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Rebuild breseq #51221

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merged 3 commits into from
Oct 7, 2024
Merged

Rebuild breseq #51221

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4763f4a
Rebuild breseq
mencian Oct 7, 2024
d37a254
add automake
mencian Oct 7, 2024
fcc0683
add m4 build_prefix
mencian Oct 7, 2024
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14 changes: 12 additions & 2 deletions recipes/breseq/build.sh
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Original file line number Diff line number Diff line change
@@ -1,5 +1,15 @@
#!/bin/bash

set -eux
./configure --prefix=$PREFIX
make -j ${CPU_COUNT}

export INCLUDES="-I${PREFIX}/include"
export LIBPATH="-L${PREFIX}/lib"
export LDFLAGS="${LDFLAGS} -L${PREFIX}/lib"

autoreconf -if
./configure --prefix="${PREFIX}" \
CXX="${CXX}" \
CXXFLAGS="${CXXFLAGS} -O3 -I${PREFIX}/include" \
LDFLAGS="${LDFLAGS}"
make -j "${CPU_COUNT}"
make install
14 changes: 9 additions & 5 deletions recipes/breseq/meta.yaml
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Expand Up @@ -9,19 +9,17 @@ source:
sha256: "39b35e246ecd2b497c82a99765ca4d78a0400bc4a7518b7506b140229ccc0247"

build:
number: 1
number: 2
run_exports:
- {{ pin_subpackage('breseq', max_pin="x.x") }}

requirements:
build:
- make
- {{ compiler("c") }}
- {{ compiler("cxx") }}
host:
- zlib
run:
- zlib
- r-base
- r-cairo
- bowtie2 >=2.0.0,!=2.0.3,!=2.0.4,!=2.3.1
Expand All @@ -36,11 +34,17 @@ about:
license: GPL-2.0-or-later
license_family: GPL
license_file: COPYING
summary: A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
data.
summary: "A computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing
data."
doc_url: "https://barricklab.org/twiki/pub/Lab/ToolsBacterialGenomeResequencing/documentation/"
dev_url: https://github.com/barricklab/breseq

extra:
additional-platforms:
- linux-aarch64
- osx-arm64
identifiers:
- biotools:breseq
- biotools:breseq_bam2aln
- biotools:breseq_bam2cov
- usegalaxy-eu:breseq
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