[med-svn] [Git][med-team/abyss][upstream] New upstream version 2.3.10

Étienne Mollier (@emollier) gitlab at salsa.debian.org
Sat Nov 2 13:04:14 GMT 2024 

Étienne Mollier pushed to branch upstream at Debian Med / abyss


Commits:
9a865ba8 by Étienne Mollier at 2024-11-02T13:43:30+01:00
New upstream version 2.3.10
- - - - -


9 changed files:

- ChangeLog
- Misc/samtobreak.hs
- README.md
- azure-pipelines.yml
- bin/abyss-pe
- configure.ac
- doc/ABYSS.1
- doc/abyss-pe.1
- doc/abyss-tofastq.1


Changes:

=====================================
ChangeLog
=====================================
@@ -1,3 +1,10 @@
+2024-10-18 Lauren Coombe <lcoombe at bcgsc.ca>
+
+  * Release version 2.3.10
+
+      General:
+	    * Fix usage of `N` and `S` parameters for scaffolding stage
+
 2024-09-11 Johnathan Wong <jowong at bcgsc.ca>
 
   * Release version 2.3.9


=====================================
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) 2.3.9\n"
+  version = "abyss-samtobreak (ABySS) 2.3.10\n"
   usage = "Usage: samtobreak [OPTION]... [FILE]...\n\
 \Calculate contig and scaffold contiguity and correctness metrics.\n"
 


=====================================
README.md
=====================================
@@ -1,5 +1,5 @@
 [![Release](https://img.shields.io/github/release/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/releases)
-[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.3.9/abyss-2.3.9.tar.gz)
+[![Downloads](https://img.shields.io/github/downloads/bcgsc/abyss/total?logo=github)](https://github.com/bcgsc/abyss/releases/download/2.3.10/abyss-2.3.10.tar.gz)
 [![Conda](https://img.shields.io/conda/dn/bioconda/abyss?label=Conda)](https://anaconda.org/bioconda/abyss)
 [![Issues](https://img.shields.io/github/issues/bcgsc/abyss.svg)](https://github.com/bcgsc/abyss/issues)
 


=====================================
azure-pipelines.yml
=====================================
@@ -33,13 +33,20 @@ jobs:
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
       mamba install --yes -c conda-forge -c bioconda compilers make boost-cpp sparsehash openmpi automake perl pandoc meson ninja btllib
     displayName: Install dependencies
   - script: |
@@ -50,68 +57,116 @@ jobs:
     displayName: Compiling ABySS
 
 - job:
-  displayName: mac_clang14
+  displayName: mac_clang16
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.7.0 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
-      make -j12 distcheck
-    displayName: Compiling ABySS
+      make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
+    displayName: Compiling ABySS with clang 16
 
 - job:
-  displayName: mac_clang13
+  displayName: mac_clang15
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.6.0 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
-      make -j12 distcheck
-    displayName: Compiling ABySS with clang 13
+      make -j12 distcheck AM_CXXFLAGS=-Wno-error=unused-but-set-variable
+    displayName: Compiling ABySS with clang 15
 
 - job:
-  displayName: mac_clang12
+  displayName: mac_clang14
   pool:
     vmImage: 'macOS-latest'
   steps:
-  - script: echo "##vso[task.prependpath]$CONDA/bin"
-    displayName: Add conda to PATH
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
   - script: conda create --yes --quiet --name abyss_CI
     displayName: Create Anaconda environment
   - script: |
       source activate abyss_CI
-      conda install --yes -c conda-forge mamba python=3.9
-      mamba install --yes -c conda-forge -c bioconda compilers=1.4.0 make boost-cpp sparsehash openmpi automake perl pandoc llvm-openmp btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+      mamba install --yes -c conda-forge -c bioconda compilers=1.5.2 make boost-cpp sparsehash openmpi automake perl pandoc btllib 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
     displayName: Install dependencies
   - script: |
       source activate abyss_CI
       ./autogen.sh
       ./configure
       make -j12 distcheck
-    displayName: Compiling ABySS with clang 12
+    displayName: Compiling ABySS with clang 14
 
