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https://github.com/arq5x/bedtools2/pull/1087
From eabcd3dcb9caa1fcc17acd43df2ded4170ed1449 Mon Sep 17 00:00:00 2001
From: David Seifert <soap@gentoo.org>
Date: Thu, 25 Apr 2024 11:18:47 +0200
Subject: [PATCH] Allow PYTHON from environment
* Distros need to be able to specify exactly which python
interpreter to run tests under.
--- a/test/bigchroms/test-bigchroms.sh
+++ b/test/bigchroms/test-bigchroms.sh
@@ -28,7 +28,7 @@ check obs abig.bed
rm obs
if [[ "$BT_NO_BIG_FILES" != "" ]]; then
-python make-big-chrom.py
+${PYTHON:-python} make-big-chrom.py
echo -e " bigchroms.t03...big get fasta \c"
$BT getfasta -fi bigx.fasta -bed bigx.bed | tail -1 > obs
--- a/test/fisher/cmp.sh
+++ b/test/fisher/cmp.sh
@@ -3,7 +3,7 @@ set -eo pipefail
echo "fisher,shuffled"
for i in $(seq 1000); do
- fisher=$(python ./sim.py | tail -1 | cut -f 2)
+ fisher=$(${PYTHON:-python} ./sim.py | tail -1 | cut -f 2)
shuffle=$(bash shuf.sh)
echo "$fisher,$shuffle"
done
--- a/test/genomecov/test-genomecov.sh
+++ b/test/genomecov/test-genomecov.sh
@@ -288,7 +288,7 @@ CRAM_REFERENCE=test_ref.fa $BT genomecov -ibam empty.cram > obs
check obs exp
rm obs exp
-python mk-deep.py > deep.sam
+${PYTHON:-python} mk-deep.py > deep.sam
echo -e " genomecov.t18...\c"
echo "c1 1 1000000" > exp
$BT genomecov -d -ibam deep.sam | head -1 > obs
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