From f88beae3e7809d15907daff1ee774fa95e5b9684 Mon Sep 17 00:00:00 2001 From: Lauren Coombe Date: Wed, 3 May 2023 11:08:50 -0700 Subject: [PATCH] Prepare for release v2.3.6 (#465) * Prepare for release v2.3.6 * Update gcc version for mac_gcc test to be consistent with current brew bottle * brew install gcc@12 --- ChangeLog | 11 +++++++++++ Misc/samtobreak.hs | 2 +- azure-pipelines.yml | 3 +-- bin/abyss-pe | 2 +- configure.ac | 2 +- doc/ABYSS.1 | 2 +- doc/abyss-pe.1 | 2 +- doc/abyss-tofastq.1 | 2 +- 8 files changed, 18 insertions(+), 8 deletions(-) diff --git a/ChangeLog b/ChangeLog index 19896fbd5..63a179b73 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,3 +1,14 @@ +2023-05-02 Lauren Coombe + + * Release version 2.3.6 + + General: + * btllib is now a dependency + * Documentation updates + + abyss-rresolver-short: + * btllib source code removed due to btllib now being a dependency + 2022-05-11 Vladimir Nikolic * Release version 2.3.5 diff --git a/Misc/samtobreak.hs b/Misc/samtobreak.hs index e5781aa1b..a51911e3a 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) 2.3.5\n" + version = "abyss-samtobreak (ABySS) 2.3.6\n" usage = "Usage: samtobreak [OPTION]... [FILE]...\n\ \Calculate contig and scaffold contiguity and correctness metrics.\n" diff --git a/azure-pipelines.yml b/azure-pipelines.yml index 144f80959..e56c4b94f 100644 --- a/azure-pipelines.yml +++ b/azure-pipelines.yml @@ -6,7 +6,7 @@ jobs: - script: | rm -f /usr/local/bin/2to3 # brew is having issues with installing Python brew update - brew install automake boost openmpi google-sparsehash make pandoc ghc + brew install automake boost openmpi google-sparsehash make pandoc ghc gcc@12 displayName: Install common - script: | wget https://github.com/bcgsc/btllib/releases/download/v1.5.1/btllib-1.5.1.tar.gz @@ -15,7 +15,6 @@ jobs: tar xzf btllib-1.5.1.tar.gz cd btllib-1.5.1 ./compile - pwd displayName: Install btllib - script: | ./autogen.sh diff --git a/bin/abyss-pe b/bin/abyss-pe index baff11c8d..e22319cb1 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) 2.3.5" + @echo "abyss-pe (ABySS) 2.3.6" @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 d04feaf3c..7056fe1f0 100644 --- a/configure.ac +++ b/configure.ac @@ -1,5 +1,5 @@ AC_PREREQ(2.62) -AC_INIT(ABySS, 2.3.5, abyss-users@bcgsc.ca, abyss, +AC_INIT(ABySS, 2.3.6, 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 358786f84..35333dd32 100644 --- a/doc/ABYSS.1 +++ b/doc/ABYSS.1 @@ -1,4 +1,4 @@ -.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.5" "User Commands" +.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.6" "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 e1a190b2b..c410beaf5 100644 --- a/doc/abyss-pe.1 +++ b/doc/abyss-pe.1 @@ -1,4 +1,4 @@ -.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.5" "User Commands" +.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.6" "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 d2244cd01..ac72fc1c3 100644 --- a/doc/abyss-tofastq.1 +++ b/doc/abyss-tofastq.1 @@ -1,4 +1,4 @@ -.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.5" "User Commands" +.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.6" "User Commands" .SH NAME abyss-tofastq \- convert various file formats to FASTQ format .br