[med-svn] [express] 03/08: fix bamtools path

Thu Feb 12 00:18:20 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 ab76606989f449479e77f5183d5169605852231e
Author: Michael R. Crusoe <mcrusoe at msu.edu>
Date:   Tue Feb 3 13:20:06 2015 -0500

    fix bamtools path
---
 debian/control                   | 80 +++++++++++++++++++++++++++++++++++-----
 debian/patches/fix-bamtools-path | 27 ++++++++++++++
 debian/patches/series            |  1 +
 3 files changed, 99 insertions(+), 9 deletions(-)

diff --git a/debian/control b/debian/control
index 50152dc..358d5b5 100644
--- a/debian/control
+++ b/debian/control
@@ -1,16 +1,78 @@
 Source: express
-Section: science
-Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Uploaders: Andreas Tille <tille at debian.org>
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.6
+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,
+               libbamtools-dev
+Standards-Version: 3.9.5
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/<pkg>/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/<pkg>/trunk/
-Homepage: <homepage>
+Vcs-Git: git://anonscm.debian.org/debian-med/express.git
+Homepage: http://bio.math.berkeley.edu/eXpress/index.html
 
 Package: express
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: <short_description>
- <long_description>
+Depends: ${shlibs:Depends},
+         ${misc:Depends}
+Description: Streaming quantification for high-throughput sequencing
+ 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 [1] 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, we have 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 [2]. Moreover, like the Cufflinks program
+ [3], 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 [4] 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 [5].
+ .
+ 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.
+ .
+ [1] Cappé O and Moulines E. (2009). On-line expectation–maximization algorithm
+ for latent data models. Journal of the Royal Statistical Society.
+ doi:10.1111/j.1467-9868.2009.00698.x
+ [2] Roberts A and Pachter L (2012). Streaming fragment assignment for
+ real-time analysis of sequencing experiments. Nature Methods.
+ doi:10.1038/nmeth.2251
+ [3] Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ,
+ Salzberg SL, Wold B,  Pachter L (2010). Transcript assembly and quantification
+ by RNA-Seq reveals unannotated transcripts and isoform switching during cell
+ differentiation. Nature Biotechnology. doi:10.1038/nbt.162
+ [4] Pachter, L (2011). Models for transcript quantification from RNA-Seq.
+ Submitted. arXiv:1104.3889v2
+ [5] Roberts A, Trapnell C, Donaghey J, Rinn JL, Pachter L (2011). Improving
+ RNA-Seq expression estimates by correcting for fragment bias. Genome Biology.
+ doi:10.1186/gb-2011-12-3-r22
diff --git a/debian/patches/fix-bamtools-path b/debian/patches/fix-bamtools-path
new file mode 100644
index 0000000..1b47d2b
--- /dev/null
+++ b/debian/patches/fix-bamtools-path
@@ -0,0 +1,27 @@
+--- express.orig/CMakeLists.txt
++++ express/CMakeLists.txt
+@@ -33,10 +33,11 @@
+ 
+ find_package(Protobuf)
+ if (PROTOBUF_FOUND)
+-  include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") 
++  include_directories(${Boost_INCLUDE_DIRS} ${PROTOBUF_INCLUDE_DIR}
++	  "/usr/include/bamtools") 
+ 	set(PROTO_INT 1)
+ else (PROTOBUF_FOUND)
+-  include_directories(${Boost_INCLUDE_DIRS} "${CMAKE_CURRENT_SOURCE_DIR}/bamtools/include") 
++  include_directories(${Boost_INCLUDE_DIRS} "/usr/include/bamtools") 
+ 	set(PROTO_INT 0)
+ endif(PROTOBUF_FOUND)
+ 
+--- express.orig/src/CMakeLists.txt
++++ express/src/CMakeLists.txt
+@@ -16,7 +16,7 @@
+ if(WIN32)
+   set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.lib" "${CMAKE_CURRENT_SOURCE_DIR}/../win_build/zlibd.lib")
+ else(WIN32)
+-  set(LIBRARIES ${LIBRARIES} "${CMAKE_CURRENT_SOURCE_DIR}/../bamtools/lib/libbamtools.a" "pthread")
++  set(LIBRARIES ${LIBRARIES} "libbamtools.so" "pthread")
+ endif(WIN32)
+ 
+ if (PROTOBUF_FOUND)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 0000000..e609dfb
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+fix-bamtools-path

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

