debian/patches/debian-gt-libs.patch

@@ -164,3 +164,15 @@
  	  -MT $@
  
  obj/src/core/versionfunc.o: obj/gth_config.h
+@@ -508,9 +505,9 @@
+                           -gtdonor -agacceptor -gzip
+ 	@touch $@
+ 
+-obj/old_train: ../genometools/bin/gt
++obj/old_train:
+ 	@echo "[write old BSSMs]"
+-	@../genometools/bin/gt dev gthmkbssmfiles bin/bssm
++	@gt dev gthmkbssmfiles bin/bssm
+ 	@touch $@
+ 
+ obj/gthdata:

debian/patches/series

 debian-gt-libs.patch
 gt-path-fix.patch
-skip-human-bssm-tests.patch

debian/patches/skip-human-bssm-tests.patch

---- a/testsuite/gth_include.rb
-+++ b/testsuite/gth_include.rb
-@@ -111,28 +111,28 @@
- Name "gth regression test (-exondistri)"
- Keywords "gth"
- Test do
--  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -exondistri"
-+  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -exondistri"
-   grep($last_stdout, /length distribution of all exons/)
- end
- 
- Name "gth regression test (-introndistri)"
- Keywords "gth"
- Test do
--  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -introndistri"
-+  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -introndistri"
-   grep($last_stdout, /length distribution of all introns/)
- end
- 
- Name "gth regression test (-refseqcovdistri)"
- Keywords "gth"
- Test do
--  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -refseqcovdistri"
-+  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -refseqcovdistri"
-   grep($last_stdout, /reference sequence coverage distribution/)
- end
- 
- Name "gth regression test (all distributions)"
- Keywords "gth"
- Test do
--  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -exondistri -introndistri -refseqcovdistri"
-+  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -exondistri -introndistri -refseqcovdistri"
-   grep($last_stdout, /length distribution of all exons/)
-   grep($last_stdout, /length distribution of all introns/)
-   grep($last_stdout, /reference sequence coverage distribution/)
-@@ -141,8 +141,8 @@
- Name "gth regression test (-skipindexcheck)"
- Keywords "gth"
- Test do
--  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -createindicesonly"
--  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species human -skipindexcheck | grep -v -e '^\\$' -e 'file='"
-+  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -createindicesonly"
-+  run_test "#{$bin}gth -genomic #{$testdata}gth/genomic_sequence_single_exon.fas -cdna #{$testdata}gth/cdna_sequence_single_exon.fas -species arabidopsis -skipindexcheck | grep -v -e '^\\$' -e 'file='"
-   run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gth/single_exon.out"
- end
- 
-@@ -153,7 +153,7 @@
-   FileUtils.cp("#{$testdata}gth/genomic_sequence_single_exon.fas", ".")
-   FileUtils.cp("#{$testdata}gth/cdna_sequence_single_exon.fas", ".")
-   # run gth
--  run_test "#{$bin}gth -genomic genomic_sequence_single_exon.fas -cdna cdna_sequence_single_exon.fas -species human"
-+  run_test "#{$bin}gth -genomic genomic_sequence_single_exon.fas -cdna cdna_sequence_single_exon.fas -species arabidopsis"
-   # make sure index files have been created & save mtimes
-   mtimes = {}
-   file_exists("cdna_sequence_single_exon.fas.dna.al1", mtimes)
-@@ -175,7 +175,7 @@
-   file_exists("genomic_sequence_single_exon.fas.dna.suf", mtimes)
