Update abyss to 2.3.10

recipes/abyss/build.sh

@@ -1,5 +1,8 @@
 #!/bin/bash
 
+export M4="${BUILD_PREFIX}/bin/m4"
+export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"
+
 if [[ "$(uname)" == Darwin ]]; then
     # Fix for install_name_tool error:
     #   error: install_name_tool: changing install names or rpaths can't be
@@ -9,13 +12,14 @@ if [[ "$(uname)" == Darwin ]]; then
     export LDFLAGS="$LDFLAGS -headerpad_max_install_names"
 fi
 
-./configure \
-    --prefix="$PREFIX" \
-    --with-boost="$PREFIX" \
-    --with-mpi="$PREFIX" \
-    --with-sparsehash="$PREFIX" \
-    --without-sqlite || cat config.log
-make AM_CXXFLAGS=-Wall
+autoreconf -if
+./configure --prefix="${PREFIX}" \
+	CXXFLAGS="${CXXFLAGS} -std=c++14 -O3 -I${PREFIX}/include" \
+	--with-boost="${PREFIX}" \
+	--with-mpi="${PREFIX}" \
+	--with-sparsehash="${PREFIX}" \
+	--without-sqlite || cat config.log
+make AM_CXXFLAGS="-Wall" -j"${CPU_COUNT}"
 make install
 
 $RECIPE_DIR/create-wrapper.sh "$PREFIX/bin/abyss-pe" "$PREFIX/bin/abyss-pe.Makefile"

recipes/abyss/meta.yaml

@@ -1,5 +1,5 @@
 {% set name = "abyss" %}
-{% set version = "2.3.9" %}
+{% set version = "2.3.10" %}
 
 package:
   name: {{ name|lower }}
@@ -12,20 +12,22 @@ build:
 
 source:
   url: https://github.com/bcgsc/abyss/releases/download/{{ version }}/abyss-{{ version }}.tar.gz
-  sha256: 55f0b27b67b4486dc6cbe132c0f4c228ee4f9e86c56292a7b50633df87e3212e
-  patches:
-    - config.patch
+  sha256: bbe42e00d1ebb53ec6afaad07779baaaee994aa5c65b9a38cf4ad2011bb93c65
 
 requirements:
   build:
     - {{ compiler('cxx') }}
     - make
+    - automake
+    - autoconf
+    - libtool
   host:
     - boost-cpp
     - sparsehash
     - openmpi
     - btllib
   run:
+    - boost-cpp
     - openmpi
     - make
     - util-linux  # [linux]
@@ -38,12 +40,13 @@ test:
     - abyss-pe help | grep -q "Assemble reads into contigs and scaffolds"
 
 about:
-  home: http://www.bcgsc.ca/platform/bioinfo/software/abyss
-  license: GPL-3.0-only
+  home: "https://www.bcgsc.ca/platform/bioinfo/software/abyss"
+  license: "GPL-3.0-only"
+  license_family: GPL3
   license_file: LICENSE
-  summary: Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler
-  dev_url: https://github.com/bcgsc/abyss
-  doc_url: https://github.com/bcgsc/abyss#readme
+  summary: "Assembly By Short Sequences - a de novo, parallel, paired-end short read sequence assembler."
+  dev_url: "https://github.com/bcgsc/abyss"
+  doc_url: "https://github.com/bcgsc/abyss/blob/v{{ version }}/README.md"
 
 extra:
   additional-platforms:
@@ -54,5 +57,6 @@ extra:
     extended-base: true
   identifiers:
     - biotools:abyss
+    - usegalaxy-eu:abyss-pe
     - doi:10.1101/gr.214346.116
     - doi:10.1101/gr.089532.108