+- job:
+  displayName: mac_clang13
+  pool:
+    vmImage: 'macOS-latest'
+  steps:
+  - script: |
+      mkdir -p ~/miniforge3
+      curl -L https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-MacOSX-x86_64.sh  -o ~/miniforge3/miniforge.sh
+      bash ~/miniforge3/miniforge.sh -b -u -p ~/miniforge3
+      rm -rf  ~/miniforge3/miniforge.sh
+      ~/miniforge3/bin/conda init bash
+      ~/miniforge3/bin/conda init zsh
+      export CONDA=$(realpath ~/miniforge3/bin)
+      echo "##vso[task.prependpath]$CONDA"
+    displayName: Install conda
+  - script: conda create --yes --quiet --name abyss_CI
+    displayName: Create Anaconda environment
+  - script: |
+      source activate abyss_CI
+      mamba install --yes -c conda-forge -c bioconda compilers=1.4.2 make boost-cpp sparsehash openmpi automake perl btllib pandoc 'llvm-openmp<17.0.0' 'libcxx<17.0.0'
+    displayName: Install dependencies
+  - script: |
+      source activate abyss_CI
+      ./autogen.sh
+      ./configure
+      make -j12 distcheck
+    displayName: Compiling ABySS with clang 13
 
 - job: linux_gcc12
   pool:


=====================================
bin/abyss-pe
=====================================
@@ -349,12 +349,12 @@ L?=$l
 S?=100-5000
 N?=15-20
 SCAFFOLD_DE_S?=$(shell echo $S | sed 's/-.*//')
-SCAFFOLD_DE_N?=$N
+SCAFFOLD_DE_N?=$(shell echo $N | sed 's/-.*//')
 SCAFFOLD_DE_OPTIONS?=$(DISTANCEEST_OPTIONS)
-$(foreach i,$(mp),$(eval $i_l?=$L))
-$(foreach i,$(mp),$(eval $i_s?=$(SCAFFOLD_DE_S)))
-$(foreach i,$(mp),$(eval $i_n?=$(SCAFFOLD_DE_N)))
-override scaffold_deopt=$v $(dbopt) --dot --median -j$j -k$k $(SCAFFOLD_DE_OPTIONS) -l$($*_l) -s$($*_s) -n$($*_n) $($*_de)
+$(foreach i,$(mp),$(eval $i_scaf_l?=$L))
+$(foreach i,$(mp),$(eval $i_scaf_s?=$(SCAFFOLD_DE_S)))
+$(foreach i,$(mp),$(eval $i_scaf_n?=$(SCAFFOLD_DE_N)))
+override scaffold_deopt=$v $(dbopt) --dot --median -j$j -k$k $(SCAFFOLD_DE_OPTIONS) -l$($*_scaf_l) -s$($*_scaf_s) -n$($*_scaf_n) $($*_de)
 scopt += $v $(dbopt) $(SS) -k$k
 ifdef G
 scopt += -G$G
@@ -414,7 +414,7 @@ help:
 	@echo 'Report bugs to https://github.com/bcgsc/abyss/issues or abyss-users at bcgsc.ca.'
 
 version:
-	@echo "abyss-pe (ABySS) 2.3.9"
+	@echo "abyss-pe (ABySS) 2.3.10"
 	@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, 2.3.9, abyss-users at bcgsc.ca, abyss,
+AC_INIT(ABySS, 2.3.10, abyss-users at bcgsc.ca, abyss,
 		http://www.bcgsc.ca/platform/bioinfo/software/abyss)
 
 AC_CONFIG_MACRO_DIR([m4])


=====================================
doc/ABYSS.1
=====================================
@@ -1,4 +1,4 @@
-.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.9" "User Commands"
+.TH ABYSS "1" "2015-May" "ABYSS (ABySS) 2.3.10" "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) 2.3.9" "User Commands"
+.TH abyss-pe "1" "2015-May" "abyss-pe (ABySS) 2.3.10" "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 2.3.9" "User Commands"
+.TH abyss-tofastq "1" "2015-May" "ABySS 2.3.10" "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/-/commit/9a865ba8c9b3d93aaf4174fdb3f8db70ca721fcf

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