text:
@article{geuvadis,
  title={Transcriptome and genome sequencing uncovers functional variation in humans},
  author={Lappalainen, Tuuli and Sammeth, Michael and Friedl{\"a}nder, Marc R and AC‘t Hoen, Peter and Monlong, Jean and Rivas, Manuel A and Gonzalez-Porta, Mar and Kurbatova, Natalja and Griebel, Thasso and Ferreira, Pedro G and others},
  journal={Nature},
  volume={501},
  number={7468},
  pages={506},
  year={2013},
  publisher={Nature Publishing Group}
}

@article{gtexv7,
  title={Genetic effects on gene expression across human tissues},
  author={GTEx Consortium and others},
  journal={Nature},
  volume={550},
  number={7675},
  pages={204},
  year={2017},
  publisher={Nature Publishing Group}
}

@article{predixcan,
  title={A gene-based association method for mapping traits using reference transcriptome data},
  author={Gamazon, Eric R and Wheeler, Heather E and Shah, Kaanan P and Mozaffari, Sahar V and Aquino-Michaels, Keston and Carroll, Robert J and Eyler, Anne E and Denny, Joshua C and Nicolae, Dan L and Cox, Nancy J and others},
  journal={Nature genetics},
  volume={47},
  number={9},
  pages={1091},
  year={2015},
  publisher={Nature Publishing Group}
}

@article{matrixqtl,
  title={Matrix eQTL: ultra fast eQTL analysis via large matrix operations},
  author={Shabalin, Andrey A},
  journal={Bioinformatics},
  volume={28},
  number={10},
  pages={1353--1358},
  year={2012},
  publisher={Oxford University Press}
}

@article{fastqtl,
  title={Fast and efficient QTL mapper for thousands of molecular phenotypes},
  author={Ongen, Halit and Buil, Alfonso and Brown, Andrew Anand and Dermitzakis, Emmanouil T and Delaneau, Olivier},
  journal={Bioinformatics},
  volume={32},
  number={10},
  pages={1479--1485},
  year={2016},
  publisher={Oxford University Press}
}

@article{tensorqtl,
  title={Scaling computational genomics to millions of individuals with GPUs},
  author={Taylor-Weiner, Amaro and Aguet, Fran{\c{c}}ois and Haradhvala, Nicholas J and Gosai, Sager and Anand, Shankara and Kim, Jaegil and Ardlie, Kristin and Van Allen, Eliezer M and Getz, Gad},
  journal={Genome biology},
  volume={20},
  number={1},
  pages={1--5},
  year={2019},
  publisher={BioMed Central}
}

@article{metaxcan,
  title={Exploring the phenotypic consequences of tissue specific gene expression variation inferred from GWAS summary statistics},
  author={Barbeira, Alvaro N and Dickinson, Scott P and Bonazzola, Rodrigo and Zheng, Jiamao and Wheeler, Heather E and Torres, Jason M and Torstenson, Eric S and Shah, Kaanan P and Garcia, Tzintzuni and Edwards, Todd L and others},
  journal={Nature communications},
  volume={9},
  number={1},
  pages={1--20},
  year={2018},
  publisher={Nature Publishing Group}
}

repository: hakyimlab/Training

repo_name: hakyimlab/Training

gha_language: TeX


text:
DESCRIPTION = "Pyrex is a language specially designed for writing Python extension modules. \
It's designed to bridge the gap between the nice, high-level, easy-to-use world of Python \
and the messy, low-level world of C."
SECTION = "devel/python"
PRIORITY = "optional"
LICENSE = "GPL"
SRCNAME = "Pyrex"
DEPENDS += "python"
DEPENDS_virtclass-native += "python-native"
PR = "ml2"

SRC_URI = "\
  http://www.cosc.canterbury.ac.nz/greg.ewing/python/${SRCNAME}/${SRCNAME}-${PV}.tar.gz \
  file://pyrex-fix-optimized-mode.patch \
"
S = "${WORKDIR}/${SRCNAME}-${PV}"

inherit distutils

SRC_URI[md5sum] = "3b3d8397c2c9a58fc59a90e2b49c651a"
SRC_URI[sha256sum] = "dd60bc66b1627d3cbd0950499017dfd57a0705bb12493bb0de2a7b9b5c0873bc"

BBCLASSEXTEND = "native"

NATIVE_INSTALL_WORKS = "1"

license: MIT

repository: overo/overo-oe-natty

license_type: permissive

repo_name: overo/overo-oe-natty

branch_name: HEAD

extension: bb


text:
DESCRIPTION = "SPDX 2.0 document creation and storage"
HOMEPAGE = "https://github.com/DoSOCSv2/DoSOCSv2"
SECTION = "devel/python"
LICENSE = "GPLv2"
LIC_FILES_CHKSUM = "file://LICENSE;md5=b234ee4d69f5fce4486a80fdaf4a4263"

SRC_URI = "git://github.com/DoSOCSv2/DoSOCSv2.git;branch=dev \
           file://0001-setup-py-delete-the-depends-install.patch \
           file://0001-Fix-bugs-because-python-from-2.x-to-3.x.patch \
           file://0001-Fix-a-error-as-fowllowing.patch \
           file://0001-Fix-a-magic-error-as-following.patch \
          "

S = "${WORKDIR}/git"

SRCREV = "aa84166694913bf1d2cce416f1c2bff120c3ba3b"
BRANCH = "dev"
PV = "0.16.1"

inherit distutils3 python3native setuptools3 python3-dir

DEPENDS += "python3-jinja2-native \
            python3-docopt-native \
            python3-sqlalchemy-native \
            file-native \
            fossology-nomos-native \
            python3-markupsafe-native \
            python3-magic-native "

do_install_append() {
	sed -i "s|scanner_nomos_path = /usr/local/|scanner_nomos_path = ${STAGING_DIR_NATIVE}/usr/|g" ${D}${PYTHON_SITEPACKAGES_DIR}/dosocs2/configtools.py
	sed -i "s,path_to_magic_file,${STAGING_DATADIR_NATIVE}/misc/magic," ${D}${STAGING_LIBDIR}/${PYTHON_DIR}/site-packages/dosocs2/util.py
}

BBCLASSEXTEND = "native"

repository: y-ashiduka/meta-spdxscanner

repo_name: y-ashiduka/meta-spdxscanner

branch_name: refs/heads/master