[med-svn] [seqtools] 01/01: Convert test scripts from ksh to sh
Andreas Tille
tille at debian.org
Thu Oct 26 12:15:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository seqtools.
commit d37de23ce6f51c6704e841e39209b6907ab4a78a
Author: Andreas Tille <tille at debian.org>
Date: Thu Oct 26 14:15:13 2017 +0200
Convert test scripts from ksh to sh
---
debian/patches/ksh2sh.patch | 1085 +++++++++++++++++++++++++++++++++++++++++++
debian/patches/series | 1 +
2 files changed, 1086 insertions(+)
diff --git a/debian/patches/ksh2sh.patch b/debian/patches/ksh2sh.patch
new file mode 100644
index 0000000..d7ef11c
--- /dev/null
+++ b/debian/patches/ksh2sh.patch
@@ -0,0 +1,1085 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 19 Oct 2017 16:27:56 +0200
+Description: Konvert test scripts from ksh to POSIX sh
+
+--- a/test/scripts/automated/belvu/test1
++++ b/test/scripts/automated/belvu/test1
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test saving a file to MSF format
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o MSF $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If thre were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test10
++++ b/test/scripts/automated/belvu/test10
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test the 'Print UPGMA-based subfamilies at cutoff'
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -X 0.5 $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test11
++++ b/test/scripts/automated/belvu/test11
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test the 'Print UPGMA-based subfamilies at cutoff'
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -X 0.5 $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test12
++++ b/test/scripts/automated/belvu/test12
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Create the tree using the UPGMA method and save it
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T u -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test13
++++ b/test/scripts/automated/belvu/test13
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Create the tree using the UPGMA method and save it
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T u -o tree $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test14
++++ b/test/scripts/automated/belvu/test14
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Create the tree using the Jukes-Cantor distance
+@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T j -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test15
++++ b/test/scripts/automated/belvu/test15
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Create the tree using the Kimura distance
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T k -o tree $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test16
++++ b/test/scripts/automated/belvu/test16
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Create the tree using the Kimura distance
+@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T k -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test17
++++ b/test/scripts/automated/belvu/test17
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Create the tree using the Storm and Sonnhammer distance
+@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T s -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test18
++++ b/test/scripts/automated/belvu/test18
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Create the tree using uncorrected distances and save
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T r -o tree $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test19
++++ b/test/scripts/automated/belvu/test19
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Print the distance matrix
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -p $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test2
++++ b/test/scripts/automated/belvu/test2
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test saving a file to Mul format
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Mul $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If thre were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test20
++++ b/test/scripts/automated/belvu/test20
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Make the alignment non-redundanct and save
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -n 80 -o Mul $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test21
++++ b/test/scripts/automated/belvu/test21
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Remove gappy columns and save the alignment
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -Q 60 -o MSF $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test22
++++ b/test/scripts/automated/belvu/test22
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Remove gappy sequences and save the alignment in
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -q 80 -o Selex $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test23
++++ b/test/scripts/automated/belvu/test23
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Ignore gaps in conservation calculation and print
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -i -c $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test24
++++ b/test/scripts/automated/belvu/test24
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Remove partial sequences and save in aligned-fasta format
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -P -o FastaAlign $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test25
++++ b/test/scripts/automated/belvu/test25
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Tests saving alignment without coordinates in Mul
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -C -o Mul $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test26
++++ b/test/scripts/automated/belvu/test26
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Read in an alignment that has a separator of '='
+@@ -19,7 +19,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -z '=' -C -o MSF $data_dir/PF02171_seed_separator.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test27
++++ b/test/scripts/automated/belvu/test27
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Read in an alignment that has a separator of '='
+@@ -19,7 +19,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -z '=' -R -C -o MSF $data_dir/PF02171_seed_separator.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test28
++++ b/test/scripts/automated/belvu/test28
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Output random model probabilities for HMMER
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -p $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test29
++++ b/test/scripts/automated/belvu/test29
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Output random model probabilities for HMMER
+@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -p $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test3
++++ b/test/scripts/automated/belvu/test3
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test saving an alignment as Selex format
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test30
++++ b/test/scripts/automated/belvu/test30
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Output random model probabilities for HMMER
+@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -p $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test31
++++ b/test/scripts/automated/belvu/test31
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort alphabetically on start up. Also tests saving
+@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Fasta -S a -C $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test32
++++ b/test/scripts/automated/belvu/test32
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort by organism on start up. Also tests saving
+@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o FastaAlign -S o -C $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test33
++++ b/test/scripts/automated/belvu/test33
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+
+ # Description:
+@@ -17,7 +17,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S s -C -s $data_dir/PF02171_seed.scores $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test34
++++ b/test/scripts/automated/belvu/test34
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+
+ # Description:
+@@ -16,7 +16,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S n -s $data_dir/PF02171_seed.scores $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test35
++++ b/test/scripts/automated/belvu/test35
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort by neighbour-joinging tree on start up (large alignment).
