public
/
nixpkgs
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

tebreak: Fix tests

This commit is contained in:
Sandro 2020-10-30 09:43:37 +01:00 committed by Sandro Jäckel
parent 5f2997686c
commit e166f22759
No known key found for this signature in database
GPG Key ID: 3AF5A43A3EECC2E5
1 changed files with 7 additions and 1 deletions
pkgs/applications/science/biology/tebreak
default.nix

8
pkgs/applications/science/biology/tebreak/default.nix
View File

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