diff options
| -rw-r--r-- | pkgs/by-name/sa/salmon/fetch-pufferfish.patch | 60 | ||||
| -rw-r--r-- | pkgs/by-name/sa/salmon/package.nix | 84 |
2 files changed, 144 insertions, 0 deletions
diff --git a/pkgs/by-name/sa/salmon/fetch-pufferfish.patch b/pkgs/by-name/sa/salmon/fetch-pufferfish.patch new file mode 100644 index 000000000000..7010a1a69fac --- /dev/null +++ b/pkgs/by-name/sa/salmon/fetch-pufferfish.patch @@ -0,0 +1,60 @@ +diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh +index bf2574e0..42582806 100755 +--- a/scripts/fetchPufferfish.sh ++++ b/scripts/fetchPufferfish.sh +@@ -11,10 +11,6 @@ CURR_DIR=$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd ) + EXTERNAL_DIR=${CURR_DIR}/../external + INSTALL_DIR=${CURR_DIR}/../external/install + +-if [ -d ${EXTERNAL_DIR}/pufferfish ] ; then +- rm -fr ${EXTERNAL_DIR}/pufferfish +-fi +- + if [ -d ${INSTALL_DIR}/include/pufferfish ] ; then + rm -fr ${INSTALL_DIR}/include/pufferfish + fi +@@ -23,42 +19,10 @@ if [ -d ${INSTALL_DIR}/src/pufferfish ] ; then + rm -fr ${INSTALL_DIR}/src/pufferfish + fi + +-SVER=salmon-v1.10.2 +-#SVER=develop +-#SVER=sketch-mode +- +-EXPECTED_SHA256=f225b74833f71dcf767a565345224357fb091f90ce79717abc836814d9ccd101 +- +-mkdir -p ${EXTERNAL_DIR} +-curl -k -L https://github.com/COMBINE-lab/pufferfish/archive/${SVER}.zip -o ${EXTERNAL_DIR}/pufferfish.zip +- +-hashcheck="" +-if exists sha256sum; then +- hashcheck="sha256sum" +-elif exists shasum; then +- hashcheck="shasum -a256" +-else +- unset hashcheck +-fi +- +- +-if [ -z "${hashcheck-}" ]; then +- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish"; +-else +- +- if [[ $SVER != develop && $SVER != onetbb ]]; then +- echo "${EXPECTED_SHA256} ${EXTERNAL_DIR}/pufferfish.zip" | ${hashcheck} -c - || { echo "pufferfish.zip did not match expected SHA1! Exiting."; exit 1; } +- else +- echo "not testing sha since pulling from develop" +- fi +-fi +- +- +-rm -fr ${EXTERNAL_DIR}/pufferfish +-unzip ${EXTERNAL_DIR}/pufferfish.zip -d ${EXTERNAL_DIR} +-mv ${EXTERNAL_DIR}/pufferfish-${SVER} ${EXTERNAL_DIR}/pufferfish + + mkdir -p ${INSTALL_DIR}/include/pufferfish ++# This is needed later when pufferfish is compiled for Salmon ++cp -r ${pufferFishSrc} ${EXTERNAL_DIR}/pufferfish + + cp ${EXTERNAL_DIR}/pufferfish/include/ProgOpts.hpp ${INSTALL_DIR}/include/pufferfish + cp ${EXTERNAL_DIR}/pufferfish/include/BooPHF.hpp ${INSTALL_DIR}/include/pufferfish diff --git a/pkgs/by-name/sa/salmon/package.nix b/pkgs/by-name/sa/salmon/package.nix new file mode 100644 index 000000000000..e4442e96fd6f --- /dev/null +++ b/pkgs/by-name/sa/salmon/package.nix @@ -0,0 +1,84 @@ +{ lib +, stdenv +, autoreconfHook +, bash +, boost +, bzip2 +, cereal_1_3_2 +, cmake +, curl +, fetchFromGitHub +, jemalloc +, libgff +, libiconv +, libstaden-read +, pkg-config +, tbb_2021_8 +, xz +, zlib +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "salmon"; + version = "1.10.2"; + + pufferFishSrc = fetchFromGitHub { + owner = "COMBINE-lab"; + repo = "pufferfish"; + rev = "salmon-v${finalAttrs.version}"; + hash = "sha256-JKbUFBEsqnENl4vFqve1FCd4TI3n9bRi2RNHC8QGQGc="; + }; + + src = fetchFromGitHub { + owner = "COMBINE-lab"; + repo = "salmon"; + rev = "v${finalAttrs.version}"; + hash = "sha256-kwqoUmVCqjr/xRxJjQKaFjjCQW+MFASHJ2f9OiAumNU="; + }; + + patches = [ + # Use pufferfish source fetched by nix + ./fetch-pufferfish.patch + ]; + + postPatch = "patchShebangs ."; + + buildInputs = [ + (boost.override { enableShared = false; enabledStatic = true; }) + bzip2 + cereal_1_3_2 + curl + jemalloc + libgff + libstaden-read + tbb_2021_8 + xz + zlib + ] ++ lib.optionals stdenv.isDarwin [ libiconv ]; + + nativeBuildInputs = [ cmake pkg-config ]; + + strictDeps = true; + + meta = { + description = + "Tool for quantifying the expression of transcripts using RNA-seq data"; + longDescription = '' + Salmon is a tool for quantifying the expression of transcripts + using RNA-seq data. Salmon uses new algorithms (specifically, + coupling the concept of quasi-mapping with a two-phase inference + procedure) to provide accurate expression estimates very quickly + and while using little memory. Salmon performs its inference using + an expressive and realistic model of RNA-seq data that takes into + account experimental attributes and biases commonly observed in + real RNA-seq data. + ''; + homepage = "https://combine-lab.github.io/salmon"; + downloadPage = "https://github.com/COMBINE-lab/salmon/releases"; + changelog = "https://github.com/COMBINE-lab/salmon/releases/tag/" + + "v${finalAttrs.version}"; + license = lib.licenses.gpl3Only; + platforms = lib.platforms.all; + maintainers = [ lib.maintainers.kupac ]; + }; +}) |