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S n $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test36
++++ b/test/scripts/automated/belvu/test36
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort by neighbour-joinging tree on start up (large alignment).
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S n $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test37
++++ b/test/scripts/automated/belvu/test37
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort by UPGMA tree on start up (large alignment).
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S u $data_dir/PF02171_full.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test38
++++ b/test/scripts/automated/belvu/test38
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort by UPGMA tree on start up (large alignment).
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S u $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test39
++++ b/test/scripts/automated/belvu/test39
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort by similarity to first sequence (large alignment).
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S S $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test4
++++ b/test/scripts/automated/belvu/test4
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test saving an alignment in aligned-fasta format
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o FastaAlign $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test40
++++ b/test/scripts/automated/belvu/test40
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort by similarity to first sequence
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S S $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test41
++++ b/test/scripts/automated/belvu/test41
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a neighbour-joining tree (scoredist distance correction)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T nb -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test42
++++ b/test/scripts/automated/belvu/test42
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a neighbour-joining tree (jukes-cantor distance correction)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T nj -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test43
++++ b/test/scripts/automated/belvu/test43
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a neighbour-joining tree (kimura distance correction)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T nk -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test44
++++ b/test/scripts/automated/belvu/test44
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a neighbour-joining tree (storm & sonnhammer distance correction)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T ns -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test45
++++ b/test/scripts/automated/belvu/test45
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a neighbour-joining tree (uncorrected distances)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T nr -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test46
++++ b/test/scripts/automated/belvu/test46
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a UPGMA tree (scoredist distance correction)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T ub -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test47
++++ b/test/scripts/automated/belvu/test47
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a UPGMA tree (jukes-cantor distance correction)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T uj -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test48
++++ b/test/scripts/automated/belvu/test48
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a UPGMA tree (kimura distance correction)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T uk -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test49
++++ b/test/scripts/automated/belvu/test49
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a UPGMA tree (storm & sonnhammer distance correction)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T us -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test5
++++ b/test/scripts/automated/belvu/test5
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test saving an alignment in unaligned-fasta format
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Fasta $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test50
++++ b/test/scripts/automated/belvu/test50
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test creating a UPGMA tree (uncorrected distances)
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -T ur -o tree $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test51
++++ b/test/scripts/automated/belvu/test51
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Sort by ID to first sequence
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o Selex -S i $data_dir/PF02171_seed.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test6
++++ b/test/scripts/automated/belvu/test6
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test saving a tree in new-hampshire format
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o tree $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test7
++++ b/test/scripts/automated/belvu/test7
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test the option to print the conservation table
+@@ -14,7 +14,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -c $data_dir/PF02171_seed.stock >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test8
++++ b/test/scripts/automated/belvu/test8
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test the option to print the conservation table
