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#!/bin/bash -euo | ||
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# Add workaround for SSH-based Git connections from Rust/cargo. See https://github.com/rust-lang/cargo/issues/2078 for details. | ||
# We set CARGO_HOME because we don't pass on HOME to conda-build, thus rendering the default "${HOME}/.cargo" defunct. | ||
export CARGO_NET_GIT_FETCH_WITH_CLI=true CARGO_HOME="$(pwd)/.cargo" | ||
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# build statically linked binary with Rust | ||
cargo-bundle-licenses --format yaml --output THIRDPARTY.yml | ||
RUST_BACKTRACE=1 cargo install --verbose --locked --no-track --root $PREFIX --path . | ||
cp scripts/* $PREFIX/bin |
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{% set version="0.0.1" %} | ||
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package: | ||
name: devider | ||
version: {{ version }} | ||
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source: | ||
url: https://github.com/bluenote-1577/devider/archive/v{{ version }}.tar.gz | ||
sha256: e2c5e4a2faa51dbfd0ad4cb867d0dc25ea4012e83ec8fea27c1624592fce7dce | ||
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build: | ||
number: 0 | ||
run_exports: | ||
- {{ pin_subpackage('devider', max_pin="x.x") }} | ||
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requirements: | ||
build: | ||
- {{ compiler("cxx") }} | ||
- {{ compiler('rust') }} | ||
- cargo-bundle-licenses | ||
- make | ||
- cmake >=3.12 | ||
run: | ||
- python | ||
- samtools | ||
- minimap2 | ||
- lofreq >=2.1.5 | ||
- tabix | ||
- pysam >=0.16 | ||
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test: | ||
commands: | ||
- devider -h | ||
- run_devider_pipeline -h | ||
- haplotag_bam -h | ||
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about: | ||
home: https://github.com/bluenote-1577/devider | ||
license: MIT | ||
license_file: | ||
- LICENSE | ||
- THIRDPARTY.yml | ||
summary: Haplotyping small sequences from heterogeneous long-read sequencing samples with a SNP-encoded positional de Bruijn graphs. | ||
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extra: | ||
recipe-maintainers: | ||
- bluenote-1577 |
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#!/bin/bash | ||
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set -xe | ||
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export LDFLAGS="-L$SRC_DIR/HTSLIB -L$PREFIX/lib" | ||
export CFLAGS="-I$SRC_DIR -I$SRC_DIR/HTSLIB -I$SRC_DIR/LIBDEFLATE -I$SRC_DIR/LIBDEFLATE/common -I$PREFIX/include -L$SRC_DIR/HTSLIB -L$PREFIX/lib" | ||
export CPPFLAGS="-I$SRC_DIR -I$SRC_DIR/HTSLIB -I$SRC_DIR/LIBDEFLATE -I$SRC_DIR/LIBDEFLATE/common -I$PREFIX/include -L$SRC_DIR/HTSLIB -L$PREFIX/lib" | ||
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# build HTSLIB | ||
cd HTSLIB | ||
make lib-static | ||
make -j"${CPU_COUNT}" lib-static | ||
cd - | ||
# build LIBDEFLATE | ||
cd LIBDEFLATE | ||
make | ||
make -j"${CPU_COUNT}" | ||
cd - | ||
# build fastk | ||
make | ||
make -j"${CPU_COUNT}" | ||
make install |
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#!/bin/bash -euo | ||
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set -xe | ||
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# build statically linked binary with Rust | ||
export RUST_BACKTRACE=1 | ||
cargo install --verbose --path . --root ${PREFIX} --no-track |
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{% set name = "gafpack" %} | ||
{% set version = "0.1.0" %} | ||
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package: | ||
name: {{ name|lower }} | ||
version: {{ version }} | ||
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source: | ||
url: https://github.com/pangenome/{{ name }}/archive/refs/tags/v{{ version }}.tar.gz | ||
sha256: 0b78d8047132965c7b0a9b0f3dc26682c1251d08507ebdd98583d9c1b563c758 | ||
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build: | ||
number: 0 | ||
run_exports: | ||
- {{ pin_subpackage(name, max_pin='x.x') }} | ||
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requirements: | ||
build: | ||
- {{ compiler('rust') }} | ||
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test: | ||
commands: | ||
- gafpack --help | ||
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about: | ||
home: https://github.com/pangenome/{{ name }} | ||
license: MIT | ||
license_family: MIT | ||
license_file: LICENSE | ||
summary: Convert alignments to pangenome variation graphs to coverage maps | ||
dev_url: https://github.com/pangenome/{{ name }} | ||
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extra: | ||
additional-platforms: | ||
- linux-aarch64 | ||
- osx-arm64 | ||
recipe-maintainers: | ||
- AndreaGuarracino |
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#!/bin/bash | ||
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set -xe | ||
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cd gnparser | ||
CGO_ENABLED=0 | ||
go clean | ||
|
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{% set name = "longcallr_nn" %} | ||
{% set version = "0.0.1" %} | ||
{% set hash = "294155357b7165b127fc821b06dcdbeee28c108a0caf442b28992a5a5cc3e583" %} | ||
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package: | ||
name: "{{ name|lower }}" | ||
version: "{{ version }}" | ||
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source: | ||
url: "https://github.com/huangnengCSU/longcallR-nn/archive/refs/tags/v{{ version }}.tar.gz" | ||
sha256: {{ hash }} | ||
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build: | ||
number: 0 | ||
noarch: python | ||
entry_points: | ||
- longcallR_nn=longcallR_nn.longcallR_nn:main | ||
script: | ||
- {{ PYTHON }} -m pip install . --no-deps --no-build-isolation --no-cache-dir -vvv | ||
run_exports: | ||
- {{ pin_subpackage(name, max_pin="x.x") }} | ||
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requirements: | ||
host: | ||
- pip | ||
- python 3.9.* | ||
run: | ||
- python 3.9.* | ||
- numpy 1.21.0 | ||
- pyyaml | ||
- pysam | ||
- tensorboardX | ||
- pytorch 1.13.* | ||
- torchvision | ||
- torchmetrics | ||
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test: | ||
commands: | ||
- longcallR_nn --help | ||
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about: | ||
home: "https://github.com/huangnengCSU/longcallR-nn" | ||
license: MIT | ||
license_family: MIT | ||
license_file: LICENSE | ||
summary: "longcallR_nn is a variant caller specifically designed for long-read RNA-seq data utilizing a ResNet model." | ||
dev_url: "https://github.com/huangnengCSU/longcallR-nn" | ||
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extra: | ||
recipe-maintainers: | ||
- huangnengCSU |
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#!/bin/bash | ||
export DISABLE_AUTOBREW=1 | ||
${R} CMD INSTALL --build . ${R_ARGS} |
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