Merge pull request #102140 from SuperSandro2000/patch-2

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Sandro 2020-11-26 01:00:22 +01:00 committed by GitHub
commit c2d728f195
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6 changed files with 63 additions and 20 deletions

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@ -1,14 +1,14 @@
{ lib
, python
}:
{ lib, python, fetchFromGitHub }:
with python.pkgs;
buildPythonApplication rec {
pname = "deepTools";
version = "3.5.0";
src = fetchPypi {
inherit pname version;
sha256 = "1a14a29e60be13eac11bd204dab9aef73cd72fe56a94c587333f21087584c0d8";
src = fetchFromGitHub {
owner = "deeptools";
repo = "deepTools";
rev = version;
sha256 = "1bz8ln32mfc9k8l9wgp034vw80dxh6f92dfqxhcrpggk4akwj6ml";
};
propagatedBuildInputs = [
@ -23,7 +23,7 @@ buildPythonApplication rec {
deeptoolsintervals
];
checkInputs = [ pytest ];
checkInputs = [ nose ];
meta = with lib; {
homepage = "https://deeptools.readthedocs.io/en/develop";

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@ -1,5 +1,5 @@
{ stdenv, fetchFromGitHub, last, exonerate, minia, python3Packages, bwa
, samtools, findutils }:
, samtools, findutils, python }:
python3Packages.buildPythonApplication rec {
pname = "tebreak";
@ -32,6 +32,12 @@ python3Packages.buildPythonApplication rec {
done
'';
checkPhase = ''
$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
pushd test
${python.interpreter} checktest.py
'';
meta = with stdenv.lib; {
description = "Find and characterise transposable element insertions";
homepage = "https://github.com/adamewing/tebreak";

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@ -32,6 +32,11 @@ stdenv.mkDerivation {
enableParallelBuilding = true;
doCheck = true;
checkInputs = [ nss_3_53.tools ];
preCheck = ''
substituteInPlace tests/testrun.sh \
--replace 'timestamp=`date +%Y%m%d_%H%M%S`' 'timestamp=19700101_000000' \
--replace 'TMPFOLDER=/tmp' '$(mktemp -d)'
'';
# enable deprecated soap headers required by lasso
# https://dev.entrouvert.org/issues/18771

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@ -1,18 +1,26 @@
{ stdenv, buildPythonPackage, fetchPypi, cython, numpy, pysam, matplotlib
}:
{ stdenv, buildPythonPackage, fetchFromGitHub, cython, numpy, pysam, matplotlib, python, isPy27, isPy3k }:
buildPythonPackage rec {
version = "0.12.4";
pname = "HTSeq";
src = fetchPypi {
inherit pname version;
sha256 = "e3980bb4f12899442b4fa6f24f0ba149090f71cedb1eaf7128249afe4eb921ff";
src = fetchFromGitHub {
owner = "htseq";
repo = "htseq";
rev = "release_${version}";
sha256 = "0y7vh249sljqjnv81060w4xkdx6f1y5zdqkh38yk926x6v9riijm";
};
buildInputs = [ cython numpy pysam ];
nativeBuildInputs = [ cython ];
propagatedBuildInputs = [ numpy pysam matplotlib ];
checkPhase = stdenv.lib.optionalString isPy27 ''
${python.interpreter} python2/test/test_general.py
'' + stdenv.lib.optionalString isPy3k ''
${python.interpreter} python3/test/test_general.py
'';
meta = with stdenv.lib; {
homepage = "https://htseq.readthedocs.io/";
description = "A framework to work with high-throughput sequencing data";
maintainers = with maintainers; [ unode ];
platforms = platforms.unix;

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@ -1,5 +1,6 @@
{ lib
, fetchPypi
, fetchFromGitHub
, fetchpatch
, rPackages
, rWrapper
, buildPythonPackage
@ -15,17 +16,29 @@
, pillow
, pomegranate
, pyfaidx
, python
, R
}:
buildPythonPackage rec {
pname = "CNVkit";
version = "0.9.7";
src = fetchPypi {
inherit pname version;
sha256 = "d68adc0121e17c61a3aa28c0a9ba6526510a5a0df0f0a6eb1818bab71b7e927a";
src = fetchFromGitHub {
owner = "etal";
repo = "cnvkit";
rev = "v${version}";
sha256 = "022zplgqil5l76vri647cyjx427vnbg5r2gw6lw712d2janvdjm7";
};
patches = [
# Fix: AttributeError: module 'pandas.io.common' has no attribute 'EmptyDataError'
(fetchpatch {
url = "https://github.com/etal/cnvkit/commit/392adfffedfa0415e635b72c5027835b0a8d7ab5.patch";
sha256 = "0s0gwyy0hybmhc3jij2v9l44b6lkcmclii8bkwsazzj2kc24m2rh";
})
];
propagatedBuildInputs = [
biopython
numpy
@ -39,6 +52,7 @@ buildPythonPackage rec {
future
pillow
pomegranate
rPackages.DNAcopy
];
postPatch = ''
@ -46,7 +60,16 @@ buildPythonPackage rec {
--replace "pandas >= 0.20.1, < 0.25.0" "pandas"
'';
pythonImportsCheck = [ "cnvlib" ];
checkInputs = [ R ];
checkPhase = ''
pushd test/
${python.interpreter} test_io.py
${python.interpreter} test_genome.py
${python.interpreter} test_cnvlib.py
${python.interpreter} test_commands.py
${python.interpreter} test_r.py
'';
meta = with lib; {
homepage = "https://cnvkit.readthedocs.io";

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@ -49,7 +49,8 @@ buildPythonPackage rec {
checkPhase = ''
py.test -k "not test_load_extern_incommon \
and not test_load_remote_encoding \
and not test_load_external"
and not test_load_external \
and not test_conf_syslog"
'';
meta = with stdenv.lib; {