Description: use Debian's gt path
Author: Sascha Steinbiss <satta@debian.org>
--- a/testsuite/gthbssmtrain_include.rb
+++ b/testsuite/gthbssmtrain_include.rb
@@ -37,7 +37,7 @@
 Name "gthbssmtrain (stdin, no introns)"
 Keywords "gthbssmtrain"
 Test do
-  run_test "#{$bin}../../genometools/bin/gt gff3 " +
+  run_test "gt gff3 " +
            "#{$testdata}U89959_csas.gff3 | " +
            "#{$bin}gthbssmtrain -seqfile #{$testdata}U89959_genomic.fas " +
            "-matchdesc -seed 913609837 -"
@@ -49,7 +49,7 @@
 Name "gthbssmtrain (stdin, introns)"
 Keywords "gthbssmtrain"
 Test do
-  run_test "#{$bin}../../genometools/bin/gt gff3 " +
+  run_test "gt gff3 " +
            "#{$testdata}U89959_csas_introns.gff3 | " +
            "#{$bin}gthbssmtrain -seqfile #{$testdata}U89959_genomic.fas " +
            "-matchdesc -seed 913609837 -"
@@ -71,11 +71,11 @@
   Name "gthbssmtrain (arabidopsis)"
   Keywords "gthbssmtrain"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -sort " +
+    run_test "gt gff3 -sort " +
              "#{$gthtestdata}gthbssmtrain/22329272.gff3 " +
              "#{$gthtestdata}gthbssmtrain/22330780.gff3"
-    run_test "#{$bin}../../genometools/bin/gt csa #{$last_stdout}"
-    run_test "#{$bin}../../genometools/bin/gt cds -regionmapping " +
+    run_test "gt csa #{$last_stdout}"
+    run_test "gt cds -regionmapping " +
              "#{$gthtestdata}gthbssmtrain/mapping.lua -minorflen 1 " +
              "-startcodon yes -finalstopcodon yes #{$last_stdout}",
              :maxtime => 300
--- a/testsuite/gth_include.rb
+++ b/testsuite/gth_include.rb
@@ -276,7 +276,7 @@
   run      "diff --strip-trailing-cr test_sas.gff3 #{$testdata}U89959_sas.gff3"
   run_test "#{$bin}gthconsensus -o test_csas.gff3 -gff3out -skipalignmentout " +
            "test.inter"
-  run_test "#{$bin}../../genometools/bin/gt eval test_csas.gff3 #{$testdata}U89959_csas.gff3"
+  run_test "gt eval test_csas.gff3 #{$testdata}U89959_csas.gff3"
   run      "diff --strip-trailing-cr #{$last_stdout} #{$testdata}U89959_csas.eval"
 end
 