-   file_exists("genomic_sequence_single_exon.fas.dna.tis", mtimes)
-   # run gth again
--  run_test "#{$bin}gth -genomic genomic_sequence_single_exon.fas -cdna cdna_sequence_single_exon.fas -species human"
-+  run_test "#{$bin}gth -genomic genomic_sequence_single_exon.fas -cdna cdna_sequence_single_exon.fas -species arabidopsis"
-   # make sure index files have have not changed
-   cmp_mtimes("cdna_sequence_single_exon.fas.dna.al1", mtimes)
-   cmp_mtimes("cdna_sequence_single_exon.fas.dna.des", mtimes)
-@@ -288,15 +288,16 @@
-   grep($last_stderr, /Illegal character 'x' in file/);
- end
- 
--Name "align_dna"
--Keywords "gth align_dna"
--Test do
--  run_test "#{$bin}align_dna " +
--           "#{$testdata}gth/genomic_sequence_single_exon.fas " +
--           "#{$testdata}gth/cdna_sequence_single_exon.fas"
--  run "grep -v -e '^Genomic Template:' -e 'EST Sequence:' #{$last_stdout}"
--  run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gth/align_dna.out"
--end
-+# has human BSSM (missing) hardcoded into tool
-+#Name "align_dna"
-+#Keywords "gth align_dna"
-+#Test do
-+#  run_test "#{$bin}align_dna " +
-+#           "#{$testdata}gth/genomic_sequence_single_exon.fas " +
-+#           "#{$testdata}gth/cdna_sequence_single_exon.fas"
-+#  run "grep -v -e '^Genomic Template:' -e 'EST Sequence:' #{$last_stdout}"
-+#  run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gth/align_dna.out"
-+#end
- 
- Name "gth -gff3descranges (single exon)"
- Keywords "gth gff3descranges"
-@@ -329,7 +330,7 @@
-   Name "gth (detect small initial exon)"
-   Keywords "gth gencode"
-   Test do
--    run_test "#{$bin}gth -species human -exdrop 1 -minmatchlen 12 " +
-+    run_test "#{$bin}gth -species arabidopsis -exdrop 1 -minmatchlen 12 " +
-              "-seedlength 12 -fragweightfactor 0.5 -introncutout " +
-              "-enrichchains -scoreminexonlen 1 -detectsmallexons -gff3out " +
-              "-skipalignmentout -genomic #{$gthtestdata}gencode/ENr233.fa.gz " +
-@@ -342,7 +343,7 @@
-   Name "gth (detect small terminal exon)"
-   Keywords "gth gencode"
-   Test do
--    run_test "#{$bin}gth -species human -exdrop 1 -minmatchlen 12 " +
-+    run_test "#{$bin}gth -species arabidopsis -exdrop 1 -minmatchlen 12 " +
-              "-seedlength 12 -fragweightfactor 0.5 -introncutout " +
-              "-enrichchains -scoreminexonlen 1 -detectsmallexons -gff3out " +
-              "-skipalignmentout -genomic #{$gthtestdata}gencode/ENm005.fa.gz " +
-@@ -355,7 +356,7 @@
-   Name "gth (detect small exon bug 1)"
-   Keywords "gth gencode"
-   Test do
--    run_test "#{$bin}gth -species human -exdrop 2 -minmatchlen 12 " +
-+    run_test "#{$bin}gth -species arabidopsis -exdrop 2 -minmatchlen 12 " +
-              "-maskpolyatails -noicinintroncheck " +
-              "-seedlength 12 -fragweightfactor 0.5 -introncutout " +
-              "-enrichchains -scoreminexonlen 1 -detectsmallexons -gff3out " +
-@@ -369,7 +370,7 @@
-     run_test("#{$bin}gth -fragweightfactor 0.5 -exdrop 1 -seedlength 12 " +
-              "-minmatchlen 12 -enrichchains -scoreminexonlen 1 " +
-              "-noicinintroncheck -detectsmallexons -introncutout " +
--             "-maskpolyatails -species human -genomic " +
-+             "-maskpolyatails -species arabidopsis -genomic " +
-              "#{$gthtestdata}gencode/ENm003.fa.gz " +
