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