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{ stdenv, callPackage, buildPerlPackage, fetchurl, fetchFromGitHub, perlPackages, R, bwa, samtools, pkgconfig, zlib, htslib, curl, bzip2, lzma, gnutls, nettle, gmp, p11-kit, libtasn1, perl, psmisc, time, vcftools, rWrapper, rPackages }:
let
ascat = fetchurl {
url = "https://raw.githubusercontent.com/Crick-CancerGenomics/ascat/v2.5.1/ASCAT/R/ascat.R";
sha256 = "1rja9s6rksmi0kc6lhx1vr5yqv2xazgxdlwc7mbj2m881x8nngb1";
};
libmaus2 = stdenv.mkDerivation rec {
name = "libmaus-${version}";
version = "2.0.499-release-20180606122508";
src = fetchFromGitHub {
owner = "gt1";
repo = "libmaus2";
rev = version;
sha256 = "1rk2f3jirn84vgsfml4c8pr6vl5s0xbds1d0givb5pvjmc6jz61x";
};
buildInputs = [ zlib ];
};
biobambam2 = stdenv.mkDerivation rec {
name = "biobambam-${version}";
version = "2.0.87-release-20180301132713";
src = fetchFromGitHub {
owner = "gt1";
repo = "biobambam2";
rev = version;
sha256 = "1hjh6kl62hr9afi6fa6x563823lmmmijh1y2204db0nfnaybnrn6";
};
nativeBuildInputs = [ pkgconfig ];
buildInputs = [ libmaus2 zlib ];
};
libBigWig = stdenv.mkDerivation rec {
name = "libBigWig-${version}";
version = "0.4.2";
src = fetchFromGitHub {
owner = "dpryan79";
repo = "libBigWig";
rev = version;
sha256 = "0h2smg24v5srdcqzrmz2g23cmlp4va465mgx8r2z571sfz8pv454";
};
buildInputs = [ curl ];
makeFlags = [ "prefix=$(out)" ];
};
cgpBigWig = stdenv.mkDerivation rec {
name = "cgpBigWig-${version}";
version = "1.0.2";
src = fetchFromGitHub {
owner = "cancerit";
repo = "cgpBigWig";
rev = version;
sha256 = "1piprbibmrwbh524plp9s35z5cf1yk7713dxsdik2qv363p6pfsa";
};
buildInputs = [ htslib libBigWig curl bzip2 lzma gnutls libtasn1 nettle gmp p11-kit ];
configurePhase = ''
cd c
patchShebangs .
'';
makeFlags = [ "HTSLIB=${htslib}" "LIBBIGWIG=${libBigWig}" ];
installPhase = ''
mkdir -p $out
cp -r ../bin $out
'';
};
BioDBHTS = buildPerlPackage rec {
name = "Bio-DB-HTS-${version}";
version = "2.11";
src = fetchFromGitHub {
owner = "Ensembl";
repo = "Bio-DB-HTS";
rev = version;
sha256 = "0n60vmsd39pz6zbkwz78fdzsmfg8dxgwx0m166vm8515q446922c";
};
nativeBuildInputs = with perlPackages; [ ModuleBuild ];
buildInputs = [ htslib zlib ];
#propagatedBuildInputs = [ BioRootVersion ];
configurePhase = ''
export HTSLIB_DIR=${htslib}
sed -i 's|"-Wl,-rpath,\$hts_lib",||' Build.PL
perl ./Build.PL --install_base=$out
'';
buildPhase = ''
./Build
'';
installPhase = ''
./Build install
mkdir -p $out/lib/perl5/site_perl/${perl.version}
mv $out/lib/perl5/x86_64-linux-thread-multi $out/lib/perl5/site_perl/${perl.version}
'';
};
BioPerl = buildPerlPackage rec {
name = "BioPerl-1.7.4";
src = fetchurl {
url = "mirror://cpan/authors/id/C/CD/CDRAUG/${name}.tar.gz";
sha256 = "0yvhgifs8g9rwdcq84zw4b005nq2jml6c75zgjscv6d2pd3lj1ss";
};
propagatedBuildInputs = with perlPackages; [ DBI DataStag Error GD Graph HTTPMessage HTTPMessage IOstringy IOString IPCRun LWP ListMoreUtils SetScalar TestMost TestRequiresInternet URI XMLDOM XMLDOMXPath XMLLibXML XMLLibXML libxml_perl XMLSAX XMLSAXBase XMLSAXWriter XMLTwig XMLWriter YAML DBFile ];
nativeBuildInputs = with perlPackages; [ TestException TestWarn TestDifferences TestDeep ];
};
DataStag = buildPerlPackage rec {
name = "Data-Stag-0.14";
src = fetchurl {
url = "mirror://cpan/authors/id/C/CM/CMUNGALL/${name}.tar.gz";
sha256 = "0ncf4l39ka23nb01jlm6rzxdb5pqbip01x0m38bnvf1gim825caa";
