[Genabel-commits] r1464 - pkg/ProbABEL/checks
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Dec 12 16:19:20 CET 2013
Author: lckarssen
Date: 2013-12-12 16:19:19 +0100 (Thu, 12 Dec 2013)
New Revision: 1464
Modified:
pkg/ProbABEL/checks/Makefile.am
pkg/ProbABEL/checks/test_qt.sh
Log:
Fix running the ProbABEL checks in parallel.
Since Automake v1.13 all tests are run in parallel by default. When running 'make -j4 check' most of the time one test would fail (test_qt.sh) and the others would pass. Strangely enough sometimes paralle checks would work and running 'make check' always worked.
It turns out that more than one test used output files named height_*.out.txt, so these would then either be overwritten or deleted, letting one of the checks fail. This commit renames the output filenames in test_qt.sh to start with 'linear' instead of 'height'. This is similar to test_bt.sh, where output files start with 'logist'.
Modified: pkg/ProbABEL/checks/Makefile.am
===================================================================
--- pkg/ProbABEL/checks/Makefile.am 2013-12-12 13:11:58 UTC (rev 1463)
+++ pkg/ProbABEL/checks/Makefile.am 2013-12-12 15:19:19 UTC (rev 1464)
@@ -72,46 +72,46 @@
logist_prob_domin.out.txt logist_prob_fv_recess.out.txt \
logist_prob_fv_over_domin.out.txt logist_prob_recess.out.txt
-cleanfiles_qt = height_base_add.out.txt height_base_fv_add.out.txt \
-height_allcov_add.out.txt height_allcov_fv_add.out.txt \
-height_int1_add.out.txt height_int1_fv_add.out.txt \
-height_robust_add.out.txt height_robust_fv_add.out.txt \
-height_robust_int1_add.out.txt height_robust_int1_fv_add.out.txt \
-height_ngp2_add.out.txt height_ngp2_fv_add.out.txt \
-height_ngp2_domin.out.txt height_ngp2_fv_domin.out.txt \
-height_ngp2_over_domin.out.txt height_ngp2_fv_over_domin.out.txt \
-height_ngp2_recess.out.txt height_ngp2_fv_recess.out.txt \
-height_ngp2_2df.out.txt height_ngp2_fv_2df.out.txt \
-height_ngp2_allcov_add.out.txt height_ngp2_allcov_fv_add.out.txt \
-height_ngp2_allcov_domin.out.txt height_ngp2_allcov_fv_domin.out.txt \
-height_ngp2_allcov_over_domin.out.txt \
-height_ngp2_allcov_fv_over_domin.out.txt \
-height_ngp2_allcov_recess.out.txt height_ngp2_allcov_fv_recess.out.txt \
-height_ngp2_allcov_recess.out.txt height_ngp2_allcov_fv_recess.out.txt \
-height_ngp2_int1_add.out.txt height_ngp2_int1_fv_add.out.txt \
-height_ngp2_int1_domin.out.txt height_ngp2_int1_fv_domin.out.txt \
-height_ngp2_int1_over_domin.out.txt \
-height_ngp2_int1_fv_over_domin.out.txt height_ngp2_int1_recess.out.txt \
-height_ngp2_int1_fv_recess.out.txt height_ngp2_int1_2df.out.txt \
-height_ngp2_int1_fv_2df.out.txt height_ngp2_robust_add.out.txt \
-height_ngp2_robust_fv_add.out.txt height_ngp2_robust_domin.out.txt \
-height_ngp2_robust_fv_domin.out.txt \
-height_ngp2_robust_over_domin.out.txt \
-height_ngp2_robust_fv_over_domin.out.txt \
-height_ngp2_robust_recess.out.txt height_ngp2_robust_fv_recess.out.txt \
-height_ngp2_robust_2df.out.txt height_ngp2_robust_fv_2df.out.txt \
-height_ngp2_robust_int1_add.out.txt \
-height_ngp2_robust_int1_fv_add.out.txt \