@@ -334,7 +334,7 @@
              "-enrichchains -scoreminexonlen 1 -detectsmallexons -gff3out " +
              "-skipalignmentout -genomic #{$gthtestdata}gencode/ENr233.fa.gz " +
              "-cdna #{$gthtestdata}gencode/small_initial_exon_cdna.fas"
-    run_test "#{$bin}../../genometools/bin/gt eval " +
+    run_test "gt eval " +
              "#{$gthtestdata}gencode/small_initial_exon.gff3 #{$last_stdout}"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}gencode/small_initial_exon.eval"
   end
@@ -347,7 +347,7 @@
              "-enrichchains -scoreminexonlen 1 -detectsmallexons -gff3out " +
              "-skipalignmentout -genomic #{$gthtestdata}gencode/ENm005.fa.gz " +
              "-cdna #{$gthtestdata}gencode/small_terminal_exon_cdna.fas"
-    run_test "#{$bin}../../genometools/bin/gt eval " +
+    run_test "gt eval " +
              "#{$gthtestdata}gencode/small_terminal_exon.gff3 #{$last_stdout}"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}gencode/small_terminal_exon.eval"
   end
--- a/testsuite/ngasp_include.rb
+++ b/testsuite/ngasp_include.rb
@@ -8,7 +8,7 @@
   Name "nGASP (training_confirmed_tidy.gff)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -tidy -addids no " +
+    run_test "gt gff3 -tidy -addids no " +
              "#{$gthtestdata}ngasp/confirmed.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_confirmed_tidy.gff3"
   end
@@ -16,7 +16,7 @@
   Name "nGASP (training_unconfirmed_tidy.gff)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -tidy -addids no " +
+    run_test "gt gff3 -tidy -addids no " +
              "#{$gthtestdata}ngasp/unconfirmed.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_unconfirmed_tidy.gff3"
   end
@@ -24,7 +24,7 @@
   Name "nGASP (test_confirmed_tidy.gff)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -tidy -addids no " +
+    run_test "gt gff3 -tidy -addids no " +
              "#{$gthtestdata}ngasp/test_regions_confirmed.gff3.gz"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_confirmed_tidy.gff3"
   end
@@ -32,7 +32,7 @@
   Name "nGASP (test_unconfirmed_tidy.gff)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -tidy -addids no " +
+    run_test "gt gff3 -tidy -addids no " +
              "#{$gthtestdata}ngasp/test_regions_unconfirmed.gff3.gz"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_unconfirmed_tidy.gff3"
   end
@@ -40,7 +40,7 @@
   Name "nGASP (training_confirmed_md5.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt id_to_md5 -usedesc -seqfile " +
+    run_test "gt id_to_md5 -usedesc -seqfile " +
              "#{$gthtestdata}ngasp32/training_regions.fa " +
              "#{$gthtestdata}ngasp/training_confirmed_tidy.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_confirmed_md5.gff3"
@@ -49,7 +49,7 @@
   Name "nGASP (training_unconfirmed_md5.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt id_to_md5 -usedesc -seqfile " +
+    run_test "gt id_to_md5 -usedesc -seqfile " +
              "#{$gthtestdata}ngasp32/training_regions.fa " +
              "#{$gthtestdata}ngasp/training_unconfirmed_tidy.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_unconfirmed_md5.gff3"
@@ -58,7 +58,7 @@
   Name "nGASP (test_confirmed_md5.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt id_to_md5 -usedesc -seqfile " +
+    run_test "gt id_to_md5 -usedesc -seqfile " +
              "#{$gthtestdata}ngasp32/test_regions.fa " +
              "#{$gthtestdata}ngasp/test_confirmed_tidy.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_confirmed_md5.gff3"
@@ -67,7 +67,7 @@
   Name "nGASP (test_unconfirmed_md5.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt id_to_md5 -usedesc -seqfile " +
+    run_test "gt id_to_md5 -usedesc -seqfile " +
              "#{$gthtestdata}ngasp32/test_regions.fa " +
              "#{$gthtestdata}ngasp/test_unconfirmed_tidy.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_unconfirmed_md5.gff3"
@@ -76,7 +76,7 @@
   Name "nGASP (training_confirmed_sorted.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -sort " +
+    run_test "gt gff3 -sort " +
              "#{$gthtestdata}ngasp/training_confirmed_md5.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_confirmed_sorted.gff3"
   end
@@ -84,7 +84,7 @@
   Name "nGASP (training_unconfirmed_sorted.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -sort " +
+    run_test "gt gff3 -sort " +
              "#{$gthtestdata}ngasp/training_unconfirmed_md5.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_unconfirmed_sorted.gff3"
   end
@@ -92,7 +92,7 @@
   Name "nGASP (test_confirmed_sorted.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -sort " +
+    run_test "gt gff3 -sort " +
              "#{$gthtestdata}ngasp/test_confirmed_md5.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_confirmed_sorted.gff3"
   end
@@ -100,7 +100,7 @@
   Name "nGASP (test_unconfirmed_sorted.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -sort " +
+    run_test "gt gff3 -sort " +
              "#{$gthtestdata}ngasp/test_unconfirmed_md5.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_unconfirmed_sorted.gff3"
   end
@@ -108,7 +108,7 @@
   Name "nGASP (training_ref2.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt merge " +
+    run_test "gt merge " +
              "#{$gthtestdata}ngasp/training_confirmed_sorted.gff3 " +
              "#{$gthtestdata}ngasp/training_unconfirmed_sorted.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_ref2.gff3"
@@ -117,7 +117,7 @@
   Name "nGASP (test_ref2.gff3)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt merge " +
+    run_test "gt merge " +
              "#{$gthtestdata}ngasp/test_confirmed_sorted.gff3 " +
              "#{$gthtestdata}ngasp/test_unconfirmed_sorted.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_ref2.gff3"
@@ -126,53 +126,53 @@
   Name "nGASP (training_ref1.gff3, combined)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -tidy -addids no " +
+    run_test "gt gff3 -tidy -addids no " +
              "#{$gthtestdata}ngasp/confirmed.gff3 | " +
-             "#{$bin}../../genometools/bin/gt id_to_md5 -usedesc -seqfile " +
+             "gt id_to_md5 -usedesc -seqfile " +
              "#{$gthtestdata}ngasp32/training_regions.fa | " +
-             "#{$bin}../../genometools/bin/gt gff3 -sort"
+             "gt gff3 -sort"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_ref1.gff3"
   end
 
