commit
40830f8253
30
pkgs/by-name/li/libgff/package.nix
Normal file
30
pkgs/by-name/li/libgff/package.nix
Normal file
|
@ -0,0 +1,30 @@
|
||||||
|
{ lib
|
||||||
|
, stdenv
|
||||||
|
, fetchFromGitHub
|
||||||
|
, cmake
|
||||||
|
}:
|
||||||
|
|
||||||
|
stdenv.mkDerivation (finalAttrs: {
|
||||||
|
pname = "libgff";
|
||||||
|
version = "2.0.0";
|
||||||
|
|
||||||
|
src = fetchFromGitHub {
|
||||||
|
owner = "COMBINE-lab";
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||||||
|
repo = "libgff";
|
||||||
|
rev = "v${finalAttrs.version}";
|
||||||
|
hash = "sha256-ZCb3UyuB/+ykrYFQ9E5VytT65gAAULiOzIEu5IXISTc=";
|
||||||
|
};
|
||||||
|
|
||||||
|
nativeBuildInputs = [ cmake ];
|
||||||
|
|
||||||
|
meta = {
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||||||
|
description = "A lightweight GTF/GFF parsers exposing a C++ interface";
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||||||
|
homepage = "https://github.com/COMBINE-lab/libgff";
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||||||
|
downloadPage = "https://github.com/COMBINE-lab/libgff/releases";
|
||||||
|
changelog = "https://github.com/COMBINE-lab/libgff/releases/tag/" +
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||||||
|
"v${finalAttrs.version}";
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|
license = lib.licenses.boost;
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||||||
|
platforms = lib.platforms.all;
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|
maintainers = [ lib.maintainers.kupac ];
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|
};
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||||||
|
})
|
|
@ -0,0 +1,12 @@
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|
diff --git a/Makefile.am b/Makefile.am
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|
index 31286d1..2631af1 100644
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|
--- a/Makefile.am
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|
+++ b/Makefile.am
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||||||
|
@@ -61,6 +61,7 @@ man_MANS = \
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|
man/man4/Read.4
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|
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|
pkginclude_HEADERS = \
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|
+ io_lib_config.h \
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|
io_lib/Read.h \
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|
io_lib/scf_extras.h \
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|
io_lib/translate.h \
|
47
pkgs/by-name/li/libstaden-read/package.nix
Normal file
47
pkgs/by-name/li/libstaden-read/package.nix
Normal file
|
@ -0,0 +1,47 @@
|
||||||
|
{ lib
|
||||||
|
, stdenv
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||||||
|
, autoreconfHook
|
||||||
|
, fetchFromGitHub
|
||||||
|
, bzip2
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||||||
|
, xz
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||||||
|
, zlib
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||||||
|
}:
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||||||
|
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|
stdenv.mkDerivation (finalAttrs: {
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||||||
|
# Same name as the Debian library
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|
pname = "libstaden-read";
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|
version = "1.15.0";
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|
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||||||
|
src = fetchFromGitHub {
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||||||
|
owner = "jkbonfield";
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|
repo = "io_lib";
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|
rev = "io_lib-" + builtins.replaceStrings ["."] ["-"] finalAttrs.version;
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|
fetchSubmodules = true;
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||||||
|
hash = "sha256-2Dlx+MXmqar81/Xmf0oE+6lWX461EDYijiZsZf/VD28=";
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||||||
|
};
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|
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||||||
|
patches = [
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|
# Needed so that the lib can be detected
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|
./libstaden-install-config-header.patch
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||||||
|
];
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||||||
|
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||||||
|
buildInputs = [ bzip2 xz zlib ];
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||||||
|
nativeBuildInputs = [ autoreconfHook ];
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||||||
|
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||||||
|
# autoreconfHook does not descend into htscodecs folder
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|
preAutoreconf = ''
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|
pushd ./htscodecs
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|
autoreconf --install --force --verbose
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|
pushd
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|
'';
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|
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|
meta = {
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|
description = "C library for reading/writing various DNA sequence formats";
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|
homepage = "https://staden.sourceforge.net";
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|
downloadPage = "https://github.com/jkbonfield/io_lib/releases";
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|
changelog = "https://github.com/jkbonfield/io_lib/blob/${finalAttrs.src.rev}/CHANGES";
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|
license = with lib.licenses; [ bsd3 free ];
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|
platforms = lib.platforms.all;
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|
maintainers = [ lib.maintainers.kupac ];
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|
};
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|
})
|
60
pkgs/by-name/sa/salmon/fetch-pufferfish.patch
Normal file
60
pkgs/by-name/sa/salmon/fetch-pufferfish.patch
Normal file
|
@ -0,0 +1,60 @@
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|
diff --git a/scripts/fetchPufferfish.sh b/scripts/fetchPufferfish.sh
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|
index bf2574e0..42582806 100755
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|
--- a/scripts/fetchPufferfish.sh
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|
+++ b/scripts/fetchPufferfish.sh
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|
@@ -11,10 +11,6 @@ CURR_DIR=$( 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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|
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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 ${EXTERNAL_DIR}/pufferfish.zip
|
||||||
|
-
|
||||||
|
-hashcheck=""
|
||||||
|
-if exists sha256sum; then
|
||||||
|
- hashcheck="sha256sum"
|
||||||
|
-elif exists shasum; then
|
||||||
|
- hashcheck="shasum -a256"
|
||||||
|
-else
|
||||||
|
- unset hashcheck
|
||||||
|
-fi
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|
-
|
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|
-
|
||||||
|
-if [ -z "${hashcheck-}" ]; then
|
||||||
|
- echo "Couldn't find shasum command; can't verify contents of downloaded pufferfish";
|
||||||
|
-else
|
||||||
|
-
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||||||
|
- 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 ${INSTALL_DIR}/include/pufferfish
|
84
pkgs/by-name/sa/salmon/package.nix
Normal file
84
pkgs/by-name/sa/salmon/package.nix
Normal file
|
@ -0,0 +1,84 @@
|
||||||
|
{ lib
|
||||||
|
, stdenv
|
||||||
|
, autoreconfHook
|
||||||
|
, bash
|
||||||
|
, boost
|
||||||
|
, bzip2
|
||||||
|
, cereal_1_3_2
|
||||||
|
, cmake
|
||||||
|
, curl
|
||||||
|
, fetchFromGitHub
|
||||||
|
, jemalloc
|
||||||
|
, libgff
|
||||||
|
, libiconv
|
||||||
|
, libstaden-read
|
||||||
|
, pkg-config
|
||||||
|
, tbb_2021_8
|
||||||
|
, xz
|
||||||
|
, zlib
|
||||||
|
}:
|
||||||
|
|
||||||
|
stdenv.mkDerivation (finalAttrs: {
|
||||||
|
pname = "salmon";
|
||||||
|
version = "1.10.2";
|
||||||
|
|
||||||
|
pufferFishSrc = fetchFromGitHub {
|
||||||
|
owner = "COMBINE-lab";
|
||||||
|
repo = "pufferfish";
|
||||||
|
rev = "salmon-v${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 ];
|
||||||
|
};
|
||||||
|
})
|
Loading…
Reference in New Issue
Block a user