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Signed-off-by: Martin Tzvetanov Grigorov <[email protected]>
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@@ -0,0 +1,13 @@ | ||
#!/usr/bin/env bash | ||
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set -xe | ||
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# no need to build SeqAn's documentation/demos | ||
rm -rf external/seqan-library-2.2.0/share/doc/seqan/ | ||
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mkdir build | ||
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CXX="${CXX} -std=c++14" make -j"${CPU_COUNT}" | ||
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mkdir -p ${PREFIX}/bin | ||
install -m 755 popins2 ${PREFIX}/bin |
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{% set name = "popins2" %} | ||
{% set version = "0.13.0" %} | ||
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package: | ||
name: {{ name }} | ||
version: {{ version }} | ||
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build: | ||
number: 0 | ||
run_exports: | ||
- {{ pin_subpackage(name, max_pin='x.x') }} | ||
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source: | ||
git_url: https://github.com/kehrlab/PopIns2 | ||
git_rev: v{{ version }} | ||
patches: | ||
- popins2.patch | ||
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requirements: | ||
build: | ||
- make | ||
- {{ compiler('cxx') }} | ||
host: | ||
- bifrost | ||
- bwa | ||
- htslib | ||
- samtools | ||
- sickle-trim | ||
- zlib | ||
run: | ||
- bifrost | ||
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test: | ||
commands: | ||
- popins2 --help | ||
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about: | ||
home: https://github.com/kehrlab/PopIns2 | ||
license: GPL-2.0-only | ||
license_family: GPL | ||
license_file: LICENSE | ||
summary: Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs | ||
doc_url: https://github.com/kehrlab/PopIns2 | ||
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extra: | ||
additional-platforms: | ||
- linux-aarch64 | ||
- osx-arm64 | ||
skip-lints: | ||
- missing_hash | ||
- uses_vcs_url |
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diff --git i/Makefile w/Makefile | ||
index de28bc8..613fa79 100644 | ||
--- i/Makefile | ||
+++ w/Makefile | ||
@@ -6,7 +6,7 @@ SRCS := $(shell find $(SRC_DIR) -type f -name *.cpp) | ||
OBJS := $(patsubst $(SRC_DIR)/%,$(BUILD_DIR)/%,$(SRCS:.cpp=.o)) | ||
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# Compiler | ||
-CXX = g++ -std=c++14 | ||
+CXX ?= g++ -std=c++14 | ||
CC = $(CXX) | ||
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# SeqAn | ||
@@ -29,7 +29,7 @@ CXXFLAGS += -march=native -DMAX_KMER_SIZE=64 | ||
CXXFLAGS += -I$(SEQAN_LIB) | ||
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# Linker flags | ||
-LDLIBS = -lbifrost -pthread -lz -rdynamic -DMAX_KMER_SIZE=64 | ||
+LDLIBS = -L"${PREFIX}/lib" -lbifrost -pthread -lz -rdynamic -DMAX_KMER_SIZE=64 | ||
# MacOS users might have to comment out the next line | ||
LDLIBS += -lrt | ||
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diff --git i/src/Traceback.h w/src/Traceback.h | ||
index 745db68..6323e80 100644 | ||
--- i/src/Traceback.h | ||
+++ w/src/Traceback.h | ||
@@ -6,6 +6,7 @@ | ||
#ifndef TRACEBACK_ | ||
#define TRACEBACK_ | ||
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+#include <cstdint> | ||
#include <iostream> | ||
#include <fstream> | ||
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