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rtg-tools: fix path for hap.py and add tests.

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Hap.py can call vfceval for rtg-tools but some executables cannot
be found.
This commit is contained in:
Alexis Praga 2025-05-11 23:54:30 +02:00 • committed by Gaetan Lepage
parent bf43db0cc5
commit 023b50d066
1 changed files with 12 additions and 1 deletions
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13
pkgs/by-name/rt/rtg-tools/package.nix
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@ -5,6 +5,9 @@
jdk, jdk,
ant, ant,
git, git,
coreutils,
hostname,
gawk,
unzip, unzip,
}: }:
@ -44,11 +47,19 @@ stdenv.mkDerivation rec {
# Use a location outside nix (must be writable) # Use a location outside nix (must be writable)
substituteInPlace installer/rtg \ substituteInPlace installer/rtg \
--replace-fail '$THIS_DIR/rtg.cfg' '$HOME/.config/rtg-tools/rtg.cfg' \ --replace-fail '$THIS_DIR/rtg.cfg' '$HOME/.config/rtg-tools/rtg.cfg' \
--replace-fail 'RTG_JAVA="java"' 'RTG_JAVA="${jdk}/lib/openjdk/bin/java"' --replace-fail 'RTG_JAVA="java"' 'RTG_JAVA="${jdk}/lib/opendk/bin/java"' \
--replace-fail uname ${lib.getExe' coreutils "uname"} \
--replace-fail awk ${lib.getExe gawk} \
--replace-fail "hostname -s" "${lib.getExe hostname} -s"
sed -i '/USER_JAVA_OPTS=$RTG_JAVA_OPTS/a mkdir -p $HOME/.config/rtg-tools' installer/rtg sed -i '/USER_JAVA_OPTS=$RTG_JAVA_OPTS/a mkdir -p $HOME/.config/rtg-tools' installer/rtg
''; '';
checkPhase = ''
ant runalltests
'';
meta = with lib; { meta = with lib; {
homepage = "https://github.com/RealTimeGenomics/rtg-tools"; homepage = "https://github.com/RealTimeGenomics/rtg-tools";
description = "Useful utilities for dealing with VCF files and sequence data, especially vcfeval"; description = "Useful utilities for dealing with VCF files and sequence data, especially vcfeval";