   Name "nGASP (training_ref2.gff3, combined)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -tidy -addids no " +
+    run_test "gt gff3 -tidy -addids no " +
              "#{$gthtestdata}ngasp/confirmed.gff3 " +
              "#{$gthtestdata}ngasp/unconfirmed.gff3 | " +
-             "#{$bin}../../genometools/bin/gt id_to_md5 -usedesc -seqfile " +
+             "gt id_to_md5 -usedesc -seqfile " +
              "#{$gthtestdata}ngasp32/training_regions.fa | " +
-             "#{$bin}../../genometools/bin/gt gff3 -sort"
+             "gt gff3 -sort"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_ref2.gff3"
   end
 
   Name "nGASP (test_ref1.gff3, combined)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -tidy -addids no " +
+    run_test "gt gff3 -tidy -addids no " +
              "#{$gthtestdata}ngasp/test_regions_confirmed.gff3.gz | " +
-             "#{$bin}../../genometools/bin/gt id_to_md5 -usedesc -seqfile " +
+             "gt id_to_md5 -usedesc -seqfile " +
              "#{$gthtestdata}ngasp32/test_regions.fa | " +
-             "#{$bin}../../genometools/bin/gt gff3 -sort"
+             "gt gff3 -sort"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_ref1.gff3"
   end
 
   Name "nGASP (test_ref2.gff3, combined)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt gff3 -tidy -addids no " +
+    run_test "gt gff3 -tidy -addids no " +
              "#{$gthtestdata}ngasp/test_regions_confirmed.gff3.gz " +
              "#{$gthtestdata}ngasp/test_regions_unconfirmed.gff3.gz | " +
-             "#{$bin}../../genometools/bin/gt id_to_md5 -usedesc -seqfile " +
+             "gt id_to_md5 -usedesc -seqfile " +
              "#{$gthtestdata}ngasp32/test_regions.fa | " +
-             "#{$bin}../../genometools/bin/gt gff3 -sort"
+             "gt gff3 -sort"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/test_ref2.gff3"
   end
 
   Name "nGASP (protein_matches.fa)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt seqtransform -addstopaminos " +
+    run_test "gt seqtransform -addstopaminos " +
              "#{$gthtestdata}ngasp32/protein_matches_complete_filtered.fa",
              :maxtime => 300
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp32/protein_matches.fa"
@@ -181,7 +181,7 @@
   Name "nGASP (splice site info)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt splicesiteinfo -seqfile " +
+    run_test "gt splicesiteinfo -seqfile " +
              "#{$gthtestdata}ngasp32/training_regions.fa " +
              "#{$gthtestdata}ngasp/training_ref2.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/training_ref2.splicesiteinfo"
@@ -201,7 +201,7 @@
   Name "nGASP (intron length distribution)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt stat -intronlengthdistri " +
+    run_test "gt stat -intronlengthdistri " +
              "#{$gthtestdata}ngasp/training_ref2.gff3"
     run "diff --strip-trailing-cr #{$last_stdout} " +
         "#{$gthtestdata}ngasp/training_ref2.intronlengthdistri"
@@ -212,10 +212,10 @@
   Name "nGASP (genometools triad)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt filter -mingenescore 0.85 " +
+    run_test "gt filter -mingenescore 0.85 " +
              "#{$gthtestdata}ngasp/ngasp.inter.gff3 | " +
-             "#{$bin}../../genometools/bin/gt csa | " +
-             "#{$bin}../../genometools/bin/gt cds -seqfile " +
+             "gt csa | " +
+             "gt cds -seqfile " +
              "#{$gthtestdata}ngasp32/test_regions.fa " +
              "-startcodon yes -o ngasp.gff3", :maxtime => 300
     run "diff --strip-trailing-cr ngasp.gff3 #{$gthtestdata}ngasp/ngasp.gff3"
@@ -225,7 +225,7 @@
   Name "nGASP (sensitivity)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt eval " +
+    run_test "gt eval " +
              "#{$gthtestdata}ngasp/test_ref1.gff3 " +
              "#{$gthtestdata}ngasp/ngasp.gff3", :maxtime => 120
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/ngasp.sensitivity"
@@ -234,7 +234,7 @@
   Name "nGASP (specificity)"
   Keywords "gth ngasp diss"
   Test do
-    run_test "#{$bin}../../genometools/bin/gt eval " +
+    run_test "gt eval " +
              "#{$gthtestdata}ngasp/test_ref2.gff3 " +
              "#{$gthtestdata}ngasp/ngasp.gff3", :maxtime => 300
     run "diff --strip-trailing-cr #{$last_stdout} #{$gthtestdata}ngasp/ngasp.specificity"