Merge pull request #102140 from SuperSandro2000/patch-2
This commit is contained in:
commit
c2d728f195
@ -1,14 +1,14 @@
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{ lib
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, python
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}:
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{ lib, python, fetchFromGitHub }:
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with python.pkgs;
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buildPythonApplication rec {
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pname = "deepTools";
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version = "3.5.0";
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src = fetchPypi {
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inherit pname version;
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sha256 = "1a14a29e60be13eac11bd204dab9aef73cd72fe56a94c587333f21087584c0d8";
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src = fetchFromGitHub {
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owner = "deeptools";
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repo = "deepTools";
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rev = version;
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sha256 = "1bz8ln32mfc9k8l9wgp034vw80dxh6f92dfqxhcrpggk4akwj6ml";
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};
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propagatedBuildInputs = [
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@ -23,7 +23,7 @@ buildPythonApplication rec {
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deeptoolsintervals
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];
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checkInputs = [ pytest ];
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checkInputs = [ nose ];
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meta = with lib; {
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homepage = "https://deeptools.readthedocs.io/en/develop";
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@ -1,5 +1,5 @@
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{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
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, samtools, findutils }:
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, samtools, findutils, python }:
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python3Packages.buildPythonApplication rec {
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pname = "tebreak";
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@ -32,6 +32,12 @@ python3Packages.buildPythonApplication rec {
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done
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'';
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checkPhase = ''
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$out/bin/tebreak -b test/data/example.ins.bam -r test/data/Homo_sapiens_chr4_50000000-60000000_assembly19.fasta -p 4 --pickle test/example.pickle --detail_out test/example.tebreak.detail.out -i lib/teref.human.fa
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pushd test
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${python.interpreter} checktest.py
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'';
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meta = with stdenv.lib; {
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description = "Find and characterise transposable element insertions";
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homepage = "https://github.com/adamewing/tebreak";
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@ -32,6 +32,11 @@ stdenv.mkDerivation {
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enableParallelBuilding = true;
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doCheck = true;
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checkInputs = [ nss_3_53.tools ];
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preCheck = ''
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substituteInPlace tests/testrun.sh \
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--replace 'timestamp=`date +%Y%m%d_%H%M%S`' 'timestamp=19700101_000000' \
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--replace 'TMPFOLDER=/tmp' '$(mktemp -d)'
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'';
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# enable deprecated soap headers required by lasso
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# https://dev.entrouvert.org/issues/18771
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@ -1,18 +1,26 @@
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{ stdenv, buildPythonPackage, fetchPypi, cython, numpy, pysam, matplotlib
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}:
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{ stdenv, buildPythonPackage, fetchFromGitHub, cython, numpy, pysam, matplotlib, python, isPy27, isPy3k }:
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buildPythonPackage rec {
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version = "0.12.4";
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pname = "HTSeq";
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src = fetchPypi {
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inherit pname version;
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sha256 = "e3980bb4f12899442b4fa6f24f0ba149090f71cedb1eaf7128249afe4eb921ff";
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src = fetchFromGitHub {
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owner = "htseq";
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repo = "htseq";
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rev = "release_${version}";
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sha256 = "0y7vh249sljqjnv81060w4xkdx6f1y5zdqkh38yk926x6v9riijm";
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};
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buildInputs = [ cython numpy pysam ];
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nativeBuildInputs = [ cython ];
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propagatedBuildInputs = [ numpy pysam matplotlib ];
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checkPhase = stdenv.lib.optionalString isPy27 ''
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${python.interpreter} python2/test/test_general.py
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'' + stdenv.lib.optionalString isPy3k ''
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${python.interpreter} python3/test/test_general.py
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'';
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meta = with stdenv.lib; {
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homepage = "https://htseq.readthedocs.io/";
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description = "A framework to work with high-throughput sequencing data";
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maintainers = with maintainers; [ unode ];
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platforms = platforms.unix;
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@ -1,5 +1,6 @@
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{ lib
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, fetchPypi
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, fetchFromGitHub
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, fetchpatch
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, rPackages
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, rWrapper
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, buildPythonPackage
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@ -15,17 +16,29 @@
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, pillow
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, pomegranate
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, pyfaidx
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, python
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, R
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}:
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buildPythonPackage rec {
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pname = "CNVkit";
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version = "0.9.7";
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src = fetchPypi {
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inherit pname version;
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sha256 = "d68adc0121e17c61a3aa28c0a9ba6526510a5a0df0f0a6eb1818bab71b7e927a";
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src = fetchFromGitHub {
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owner = "etal";
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repo = "cnvkit";
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rev = "v${version}";
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sha256 = "022zplgqil5l76vri647cyjx427vnbg5r2gw6lw712d2janvdjm7";
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};
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patches = [
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# Fix: AttributeError: module 'pandas.io.common' has no attribute 'EmptyDataError'
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(fetchpatch {
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url = "https://github.com/etal/cnvkit/commit/392adfffedfa0415e635b72c5027835b0a8d7ab5.patch";
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sha256 = "0s0gwyy0hybmhc3jij2v9l44b6lkcmclii8bkwsazzj2kc24m2rh";
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})
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];
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propagatedBuildInputs = [
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biopython
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numpy
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@ -39,6 +52,7 @@ buildPythonPackage rec {
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future
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pillow
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pomegranate
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rPackages.DNAcopy
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];
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postPatch = ''
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@ -46,7 +60,16 @@ buildPythonPackage rec {
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--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
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'';
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pythonImportsCheck = [ "cnvlib" ];
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checkInputs = [ R ];
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checkPhase = ''
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pushd test/
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${python.interpreter} test_io.py
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${python.interpreter} test_genome.py
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${python.interpreter} test_cnvlib.py
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${python.interpreter} test_commands.py
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${python.interpreter} test_r.py
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'';
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meta = with lib; {
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homepage = "https://cnvkit.readthedocs.io";
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@ -49,7 +49,8 @@ buildPythonPackage rec {
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checkPhase = ''
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py.test -k "not test_load_extern_incommon \
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and not test_load_remote_encoding \
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and not test_load_external"
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and not test_load_external \
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and not test_conf_syslog"
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'';
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meta = with stdenv.lib; {
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