-height_ngp2_robust_int1_domin.out.txt \
-height_ngp2_robust_int1_fv_domin.out.txt \
-height_ngp2_robust_int1_over_domin.out.txt \
-height_ngp2_robust_int1_fv_over_domin.out.txt \
-height_ngp2_robust_int1_recess.out.txt \
-height_ngp2_robust_int1_fv_recess.out.txt \
-height_ngp2_robust_int1_2df.out.txt \
-height_ngp2_robust_int1_fv_2df.out.txt \
-height_ngp2_allcov_fv_2df.out.txt height_ngp2_robust_fv_add.out.txt \
-height_ngp2_allcov_2df.out.txt
+cleanfiles_qt = linear_base_add.out.txt linear_base_fv_add.out.txt \
+linear_allcov_add.out.txt linear_allcov_fv_add.out.txt \
+linear_int1_add.out.txt linear_int1_fv_add.out.txt \
+linear_robust_add.out.txt linear_robust_fv_add.out.txt \
+linear_robust_int1_add.out.txt linear_robust_int1_fv_add.out.txt \
+linear_ngp2_add.out.txt linear_ngp2_fv_add.out.txt \
+linear_ngp2_domin.out.txt linear_ngp2_fv_domin.out.txt \
+linear_ngp2_over_domin.out.txt linear_ngp2_fv_over_domin.out.txt \
+linear_ngp2_recess.out.txt linear_ngp2_fv_recess.out.txt \
+linear_ngp2_2df.out.txt linear_ngp2_fv_2df.out.txt \
+linear_ngp2_allcov_add.out.txt linear_ngp2_allcov_fv_add.out.txt \
+linear_ngp2_allcov_domin.out.txt linear_ngp2_allcov_fv_domin.out.txt \
+linear_ngp2_allcov_over_domin.out.txt \
+linear_ngp2_allcov_fv_over_domin.out.txt \
+linear_ngp2_allcov_recess.out.txt linear_ngp2_allcov_fv_recess.out.txt \
+linear_ngp2_allcov_recess.out.txt linear_ngp2_allcov_fv_recess.out.txt \
+linear_ngp2_int1_add.out.txt linear_ngp2_int1_fv_add.out.txt \
+linear_ngp2_int1_domin.out.txt linear_ngp2_int1_fv_domin.out.txt \
+linear_ngp2_int1_over_domin.out.txt \
+linear_ngp2_int1_fv_over_domin.out.txt linear_ngp2_int1_recess.out.txt \
+linear_ngp2_int1_fv_recess.out.txt linear_ngp2_int1_2df.out.txt \
+linear_ngp2_int1_fv_2df.out.txt linear_ngp2_robust_add.out.txt \
+linear_ngp2_robust_fv_add.out.txt linear_ngp2_robust_domin.out.txt \
+linear_ngp2_robust_fv_domin.out.txt \
+linear_ngp2_robust_over_domin.out.txt \
+linear_ngp2_robust_fv_over_domin.out.txt \
+linear_ngp2_robust_recess.out.txt linear_ngp2_robust_fv_recess.out.txt \
+linear_ngp2_robust_2df.out.txt linear_ngp2_robust_fv_2df.out.txt \
+linear_ngp2_robust_int1_add.out.txt \
+linear_ngp2_robust_int1_fv_add.out.txt \
+linear_ngp2_robust_int1_domin.out.txt \
+linear_ngp2_robust_int1_fv_domin.out.txt \
+linear_ngp2_robust_int1_over_domin.out.txt \
+linear_ngp2_robust_int1_fv_over_domin.out.txt \
+linear_ngp2_robust_int1_recess.out.txt \
+linear_ngp2_robust_int1_fv_recess.out.txt \
+linear_ngp2_robust_int1_2df.out.txt \
+linear_ngp2_robust_int1_fv_2df.out.txt \
+linear_ngp2_allcov_fv_2df.out.txt linear_ngp2_robust_fv_add.out.txt \
+linear_ngp2_allcov_2df.out.txt
cleanfiles_mms = mmscore_dose_add.out.txt mmscore_dose_fv_add.out.txt \
mmscore_prob_fv_over_domin.out.txt mmscore_prob_fv_domin.out.txt \
Modified: pkg/ProbABEL/checks/test_qt.sh
===================================================================
--- pkg/ProbABEL/checks/test_qt.sh 2013-12-12 13:11:58 UTC (rev 1463)
+++ pkg/ProbABEL/checks/test_qt.sh 2013-12-12 15:19:19 UTC (rev 1464)
