Add Cloudspades

recipes/cloudspades/0001-change-verbosity-remove-expr.patch

@@ -0,0 +1,43 @@
+diff -Naur a/assembler/spades_compile.sh b/assembler/spades_compile.sh
+--- a/assembler/spades_compile.sh	2024-05-26 14:36:40
++++ b/assembler/spades_compile.sh	2024-05-27 13:00:03
+@@ -37,10 +37,10 @@ check_whether_OPTARG_is_an_integer() {
+ }
+
+ # return the argument first character
+-str_head() { echo "$(expr substr "$1" 1 1)"; }
++str_head() { echo "${1::1}"; }
+
+ # return the argument without the first character
+-str_tail() { echo "$(expr substr "$1" 2 $((${#1}-1)))"; }
++str_tail() { echo "${1:1}"; }
+
+ print_help() {
+   echo
+@@ -221,11 +221,21 @@ else
+   ADDITIONAL_FLAGS="$ADDITIONAL_FLAGS -DSPADES_BUILD_INTERNAL=OFF"
+ fi
+
+-cd "$WORK_DIR"
+-cmake -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="$PREFIX" $ADDITIONAL_FLAGS "$BASEDIR/src"
+-make -j $AMOUNT_OF_THREADS
+-make install
+-cd "$PREFIX"
++if [[ `uname` == "Darwin" ]]; then
++        export CONFIG_ARGS="-DCMAKE_FIND_FRAMEWORK=NEVER -DCMAKE_FIND_APPBUNDLE=NEVER"
++       export CFLAGS="${CFLAGS} -Wunused-command-line-argument"
++       export CXXFLAGS="${CXXFLAGS} -D_LIBCPP_DISABLE_AVAILABILITY"
++else
++        export CONFIG_ARGS=""
++fi
++
++cd "${WORK_DIR}"
++cmake -S "${BASEDIR}/src" -B . -G "Unix Makefiles" -DCMAKE_INSTALL_PREFIX="${PREFIX}" \
++       -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER="${CXX}" \
++       -DCMAKE_CXX_FLAGS="${CXXFLAGS}" -DCMAKE_C_COMPILER="${CC}" \
++       -DCMAKE_C_FLAGS="${CFLAGS}" "${ADDITIONAL_FLAGS}" \
++       "${CONFIG_ARGS}"
++cmake --build . --target install -j "${AMOUNT_OF_THREADS}" -v
+
+ if [ $RUN_TESTS = "y" ]; then
+   cd "$BASEDIR"

recipes/cloudspades/build.sh

@@ -0,0 +1,20 @@
+#!/bin/bash
+
+set -e -o pipefail -x
+
+export LIBRARY_PATH="${PREFIX}/lib"
+export INCLUDE_PATH="${PREFIX}/include"
+export CFLAGS="${CFLAGS} -O3 -fcommon"
+export CXXFLAGS="${CFLAGS} -O3 -fcommon -I${PREFIX}/include -D_LIBCPP_DISABLE_AVAILABILITY"
+
+case $(uname) in
+	Linux)
+		THREADS="-rj${CPU_COUNT}"
+		;;
+	Darwin)
+		THREADS=""
+		;;
+esac
+
+cd assembler
+PREFIX="${PREFIX}" bash spades_compile.sh "${THREADS}" -DSPADES_ENABLE_PROJECTS="all"

recipes/cloudspades/meta.yaml

@@ -0,0 +1,54 @@
+{% set name = "cloudspades" %}
+{% set version = "3.16.0" %}
+{% set sha256 = "5972a76722fadf9527675fea3884a03ca864b153b8de9dd94532b1b797de04aa" %}
+
+package:
+  name: {{ name }}
+  version: {{ version }}
+
+source:
+  url: https://github.com/ablab/spades/archive/refs/tags/cloudspades-0.1.tar.gz
+  sha256: {{ sha256 }}
+
+build:
+  number: 0
+  skip: True  # [osx]
+  run_exports:
+    - {{ pin_subpackage('cloudspades', max_pin="x") }}
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - cmake
+    - make
+    - pkg-config
+  host:
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+    - zlib
+    - bzip2
+  run:
+    - libgomp  # [linux]
+    - llvm-openmp  # [osx]
+    - python >=3.8
+
+test:
+  commands:
+    - spades.py --version 2>&1 | grep {{ version }}
+    - metaspades.py --version 2>&1 | grep {{ version }}
+    - spades-kmercount -h 2>&1 | grep spades-kmercount
+    - spades-gmapper 2>&1 | grep spades-gmapper
+    - spades-gbuilder 2>&1 | grep spades-gbuilder
+
+about:
+  home: "https://github.com/ablab/spades"
+  license: "GPL-2.0-only"
+  license_family: GPL
+  license_file: 'assembler/LICENSE'
+  summary: "A module of the SPAdes assembler aimed at genome assembly from linked read technologies (10x, Tellseq, Haplotagging)."
+  dev_url: "https://github.com/ablab/spades/tree/cloudspades-0.1"
+  doc_url: "https://github.com/ablab/spades/tree/cloudspades-ismb"
+
+extra:
+  recipe-maintainers:
+    - pdimens