[med-svn] [Git][med-team/abyss][master] 4 commits: New upstream version 2.2.2
Michael R. Crusoe
gitlab at salsa.debian.org
Sat Aug 17 08:29:54 BST 2019
Michael R. Crusoe pushed to branch master at Debian Med / abyss
Commits:
6ab3b099 by Michael R. Crusoe at 2019-08-17T06:53:02Z
New upstream version 2.2.2
- - - - -
0a1fc576 by Michael R. Crusoe at 2019-08-17T06:53:04Z
Update upstream source from tag 'upstream/2.2.2'
Update to upstream version '2.2.2'
with Debian dir d6b938f5772465a8fcf0713e7e5fec7a945c4c33
- - - - -
8ae4d426 by Michael R. Crusoe at 2019-08-17T06:53:05Z
New upstream version
- - - - -
74298696 by Michael R. Crusoe at 2019-08-17T07:23:45Z
spelling fixes + Upload to unstable
- - - - -
17 changed files:
- .circleci/config.yml
- ChangeLog
- Map/index.cc
- Map/map.cc
- Map/overlap.cc
- Misc/samtobreak.hs
- azure-pipelines.yml
- bin/abyss-pe
- configure.ac
- debian/changelog
- + debian/clean
- debian/patches/series
- + debian/patches/spelling
- debian/rules
- doc/ABYSS.1
- doc/abyss-pe.1
- doc/abyss-tofastq.1
Changes:
=====================================
.circleci/config.yml
=====================================
@@ -21,6 +21,7 @@ jobs:
- checkout
- run: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=clang-6.0 CXX=clang++-6.0"
./configure CC=clang-6.0 CXX=clang++-6.0 --with-mpi=/usr/lib/openmpi
- run: make -j12 distcheck
@@ -34,6 +35,7 @@ jobs:
- checkout
- run: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-5 CXX=g++-5"
./configure CC=gcc-5 CXX=g++-5 --with-mpi=/usr/lib/openmpi
- run: make -j12 distcheck
@@ -47,6 +49,7 @@ jobs:
- checkout
- run: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-6 CXX=g++-6"
./configure CC=gcc-6 CXX=g++-6 --with-mpi=/usr/lib/openmpi
- run: make -j12 distcheck
@@ -60,6 +63,7 @@ jobs:
- checkout
- run: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-7 CXX=g++-7"
./configure CC=gcc-7 CXX=g++-7 --with-mpi=/usr/lib/openmpi
- run: make -j12 distcheck
@@ -73,6 +77,7 @@ jobs:
- checkout
- run: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8"
./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi
- run: make -j12 distcheck
=====================================
ChangeLog
=====================================
@@ -1,3 +1,8 @@
+2019-08-16 Johnathan Wong <jowong at bcgsc.ca>
+
+ * Release version 2.2.2
+ * Fix abyss-overlap for 32-bit systems
+
2019-08-12 Johnathan Wong <jowong at bcgsc.ca>
* Release version 2.2.1
=====================================
Map/index.cc
=====================================
@@ -146,7 +146,7 @@ static void buildFMIndex(FMIndex& fm, const string& path)
std::vector<FMIndex::value_type> s;
readFile(path.c_str(), s);
- size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
+ uint64_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
if (s.size() > MAX_SIZE) {
std::cerr << PROGRAM << ": `" << path << "', "
<< toSI(s.size())
=====================================
Map/map.cc
=====================================
@@ -505,7 +505,7 @@ static void buildFMIndex(FMIndex& fm, const char* path)
std::vector<FMIndex::value_type> s;
readFile(path, s);
- size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
+ uint64_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
if (s.size() > MAX_SIZE) {
std::cerr << PROGRAM << ": `" << path << "', "
<< toSI(s.size())
=====================================
Map/overlap.cc
=====================================
@@ -293,7 +293,7 @@ static void buildFMIndex(FMIndex& fm, const char* path)
std::vector<FMIndex::value_type> s;
readFile(path, s);
- size_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
+ uint64_t MAX_SIZE = numeric_limits<FMIndex::sais_size_type>::max();
if (s.size() > MAX_SIZE) {
std::cerr << PROGRAM << ": `" << path << "', "
<< toSI(s.size())
=====================================
Misc/samtobreak.hs
=====================================
@@ -279,7 +279,7 @@ parseArgs = do
where
help = putStr (usageInfo usage options) >> exitSuccess
tryHelp = "Try 'abyss-samtobreak --help' for more information."