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/bash -x
# This script runs checks on ProbABEL's palinear module for
# quantitative traits.
@@ -25,7 +25,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 \
- -o height_base \
+ -o linear_base \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -33,12 +33,12 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 \
- -o height_base_fv \
+ -o linear_base_fv \
>& 3
#echo -n "QT check: dose vs. dose_fv"
-run_diff height_base_add.out.txt \
- height_base_fv_add.out.txt \
+run_diff linear_base_add.out.txt \
+ linear_base_fv_add.out.txt \
"QT check: dose vs. dose_fv"
@@ -48,7 +48,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --allcov \
- -o height_allcov \
+ -o linear_allcov \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -56,11 +56,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --allcov \
- -o height_allcov_fv \
+ -o linear_allcov_fv \
>& 3
-run_diff height_allcov_add.out.txt \
- height_allcov_fv_add.out.txt \
+run_diff linear_allcov_add.out.txt \
+ linear_allcov_fv_add.out.txt \
"QT check: allcov: dose vs. dose_fv"
@@ -71,7 +71,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --interaction=1 \
- -o height_int1 \
+ -o linear_int1 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -79,11 +79,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --interaction=1 \
- -o height_int1_fv \
+ -o linear_int1_fv \
>& 3
-run_diff height_int1_add.out.txt \
- height_int1_fv_add.out.txt \
+run_diff linear_int1_add.out.txt \
+ linear_int1_fv_add.out.txt \
"QT check: interactions: dose vs. dose_fv"
@@ -94,7 +94,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --robust \
- -o height_robust \
+ -o linear_robust \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -102,11 +102,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --robust \
- -o height_robust_fv \
+ -o linear_robust_fv \
>& 3
-run_diff height_robust_add.out.txt \
- height_robust_fv_add.out.txt \
+run_diff linear_robust_add.out.txt \
+ linear_robust_fv_add.out.txt \
"QT check: robust: dose vs. dose_fv"
@@ -117,7 +117,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --robust --interaction=1 \
- -o height_robust_int1 \
+ -o linear_robust_int1 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -125,11 +125,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --robust --interaction=1 \
- -o height_robust_int1_fv \
+ -o linear_robust_int1_fv \
>& 3
-run_diff height_robust_int1_add.out.txt \
- height_robust_int1_fv_add.out.txt \
+run_diff linear_robust_int1_add.out.txt \
+ linear_robust_int1_fv_add.out.txt \
"QT check: robust & interaction: dose vs. dose_fv"
@@ -140,7 +140,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 \
- -o height_ngp2 \
+ -o linear_ngp2 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -148,18 +148,18 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 \
- -o height_ngp2_fv \
+ -o linear_ngp2_fv \
>& 3
# Remove header from the outputs, because they differ
-run_diff height_base_add.out.txt \
- height_ngp2_add.out.txt \
+run_diff linear_base_add.out.txt \
+ linear_ngp2_add.out.txt \
"QT check: dose vs. prob (additive model)" -I SNP
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_${model}.out.txt \
- height_ngp2_fv_${model}.out.txt \
+ run_diff linear_ngp2_${model}.out.txt \
+ linear_ngp2_fv_${model}.out.txt \
"QT check ($model model): prob vs. prob_fv"
done
@@ -171,7 +171,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --allcov \
- -o height_ngp2_allcov \
+ -o linear_ngp2_allcov \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -179,12 +179,12 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --allcov \
- -o height_ngp2_allcov_fv \
+ -o linear_ngp2_allcov_fv \
>& 3
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_allcov_${model}.out.txt \
- height_ngp2_allcov_fv_${model}.out.txt \
+ run_diff linear_ngp2_allcov_${model}.out.txt \
+ linear_ngp2_allcov_fv_${model}.out.txt \
"QT check --allcov ($model model): prob vs. prob_fv"
done
@@ -196,7 +196,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --interaction=1 \
- -o height_ngp2_int1 \
+ -o linear_ngp2_int1 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -204,12 +204,12 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --interaction=1 \
- -o height_ngp2_int1_fv \
+ -o linear_ngp2_int1_fv \
>& 3
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_int1_${model}.out.txt \
- height_ngp2_int1_fv_${model}.out.txt \
+ run_diff linear_ngp2_int1_${model}.out.txt \
+ linear_ngp2_int1_fv_${model}.out.txt \
"QT check --interactions ($model model): prob vs. prob_fv"
done
@@ -221,7 +221,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --robust \
- -o height_ngp2_robust \
+ -o linear_ngp2_robust \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -229,12 +229,12 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --robust \
- -o height_ngp2_robust_fv \
+ -o linear_ngp2_robust_fv \
>& 3
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_robust_${model}.out.txt \
- height_ngp2_robust_fv_${model}.out.txt \
+ run_diff linear_ngp2_robust_${model}.out.txt \
+ linear_ngp2_robust_fv_${model}.out.txt \
"QT check --robust ($model model): prob vs. prob_fv"
done
@@ -246,7 +246,7 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --robust --interaction=1 \
- -o height_ngp2_robust_int1 \
+ -o linear_ngp2_robust_int1 \
>& 3
../src/palinear \
-p ${inputdir}/height.txt \
@@ -254,11 +254,11 @@
-i ${inputdir}/test.mlinfo \
-m ${inputdir}/test.map \
-c 19 --ngp=2 --robust --interaction=1 \
- -o height_ngp2_robust_int1_fv \
+ -o linear_ngp2_robust_int1_fv \
>& 3
for model in add domin over_domin recess 2df; do
- run_diff height_ngp2_robust_int1_${model}.out.txt \
- height_ngp2_robust_int1_fv_${model}.out.txt \
+ run_diff linear_ngp2_robust_int1_${model}.out.txt \
+ linear_ngp2_robust_int1_fv_${model}.out.txt \
"QT check --robust --interactions ($model model): prob vs. prob_fv"
done
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