[Genabel-commits] r1518 - pkg/ProbABEL/checks

[noreply at r-forge.r-project.org]

Author: lckarssen
Date: 2013-12-30 15:48:15 +0100 (Mon, 30 Dec 2013)
New Revision: 1518

Modified:
   pkg/ProbABEL/checks/test_bt.sh
   pkg/ProbABEL/checks/test_cox.sh
   pkg/ProbABEL/checks/test_mms.sh
   pkg/ProbABEL/checks/test_qt.sh
Log:
The basic ProbABEL test scripts can now also be run from a different directory than the one they are in. 
This is the commit that should have gone into commit r1516.


Modified: pkg/ProbABEL/checks/test_bt.sh
===================================================================
--- pkg/ProbABEL/checks/test_bt.sh	2013-12-30 14:43:27 UTC (rev 1517)
+++ pkg/ProbABEL/checks/test_bt.sh	2013-12-30 14:48:15 UTC (rev 1518)
@@ -2,27 +2,30 @@
 # This script runs checks on ProbABEL's palogist module for
 # binary traits.
 
-echo "analysing BT"
+echo "Analysing BT..."
 
 scriptdir=$(dirname $0)
 
 if [ -z ${srcdir} ]; then
     srcdir="."
+    bindir=${scriptdir}/../src/
+else
+    bindir="../src/"
 fi
 
 . ${scriptdir}/run_diff.sh
 
-inputdir=${srcdir}/inputfiles
+inputdir=${scriptdir}/inputfiles
+palogist=${bindir}/palogist
 
 # Redirect all output to file descriptor 3 to /dev/null except if
 # the first argument is "verbose" then redirect handle 3 to stdout
 exec 3>/dev/null
 if [ "$1" = "verbose" ]; then
+    echo "Verbose mode ON"
     exec 3>&1
 fi
 
-palogist=../src/palogist
-
 $palogist \
     -p ${inputdir}/logist_data.txt \
     -d ${inputdir}/test.mldose \

Modified: pkg/ProbABEL/checks/test_cox.sh
===================================================================
--- pkg/ProbABEL/checks/test_cox.sh	2013-12-30 14:43:27 UTC (rev 1517)
+++ pkg/ProbABEL/checks/test_cox.sh	2013-12-30 14:48:15 UTC (rev 1518)
@@ -7,11 +7,15 @@
 
 if [ -z ${srcdir} ]; then
     srcdir="."
+    bindir=${scriptdir}/../src/
+else
+    bindir="../src/"
 fi
 
 . ${scriptdir}/run_diff.sh
 
-inputdir=${srcdir}/inputfiles
+inputdir=${scriptdir}/inputfiles
+pacoxph=${bindir}/pacoxph
 
 # Redirect all output to file descriptor 3 to /dev/null except if
 # the first argument is "verbose" then redirect handle 3 to stdout
@@ -21,8 +25,6 @@
     exec 3>&1
 fi
 
-pacoxph=../src/pacoxph
-
 $pacoxph \
     -p ${inputdir}/coxph_data.txt \
     -d ${inputdir}/test.mldose \

Modified: pkg/ProbABEL/checks/test_mms.sh
===================================================================
--- pkg/ProbABEL/checks/test_mms.sh	2013-12-30 14:43:27 UTC (rev 1517)
+++ pkg/ProbABEL/checks/test_mms.sh	2013-12-30 14:48:15 UTC (rev 1518)
@@ -2,24 +2,30 @@
 # This script runs checks on ProbABEL's palinear module for
 # quantitative traits combined with the mmscore option.
 
-echo "analysis using MMScore"
+echo "Analysis using MMScore..."
+
+scriptdir=$(dirname $0)
+
 if [ -z ${srcdir} ]; then
     srcdir="."
+    bindir=${scriptdir}/../src/
+else
+    bindir="../src/"
 fi
 
-. ${srcdir}/run_diff.sh
+. ${scriptdir}/run_diff.sh
 
-inputdir=${srcdir}/inputfiles
+inputdir=${scriptdir}/inputfiles
+palinear=${bindir}/palinear
 
 # Redirect all output to file descriptor 3 to /dev/null except if
 # the first argument is "verbose" then redirect handle 3 to stdout
 exec 3>/dev/null
 if [ "$1" = "verbose" ]; then
+    echo "Verbose mode ON"
     exec 3>&1
 fi
 
-palinear=../src/palinear
-
 $palinear \
     -p ${inputdir}/mmscore_pheno.PHE \
     -i ${inputdir}/mmscore_gen.mlinfo \

Modified: pkg/ProbABEL/checks/test_qt.sh
===================================================================
--- pkg/ProbABEL/checks/test_qt.sh	2013-12-30 14:43:27 UTC (rev 1517)
+++ pkg/ProbABEL/checks/test_qt.sh	2013-12-30 14:48:15 UTC (rev 1518)
@@ -2,27 +2,30 @@
 # This script runs checks on ProbABEL's palinear module for
 # quantitative traits.
 
-echo "analysing QT"
+echo "Analysing QT..."
 
 scriptdir=$(dirname $0)
 
 if [ -z ${srcdir} ]; then
     srcdir="."
+    bindir=${scriptdir}/../src/
+else
+    bindir="../src/"
 fi
 
 . ${scriptdir}/run_diff.sh
 
-inputdir=${srcdir}/inputfiles
+inputdir=${scriptdir}/inputfiles
+palinear=${bindir}/palinear
 
 # Redirect all output to file descriptor 3 to /dev/null except if
 # the first argument is "verbose" then redirect handle 3 to stdout
 exec 3>/dev/null
 if [ "$1" = "verbose" ]; then
+    echo "Verbose mode ON"
     exec 3>&1
 fi
 
-palinear="../src/palinear"
-
 echo "base analysis"
 $palinear \
     -p ${inputdir}/height.txt \