From 23a6e4f4925dd0895b0238bb3fa63864b5433171 Mon Sep 17 00:00:00 2001 From: vlad0x00 Date: Mon, 20 Dec 2021 11:04:35 -0800 Subject: [PATCH] Update version and drop gcc5 support --- ChangeLog | 14 +++++++++++++- Misc/samtobreak.hs | 2 +- README.md | 4 ++-- azure-pipelines.yml | 21 --------------------- bin/abyss-pe | 2 +- configure.ac | 2 +- doc/ABYSS.1 | 2 +- doc/abyss-pe.1 | 2 +- doc/abyss-tofastq.1 | 2 +- 9 files changed, 21 insertions(+), 30 deletions(-) diff --git a/ChangeLog b/ChangeLog index f6bb568b1..66ba323f3 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,15 @@ +2021-12-20 Vladimir Nikolic + + * Release version 2.3.4 + + General: + * Dropped support for gcc5 due to lack of support for more recent C++ features. + + abyss-rresolver-short: + * Reduced memory consumption. + * Better calculation of read size proportions in the input dataset. + * Increased max read read size allowed. + 2021-11-10 Vladimir Nikolic * Release version 2.3.3 @@ -7,7 +19,7 @@ abyss-rresolver-short: * Multiple read sizes are better handled. E.g. 150 and 151 are processed as one read size. - * Updated default parameters. + * Updated default parameters. 2021-10-13 Vladimir Nikolic diff --git a/Misc/samtobreak.hs b/Misc/samtobreak.hs index f2e5195f5..a8cfb6050 100644 --- a/Misc/samtobreak.hs +++ b/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) 2.3.3\n" + version = "abyss-samtobreak (ABySS) 2.3.4\n" usage = "Usage: samtobreak [OPTION]... [FILE]...\n\ \Calculate contig and scaffold contiguity and correctness metrics.\n" diff --git a/README.md b/README.md index cbb371257..37910b95c 100644 --- a/README.md +++ b/README.md @@ -156,10 +156,10 @@ This installs ABySS at the provided path, in this case `/path/to/abyss`. Not specifying `--prefix` would install in `/usr/local`, which requires sudo privileges when running `make install`. -ABySS requires a modern compiler such as GCC 4.2 or greater. If you have multiple +ABySS requires a modern compiler such as GCC 6 or greater. If you have multiple versions of GCC installed, you can specify a different compiler: - ../configure CC=gcc-4.6 CXX=g++-4.6 + ../configure CC=gcc-10 CXX=g++-10 If Boost is installed at a non-standard location, you can specify the path to it: diff --git a/azure-pipelines.yml b/azure-pipelines.yml index e165c7f4d..f4fd250f4 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -131,27 +131,6 @@ jobs: make -j12 distcheck displayName: Compiling ABySS with clang 10 -- job: linux_gcc5 - pool: - vmImage: ubuntu-latest - steps: - - script: | - sudo apt-get update -qq - sudo apt-get install -qq software-properties-common - sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic main universe security" - sudo add-apt-repository -y "deb http://us.archive.ubuntu.com/ubuntu bionic-updates main universe restricted" - sudo apt-get update -qq - sudo apt-get install -qq autoconf automake gcc g++ libboost-dev libgtest-dev libopenmpi-dev libsparsehash-dev make pandoc - displayName: Install common - - script: sudo apt-get install -qq gcc-5 g++-5 - 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 - - job: linux_gcc6 pool: vmImage: ubuntu-latest diff --git a/bin/abyss-pe b/bin/abyss-pe index bf6a212a4..0f7d916c1 100755 --- a/bin/abyss-pe +++ b/bin/abyss-pe @@ -414,7 +414,7 @@ help: @echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users@bcgsc.ca.' version: - @echo "abyss-pe (ABySS) 2.3.3" + @echo "abyss-pe (ABySS) 2.3.4" @echo "Written by Shaun Jackman and Anthony Raymond." @echo @echo "Copyright 2012 Canada's Michael Smith Genome Science Centre" diff --git a/configure.ac b/configure.ac index 61dc4c13c..cf102f9e9 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.62) -AC_INIT(ABySS, 2.3.3, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 2.3.4, abyss-users@bcgsc.ca, abyss, http://www.bcgsc.ca/platform/bioinfo/software/abyss) AC_CONFIG_MACRO_DIR([m4]) diff --git a/doc/ABYSS.1 b/doc/ABYSS.1 index a9f9d161d..417b1a9f0 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.3" "User Commands" +.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.4" "User Commands" .SH NAME ABYSS \- assemble short reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-pe.1 b/doc/abyss-pe.1 index feb262a63..f410a47c5 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.3" "User Commands" +.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.4" "User Commands" .SH NAME abyss-pe - assemble reads into contigs .SH SYNOPSIS diff --git a/doc/abyss-tofastq.1 b/doc/abyss-tofastq.1 index e7d201db6..131a29aca 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.3" "User Commands" +.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.4" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br