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salmon: init at 1.10.2
Co-authored-by: Arne Keller <2012gdwu+github@posteo.de> Co-authored-by: a-n-n-a-l-e-e <150648636+a-n-n-a-l-e-e@users.noreply.github.com>
This commit is contained in:
László Kupcsik
parent
dcb93f2776
commit
ccef24c817
60
pkgs/by-name/sa/salmon/fetch-pufferfish.patch
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60
pkgs/by-name/sa/salmon/fetch-pufferfish.patch
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@ -0,0 +1,60 @@
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diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
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index bf2574e0..42582806 100755
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--- a/scripts/fetchPufferfish.sh
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+++ b/scripts/fetchPufferfish.sh
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@@ -11,10 +11,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )
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EXTERNAL_DIR=${CURR_DIR}/../external
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INSTALL_DIR=${CURR_DIR}/../external/install
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-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then
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- rm -fr ${EXTERNAL_DIR}/pufferfish
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-fi
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-
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if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then
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rm -fr ${INSTALL_DIR}/include/pufferfish
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fi
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@@ -23,42 +19,10 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then
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rm -fr ${INSTALL_DIR}/src/pufferfish
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fi
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-SVER=salmon-v1.10.2
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-#SVER=develop
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-#SVER=sketch-mode
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-
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-EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101
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-
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-mkdir -p ${EXTERNAL_DIR}
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-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip
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-
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-hashcheck=""
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-if exists sha256sum; then
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- hashcheck="sha256sum"
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-elif exists shasum; then
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- hashcheck="shasum -a256"
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-else
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- unset hashcheck
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-fi
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-
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-
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-if [ -z "${hashcheck-}" ]; then
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- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
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-else
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-
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- if [[ $SVER != develop && $SVER != onetbb ]]; then
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- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; }
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- else
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- echo "not testing sha since pulling from develop"
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- fi
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-fi
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-
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-
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-rm -fr ${EXTERNAL_DIR}/pufferfish
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-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR}
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-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish
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mkdir -p ${INSTALL_DIR}/include/pufferfish
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+# This is needed later when pufferfish is compiled for Salmon
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+cp -r ${pufferFishSrc} ${EXTERNAL_DIR}/pufferfish
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cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish
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cp ${EXTERNAL_DIR}/pufferfish/include/BooPHF.hpp ${INSTALL_DIR}/include/pufferfish
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84
pkgs/by-name/sa/salmon/package.nix
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84
pkgs/by-name/sa/salmon/package.nix
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@ -0,0 +1,84 @@
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{ lib
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, stdenv
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, autoreconfHook
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, bash
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, boost
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, bzip2
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, cereal_1_3_2
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, cmake
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, curl
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, fetchFromGitHub
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, jemalloc
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, libgff
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, libiconv
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, libstaden-read
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, pkg-config
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, tbb_2021_8
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, xz
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, zlib
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}:
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stdenv.mkDerivation (finalAttrs: {
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pname = "salmon";
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version = "1.10.2";
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pufferFishSrc = fetchFromGitHub {
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owner = "COMBINE-lab";
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repo = "pufferfish";
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rev = "salmon-v${finalAttrs.version}";
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hash = "sha256-JKbUFBEsqnENl4vFqve1FCd4TI3n9bRi2RNHC8QGQGc=";
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};
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src = fetchFromGitHub {
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owner = "COMBINE-lab";
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repo = "salmon";
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rev = "v${finalAttrs.version}";
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hash = "sha256-kwqoUmVCqjr/xRxJjQKaFjjCQW+MFASHJ2f9OiAumNU=";
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};
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patches = [
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# Use pufferfish source fetched by nix
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./fetch-pufferfish.patch
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];
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postPatch = "patchShebangs .";
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buildInputs = [
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(boost.override { enableShared = false; enabledStatic = true; })
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bzip2
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cereal_1_3_2
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curl
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jemalloc
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libgff
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libstaden-read
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tbb_2021_8
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xz
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zlib
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] ++ lib.optionals stdenv.isDarwin [ libiconv ];
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nativeBuildInputs = [ cmake pkg-config ];
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strictDeps = true;
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meta = {
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description =
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"Tool for quantifying the expression of transcripts using RNA-seq data";
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longDescription = ''
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Salmon is a tool for quantifying the expression of transcripts
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using RNA-seq data. Salmon uses new algorithms (specifically,
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coupling the concept of quasi-mapping with a two-phase inference
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procedure) to provide accurate expression estimates very quickly
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and while using little memory. Salmon performs its inference using
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an expressive and realistic model of RNA-seq data that takes into
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account experimental attributes and biases commonly observed in
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real RNA-seq data.
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'';
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homepage = "https://combine-lab.github.io/salmon";
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downloadPage = "https://github.com/COMBINE-lab/salmon/releases";
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changelog = "https://github.com/COMBINE-lab/salmon/releases/tag/" +
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"v${finalAttrs.version}";
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license = lib.licenses.gpl3Only;
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platforms = lib.platforms.all;
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maintainers = [ lib.maintainers.kupac ];
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};
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})
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