-              "-cdna #{$gthtestdata}gencode/detect_small_exon_bug_2_cdna.fas",
-              :maxtime => 900)
-@@ -381,7 +382,7 @@
-     run_test("#{$bin}gth -fragweightfactor 0.5 -exdrop 1 -seedlength 12 " +
-              "-minmatchlen 12 -enrichchains -scoreminexonlen 1 " +
-              "-noicinintroncheck -detectsmallexons -introncutout " +
--             "-maskpolyatails -species human -genomic " +
-+             "-maskpolyatails -species arabidopsis -genomic " +
-              "#{$gthtestdata}gencode/ENm004.fa.gz " +
-              "-cdna #{$gthtestdata}gencode/detect_small_exon_bug_3_cdna.fas",
-              :maxtime => 300)
-@@ -393,7 +394,7 @@
-     run_test("#{$bin}gth -fragweightfactor 0.5 -exdrop 1 -seedlength 12 " +
-              "-minmatchlen 12 -enrichchains -scoreminexonlen 1 " +
-              "-noicinintroncheck -detectsmallexons -introncutout " +
--             "-maskpolyatails -species human -genomic " +
-+             "-maskpolyatails -species arabidopsis -genomic " +
-              "#{$gthtestdata}gencode/ENm004.fa.gz " +
-              "-cdna #{$gthtestdata}gencode/detect_small_exon_bug_4_cdna.fas",
-              :maxtime => 300)
-@@ -405,7 +406,7 @@
-     run_test("#{$bin}gth -fragweightfactor 0.5 -exdrop 1 -seedlength 12 " +
-              "-minmatchlen 12 -enrichchains -scoreminexonlen 1 " +
-              "-noicinintroncheck -detectsmallexons -introncutout " +
--             "-maskpolyatails -species human -genomic " +
-+             "-maskpolyatails -species arabidopsis -genomic " +
-              "#{$gthtestdata}gencode/ENm014.fa.gz " +
-              "-cdna #{$gthtestdata}gencode/detect_small_exon_bug_5_cdna.fas",
-              :maxtime => 600)
---- a/testsuite/gthbssmfileinfo_include.rb
-+++ b/testsuite/gthbssmfileinfo_include.rb
-@@ -5,9 +5,10 @@
-   run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmfileinfo/arabidopsis.out"
- end
- 
--Name "gthbssmfileinfo (human)"
--Keywords "gthbssmfileinfo"
--Test do
--  run_test "#{$bin}gthbssmfileinfo human"
--  run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmfileinfo/human.out"
--end
-+# human BSSM file is missing
-+#Name "gthbssmfileinfo (human)"
-+#Keywords "gthbssmfileinfo"
-+#Test do
-+#  run_test "#{$bin}gthbssmfileinfo human"
-+#  run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmfileinfo/human.out"
-+#end
---- a/testsuite/gthbssmprint_include.rb
-+++ b/testsuite/gthbssmprint_include.rb
-@@ -5,9 +5,10 @@
-   run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmprint/arabidopsis.out"
- end
- 
--Name "gthbssmprint (human)"
--Keywords "gthbssmprint"
--Test do
--  run_test "#{$bin}gthbssmprint human.bssm"
--  run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmprint/human.out"
--end
-+# human BSSM is missing
-+#Name "gthbssmprint (human)"
-+#Keywords "gthbssmprint"
-+#Test do
-+#  run_test "#{$bin}gthbssmprint human.bssm"
-+#  run "diff --strip-trailing-cr #{$last_stdout} #{$testdata}gthbssmprint/human.out"
-+#end

debian/rules

@@ -13,8 +13,7 @@ override_dh_clean:
 
 override_dh_auto_build:
 	make licensemanager=no opt=yes 64bit=yes
-	make licensemanager=no opt=yes 64bit=yes obj/train
-	make licensemanager=no opt=yes 64bit=yes obj/gthdata
+	make licensemanager=no opt=yes 64bit=yes train
 
 override_dh_auto_install:
 	mv bin/bssm debian/bssm