};
propagatedBuildInputs = with perlPackages; [ IOString Graph XMLLibXSLT ];
};
XMLDOMXPath = buildPerlPackage rec {
name = "XML-DOM-XPath-0.14";
src = fetchurl {
url = "mirror://cpan/authors/id/M/MI/MIROD/${name}.tar.gz";
sha256 = "1si9m1pqih3ibbd6jnw69fh98dd4krxpx90p65x9j4aja55afwq1";
};
propagatedBuildInputs = with perlPackages; [ XMLDOM XMLXPathEngine ];
doCheck = false;
};
pcapCore = buildPerlPackage rec {
name = "PCAP-core-${version}";
version = "4.2.3";
src = fetchFromGitHub {
owner = "cancerit";
repo = "PCAP-core";
rev = version;
sha256 = "0ia9z0k4jpa02596smivpkw85vi9sv7sbxnysv7jdyh2g1rv1s5c";
};
nativeBuildInputs = with perlPackages; [ TestFatal TestWarn ];
propagatedBuildInputs = with perlPackages; [
bwa
samtools
biobambam2
cgpBigWig
ConstFast
FileWhich
IPCSystemSimple
CaptureTiny
TermUI
BioDBHTS
DataUUID
YAML
BioPerl
JSON
psmisc
];
preConfigure = ''
sed -i 's|/usr/bin/time|${time}/bin/time|' lib/PCAP/Threaded.pm
sed -i 's|/bin/bash|${stdenv.shell}|' lib/PCAP/Threaded.pm
'';
};
cgpVcf = buildPerlPackage rec {
name = "cgpVCF-${version}";
version = "2.0.4";
outputs = [ "out" "dev" ];
src = fetchFromGitHub {
owner = "cancerit";
repo = "cgpVcf";
rev = "v${version}";
sha256 = "0j8spk02v4l0nrqsa42d57djb4nm71daz5hvlm5fwakfq8037yx4";
};
nativeBuildInputs = with perlPackages; [ TestFatal TestWarn ];
propagatedBuildInputs = with perlPackages; [
ConstFast
samtools
vcftools
DataUUID
DateTime
IPCSystemSimple
];
};
BDebug = buildPerlPackage rec {
name = "B-Debug-1.26";
src = fetchurl {
url = "mirror://cpan/authors/id/R/RU/RURBAN/${name}.tar.gz";
sha256 = "0fhdaxpkirgnwivd0a7x83dvfwqbngsq2rcfwvfxipgh6i8kyvcd";
};
};
DevelCover = buildPerlPackage rec {
name = "Devel-Cover-1.31";
src = fetchurl {
url = "mirror://cpan/authors/id/P/PJ/PJCJ/${name}.tar.gz";
sha256 = "0wsd7fkpy5qwnz68hz624frnbqii5igg6l2q7n1mx1lh32vn0kcr";
};
nativeBuildInputs = with perlPackages; [ BDebug ];
doCheck = false;
};
alleleCount = stdenv.mkDerivation rec {
name = "alleleCount-${version}";
version = "4.0.1";
src = fetchFromGitHub {
owner = "cancerit";
repo = "alleleCount";
rev = "v${version}";
sha256 = "0nkwnjqglgshzhlmz1r0khdjai9mfz4ih8bzrzg0g18d1725k6gp";
};
buildInputs = [ htslib perl zlib bzip2 lzma ];
preConfigure = "cd c";
installPhase = ''
mkdir -p $out/bin
cp bin/* $out/bin
'';
};
alleleCountPerl = buildPerlPackage rec {
name = "alleleCount.pl-${version}";
version = "4.0.1";
src = fetchFromGitHub {
owner = "cancerit";
repo = "alleleCount";
rev = "v${version}";
sha256 = "0nkwnjqglgshzhlmz1r0khdjai9mfz4ih8bzrzg0g18d1725k6gp";
};
preConfigure = ''
cd perl
'';
nativeBuildInputs = with perlPackages; [
TestFatal
];
propagatedBuildInputs = with perlPackages; [
ConstFast
DevelCover
FileSlurp
FileWhich
PodCoverage
TryTiny
alleleCount
IPCSystemSimple
];
};
ascatR = rWrapper.overrideAttrs (attrs: {
packages = with rPackages; [ RColorBrewer ];
});
ascatNGS = buildPerlPackage rec {
name = "ascatNGS-${version}";
version = "4.1.2";
src = fetchFromGitHub {
owner = "cancerit";
repo = "ascatNgs";
rev = "v${version}";
sha256 = "0qc1wp37k2c9vya992cfiphp2jpp8hvfvqz5ydi2d5b71prfaw82";
};
preConfigure = ''
cd perl
cp ${ascat} share/ascat/ascat.R
'';
nativeBuildInputs = with perlPackages; [ TestFatal TestWarn ];
propagatedBuildInputs = with perlPackages; [
ascatR
FileShareDirInstall
pcapCore
FileShareDir
cgpVcf
alleleCountPerl
];
};
in
ascatNGS
|