- version = "abyss-samtobreak (ABySS) 2.2.1\n"
+ version = "abyss-samtobreak (ABySS) 2.2.2\n"
usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
\Calculate contig and scaffold contiguity and correctness metrics.\n"
=====================================
azure-pipelines.yml
=====================================
@@ -16,6 +16,7 @@ jobs:
displayName: Install 32-bit compilation support
- script: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=\"gcc-8 -m32\" CXX=\"g++-8 -m32\" --build=i386-linux-gnu"
./configure CC=gcc-8 CXX=g++-8 --build=i686-linux-gnu "CFLAGS=-m32" "CXXFLAGS=-m32" "LDFLAGS=-m32" --with-mpi=/usr/lib/openmpi
make -j12 distcheck
displayName: Compiling ABySS with gcc-8
@@ -35,6 +36,7 @@ jobs:
displayName: Install clang-6.0
- script: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=clang-6.0 CXX=clang++-6.0"
./configure CC=clang-6.0 CXX=clang++-6.0 --with-mpi=/usr/lib/openmpi
make -j12 distcheck
displayName: Compiling ABySS with clang 6.0
@@ -54,6 +56,7 @@ jobs:
displayName: Install gcc-5
- script: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-5 CXX=g++-5"
./configure CC=gcc-5 CXX=g++-5 --with-mpi=/usr/lib/openmpi
make -j12 distcheck
displayName: Compiling ABySS with gcc-5
@@ -73,6 +76,7 @@ jobs:
displayName: Install gcc-6
- script: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-6 CXX=g++-6"
./configure CC=gcc-6 CXX=g++-6 --with-mpi=/usr/lib/openmpi
make -j12 distcheck
displayName: Compiling ABySS with gcc-6
@@ -92,6 +96,7 @@ jobs:
displayName: Install gcc-7
- script: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-7 CXX=g++-7"
./configure CC=gcc-7 CXX=g++-7 --with-mpi=/usr/lib/openmpi
make -j12 distcheck
displayName: Compiling ABySS with gcc-7
@@ -111,6 +116,7 @@ jobs:
displayName: Install gcc-8
- script: |
./autogen.sh
+ export DISTCHECK_CONFIGURE_FLAGS="CC=gcc-8 CXX=g++-8"
./configure CC=gcc-8 CXX=g++-8 --with-mpi=/usr/lib/openmpi
make -j12 distcheck
displayName: Compiling ABySS with gcc-8
@@ -140,7 +146,7 @@ jobs:
- script: make clang-format
displayName: Run clang-format
-- job: macOS_gcc8
+- job: macOS_default_gcc
pool:
vmImage: macOS-10.14
steps:
@@ -148,10 +154,8 @@ jobs:
brew update
brew install automake boost at 1.70 openmpi google-sparsehash make pandoc ghc
displayName: Install common
- - script: brew install gcc at 8
- displayName: Install gcc
- script: |
./autogen.sh
- ./configure CC=gcc-8 CXX=g++-8 --with-boost=/usr/local/Cellar/boost/1.70.0/include/ --with-mpi=/usr/local/Cellar/open-mpi/4.0.1_2/ CPPFLAGS=-I/usr/local/Cellar/google-sparsehash/2.0.3/include/
+ ./configure --with-boost=/usr/local/Cellar/boost/1.70.0/include/ --with-mpi=/usr/local/Cellar/open-mpi/4.0.1_2/ CPPFLAGS=-I/usr/local/Cellar/google-sparsehash/2.0.3/include/
make -j12 distcheck
- displayName: Compiling ABySS with gcc 8
+ displayName: Compiling ABySS with default gcc
=====================================
bin/abyss-pe
=====================================
@@ -398,7 +398,7 @@ help:
@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users at bcgsc.ca.'
version:
- @echo "abyss-pe (ABySS) 2.2.1"
+ @echo "abyss-pe (ABySS) 2.2.2"
@echo "Written by Shaun Jackman and Anthony Raymond."
@echo
@echo "Copyright 2012 Canada's Michael Smith Genome Science Centre"
=====================================
configure.ac
=====================================
@@ -1,5 +1,5 @@
AC_PREREQ(2.62)
-AC_INIT(ABySS, 2.2.1, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.2.2, abyss-users at bcgsc.ca, abyss,
http://www.bcgsc.ca/platform/bioinfo/software/abyss)
AC_CONFIG_MACRO_DIR([m4])
=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+abyss (2.2.2-1) unstable; urgency=medium
+
+ * New upstream version
+
+ -- Michael R. Crusoe <michael.crusoe at gmail.com> Sat, 17 Aug 2019 08:53:07 +0200
+
abyss (2.2.1-1) unstable; urgency=medium
* New upstream release, should fix failing builds on 32-bit architectures.
=====================================
debian/clean
=====================================
@@ -0,0 +1 @@
+Sealer/abyss-sealer.1
=====================================
debian/patches/series
=====================================
@@ -2,3 +2,4 @@ abyss-pe.patch
# gtest.patch
abyss-32-bit.patch
strict_alignment.patch
+spelling
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,41 @@
+From: Michael R. Crusoe <michael.crusoe at gmail.com>
+Subject: typo fixes, courtesy lintian
+--- abyss.orig/Sealer/README.md
++++ abyss/Sealer/README.md
+@@ -24,7 +24,7 @@
+ Description
+ ===========
+
+-Sealer is an application of Konnector that closes intra-scaffold gaps. It performs three sequential functions. First, regions with Ns are identified from an input scaffold. Flanking nucleotues (2 x 100bp) are extracted from those regions while respecting the strand (5' to 3') direction on the sequence immediately downstream of each gap. In the second step, flanking sequence pairs are used as input to Konnector along with a set of reads with a high level of coverage redundancy. Ideally, the reads should represent the original dataset from which the draft assembly is generated, or further whole genome shotgun (WGS) sequencing data generated from the same sample. Within Konnector, the input WGS reads are used to populate a Bloom filter, tiling the reads with a sliding window of length *k*, thus generating a probabilistic representation of all the *k*-mers in the reads. Konnector also uses crude error removal and correctional algorithms, eliminating singletons (*k*-mers that are observed only once) and fixing base mismatches in the flanking sequence pairs. Sealer launches Konnector processes using a user-input range of *k*-mer lengths. In the third and final operation, succesfully merged sequences are inserted into the gaps of the original scaffolds, and Sealer outputs a new gap-filled scaffold file.
