from sampled subsequences. Example applications include
+ transcript-level RNA-Seq quantification, allele-specific/haplotype
+ expression analysis (from RNA-Seq), transcription factor binding
+ quantification in ChIP-Seq, and analysis of metagenomic data. It is
+ based on an online-EM algorithm that results in space (memory)
+ requirements proportional to the total size of the target sequences and
+ time requirements that are proportional to the number of sampled
+ fragments. Thus, in applications such as RNA-Seq, eXpress can accurately
+ quantify much larger samples than other currently available tools
+ greatly reducing computing infrastructure requirements. eXpress can be
+ used to build lightweight high-throughput sequencing processing
+ pipelines when coupled with a streaming aligner (such as Bowtie), as
+ output can be piped directly into eXpress, effectively eliminating the
+ need to store read alignments in memory or on disk.
+ .
+ In an analysis of the performance of eXpress for RNA-Seq data, it was
+ observed that this efficiency does not come at a cost of accuracy.
+ eXpress is more accurate than other available tools, even when limited
+ to smaller datasets that do not require such efficiency. Moreover, like
+ the Cufflinks program, eXpress can be used to estimate transcript
+ abundances in multi-isoform genes. eXpress is also able to resolve
+ multi-mappings of reads across gene families, and does not require a
+ reference genome so that it can be used in conjunction with de novo
+ assemblers such as Trinity, Oases, or Trans-ABySS. The underlying model
+ is based on previously described probabilistic models developed for
+ RNA-Seq but is applicable to other settings where target sequences are
+ sampled, and includes parameters for fragment length distributions,
+ errors in reads, and sequence-specific fragment bias.
+ .
+ eXpress can be used to resolve ambiguous mappings in other
+ high-throughput sequencing based applications. The only required inputs
+ to eXpress are a set of target sequences and a set of sequenced
+ fragments multiply-aligned to them. While these target sequences will
+ often be gene isoforms, they need not be. Haplotypes can be used as the
+ reference for allele-specific expression analysis, binding regions for
+ ChIP-Seq, or target genomes in metagenomics experiments. eXpress is
+ useful in any analysis where reads multi-map to sequences that differ in
+ abundance.
diff --git a/debian/express.install b/debian/express.install
deleted file mode 100644
index 56b07e6..0000000
--- a/debian/express.install
+++ /dev/null
@@ -1 +0,0 @@
-usr/bin/express
diff --git a/debian/express.manpages b/debian/express.manpages
deleted file mode 100644
index fd29734..0000000
--- a/debian/express.manpages
+++ /dev/null
@@ -1 +0,0 @@
-debian/express.1
diff --git a/debian/patches/fix-bamtools-path b/debian/patches/fix-bamtools-path
index 8c647f7..894a261 100644
--- a/debian/patches/fix-bamtools-path
+++ b/debian/patches/fix-bamtools-path
@@ -29,3 +29,23 @@ Description: Fix path to Debian packaged bamtools
endif(WIN32)
if (PROTOBUF_FOUND)
+--- express.orig/src/mismatchmodel.cpp
++++ express/src/mismatchmodel.cpp
+@@ -126,7 +126,7 @@
+ size_t k = 0;
+ do {
+ if (k > max_indel_size) {
+- logger.warn("Paramater file '%s' insertion distribution is being "
++ logger.warn("Parameter file '%s' insertion distribution is being "
+ "truncated at max indel length of %d.",
+ param_file_name.c_str(), max_indel_size);
+ break;
+@@ -143,7 +143,7 @@
+ k = 0;
+ do {
+ if (k > max_indel_size) {
+- logger.warn("Paramater file '%s' deletion distribution is being "
++ logger.warn("Parameter file '%s' deletion distribution is being "
+ "truncated at max indel length of %d.",
+ param_file_name.c_str(), max_indel_size);
+ break;
diff --git a/debian/patches/series b/debian/patches/series
index e609dfb..2c4a4bc 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,2 @@
+spelling-fixes
fix-bamtools-path
diff --git a/debian/patches/spelling-fixes b/debian/patches/spelling-fixes
new file mode 100644
index 0000000..99d65c7
--- /dev/null
+++ b/debian/patches/spelling-fixes
@@ -0,0 +1,37 @@
+Author: Michael R. Crusoe <crusoe at ucdavis.edu>
+Last-Update: Fri, 21 Aug 2015 09:21:09 +0100
+Description: Correct upstream typos
+
+--- express.orig/src/lengthdistribution.cpp
++++ express/src/lengthdistribution.cpp
+@@ -72,7 +72,7 @@
+ char line_buff[BUFF_SIZE];
+
+ if (!infile.is_open()) {
+- logger.severe("Unable to open paramater file '%s'.",
++ logger.severe("Unable to open parameter file '%s'.",
+ param_file_name.c_str());
+ }
+
+--- express.orig/src/main.cpp
++++ express/src/main.cpp
+@@ -683,7 +683,7 @@
+ break;
+ }
+ {
+- // Block the bias update thread from updating the paramater tables
++ // Block the bias update thread from updating the parameter tables
+ // during processing. We don't need to do this during multi-threaded
+ // processing since the parameters are burned out before we start
+ // the threads.
+--- express.orig/src/markovmodel.h
++++ express/src/markovmodel.h
+@@ -125,7 +125,7 @@
+ double marginal_prob(size_t w, size_t nuc) const;
+ /**
+ * Slides a window along the given sequence, incrementing the highest order
+- * transition paramaters by the given mass multiplied by the probability of
++ * transition parameters by the given mass multiplied by the probability of
+ * observing a fragment at that distance from the end.
+ * @param seq the sequence to slide the window along.
+ * @param mass the amount to increment the parameters by.
diff --git a/debian/rules b/debian/rules
index ce8babd..5e03318 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,6 +1,6 @@
#!/usr/bin/make -f
-# DH_VERBOSE := 1
+DH_VERBOSE := 1
%:
dh $@ --parallel
--
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