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -c $data_dir/ALIGN.selex >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/belvu/test9
++++ b/test/scripts/automated/belvu/test9
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test reading a file in 'raw' format. Check that it can
+@@ -15,7 +15,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`belvu -o MSF -r $data_dir/PF02171_seed.fasta >&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/blixem/test1
++++ b/test/scripts/automated/blixem/test1
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Blixem's --help option
+@@ -18,7 +18,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`blixem -h 2>&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ RC=1
+ fi
+--- a/test/scripts/automated/blixem/test2
++++ b/test/scripts/automated/blixem/test2
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Blixem's usage text
+@@ -18,7 +18,7 @@ results_file="$test_dir/$test_name""_res
+ diffs=`blixem 2>&1 | diff "$results_file" -`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ RC=1
+ fi
+--- a/test/scripts/automated/dotter/test1
++++ b/test/scripts/automated/dotter/test1
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ #
+ # Description:
+@@ -21,7 +21,7 @@ dotter -b $output_file -q 246634 -f $dat
+ diffs=`diff $results_file $output_file`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/dotter/test2
++++ b/test/scripts/automated/dotter/test2
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ #
+ # Description:
+@@ -21,7 +21,7 @@ dotter -e $output_file -q 246634 -f $dat
+ diffs=`diff $results_file $output_file`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ print "$test_name FAILED"
+ RC=1
+--- a/test/scripts/automated/dotter/test3
++++ b/test/scripts/automated/dotter/test3
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ #
+ # Description:
+@@ -24,7 +24,7 @@ dotter -b $output_file1 -e $output_file2
+ diffs=`diff $results_file1 $output_file1`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ RC=1
+ fi
+@@ -33,7 +33,7 @@ fi
+ diffs=`diff $results_file2 $output_file2`
+
+ # If there were any problems or differences, set RC
+-if [[ $? -ne 0 || $diffs != "" ]]
++if [ $? -ne 0 -o "$diffs" != "" ]
+ then
+ RC=1
+ fi
+--- a/test/scripts/manual/belvu/test1
++++ b/test/scripts/manual/belvu/test1
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test that the residue colors and markup colors are loaded correctly
+--- a/test/scripts/manual/belvu/test2
++++ b/test/scripts/manual/belvu/test2
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test that the residue colors and markup colors are loaded correctly
+--- a/test/scripts/manual/belvu/test3
++++ b/test/scripts/manual/belvu/test3
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test reading a file without stripping coordinates
+--- a/test/scripts/manual/belvu/test4
++++ b/test/scripts/manual/belvu/test4
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ # Description:
+ # Test loading of match segments from a separate file
+ #
+--- a/test/scripts/manual/belvu/test5
++++ b/test/scripts/manual/belvu/test5
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test loading of match segments from a match-footer section
+--- a/test/scripts/manual/blixem/test1
++++ b/test/scripts/manual/blixem/test1
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Blixem in nucleotide mode. Features include nucleotide matches, transcripts
+--- a/test/scripts/manual/blixem/test2
++++ b/test/scripts/manual/blixem/test2
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Blixem in protein mode. Features include protein matches, transcripts
+--- a/test/scripts/manual/dotter/test1
++++ b/test/scripts/manual/dotter/test1
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Dotter in nucleotide->nucleotide mode. Tests the dot-matrix calculation as well
+--- a/test/scripts/manual/dotter/test2
++++ b/test/scripts/manual/dotter/test2
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Tests calling Dotter on a long sequence versus itself. Transcripts are supplied via a features
+--- a/test/scripts/manual/dotter/test3
++++ b/test/scripts/manual/dotter/test3
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Dotter in nucleotide->protein mode. Tests the dot-matrix calculation as well
+--- a/test/scripts/manual/dotter/test4
++++ b/test/scripts/manual/dotter/test4
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Dotter in nucleotide->protein mode, using the reverse-complemented version of the
+--- a/test/scripts/manual/dotter/test5
++++ b/test/scripts/manual/dotter/test5
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Dotter in nucleotide->nucleotide mode, using the reverse-complemented version of the input
+--- a/test/scripts/manual/dotter/test6
++++ b/test/scripts/manual/dotter/test6
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test Dotter in protein->protein mode.
+--- a/test/scripts/manual/dotter/test7
++++ b/test/scripts/manual/dotter/test7
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Test loading of a saved dot-matrix.
+--- a/test/scripts/manual/dotter/test8
++++ b/test/scripts/manual/dotter/test8
+@@ -1,4 +1,4 @@
+-#!/bin/ksh
++#!/bin/sh
+ #
+ # Description:
+ # Tests loading a dot-matrix plot from file for a long sequence versus itself.
diff --git a/debian/patches/series b/debian/patches/series
index 32c6ab5..af6d798 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ prevent_usage_of_blatsrc.patch
use_debian_packaged_jsoncpp.patch
fix_missing_includes.patch
spelling.patch
+ksh2sh.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/seqtools.git
More information about the debian-med-commit
mailing list