++Sealer is an application of Konnector that closes intra-scaffold gaps. It performs three sequential functions. First, regions with Ns are identified from an input scaffold. Flanking nucleotues (2 x 100bp) are extracted from those regions while respecting the strand (5' to 3') direction on the sequence immediately downstream of each gap. In the second step, flanking sequence pairs are used as input to Konnector along with a set of reads with a high level of coverage redundancy. Ideally, the reads should represent the original dataset from which the draft assembly is generated, or further whole genome shotgun (WGS) sequencing data generated from the same sample. Within Konnector, the input WGS reads are used to populate a Bloom filter, tiling the reads with a sliding window of length *k*, thus generating a probabilistic representation of all the *k*-mers in the reads. Konnector also uses crude error removal and correctional algorithms, eliminating singletons (*k*-mers that are observed only once) and fixing base mismatches in the flanking sequence pairs. Sealer launches Konnector processes using a user-input range of *k*-mer lengths. In the third and final operation, successfully merged sequences are inserted into the gaps of the original scaffolds, and Sealer outputs a new gap-filled scaffold file.
+
+ Installation
+ ============
+@@ -159,6 +159,6 @@
+ * `--help`: display this help and exit
+ * `--version`: output version information and exit
+
+-*k* is the size of *k*-mer for the de Bruijn graph. You may specify multiple values of *k*, which will increase the nubmer of gaps closed at the cost of increased run time. Multiple values of *k* ought to be specified in increasing order, as lower values of *k* have fewer coverage gaps and are less likely to misassemble.
++*k* is the size of *k*-mer for the de Bruijn graph. You may specify multiple values of *k*, which will increase the number of gaps closed at the cost of increased run time. Multiple values of *k* ought to be specified in increasing order, as lower values of *k* have fewer coverage gaps and are less likely to misassemble.
+
+ *P* is the threshold for number of paths allowed to be traversed. When set to 10, Konnector will attempt to close gaps even when there are 10 different paths found. It would attempt to create a consensus sequence between these paths. The default setting is 2.
+--- abyss.orig/doc/abyss-pe.1
++++ abyss/doc/abyss-pe.1
+@@ -113,7 +113,7 @@
+ SS=--SS to assemble in strand-specific mode
+ .br
+ Requires that all libraries are strand-specific RNA-Seq libraries.
+-Assumes that the first read in a read pair is reveresed WRT the
++Assumes that the first read in a read pair is reversed WRT the
+ transcripts sequenced.
+ .TP
+ .B t
+@@ -242,7 +242,7 @@
+
+ .SS "MPI COMPATIBILITY"
+ Due to its use of multi-threading, DIDA has known deadlocking issues
+-with OpenMPI. Using the MPICH MPI library is strongly recommmended
++with OpenMPI. Using the MPICH MPI library is strongly recommended
+ when running assemblies with DIDA. Testing was done with MPICH 3.1.3,
+ compiled with --enable-threads=funneled.
+
=====================================
debian/rules
=====================================
@@ -1,6 +1,6 @@
#!/usr/bin/make -f
-export DEB_CXXFLAGS_MAINT_APPEND = -DGTEST_USE_OWN_TR1_TUPLE=0
+export DEB_CXXFLAGS_MAINT_APPEND = -DGTEST_USE_OWN_TR1_TUPLE=0 -Wno-error=deprecated-copy -Wno-error=array-bounds
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
=====================================
doc/ABYSS.1
=====================================
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.1" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.2.2" "User Commands"
.SH NAME
ABYSS \- assemble short reads into contigs
.SH SYNOPSIS
=====================================
doc/abyss-pe.1
=====================================
@@ -1,4 +1,4 @@
-.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.1" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.2.2" "User Commands"
.SH NAME
abyss-pe - assemble reads into contigs
.SH SYNOPSIS
=====================================
doc/abyss-tofastq.1
=====================================
@@ -1,4 +1,4 @@
-.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.1" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.2.2" "User Commands"
.SH NAME
abyss-tofastq \- convert various file formats to FASTQ format
.br
View it on GitLab: https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c
--
View it on GitLab: https://salsa.debian.org/med-team/abyss/compare/acb475098819c0d7d7a34465551fe3df2d4f9804...74298696a060ea9876f79a8d32af9aada7ece73c
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