[med-svn] [Git][med-team/genomethreader][master] 2 commits: create all BSSM files
Sascha Steinbiss
gitlab at salsa.debian.org
Wed Jan 1 15:50:32 GMT 2020
Sascha Steinbiss pushed to branch master at Debian Med / genomethreader
Commits:
a9650b35 by Sascha Steinbiss at 2020-01-01T15:48:20Z
create all BSSM files
- - - - -
3eb9fa48 by Sascha Steinbiss at 2020-01-01T15:50:13Z
re-enable tests requiring human.bssm
- - - - -
4 changed files:
- debian/patches/debian-gt-libs.patch
- debian/patches/series
- − debian/patches/skip-human-bssm-tests.patch
- debian/rules
Changes:
=====================================
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 $@
+
+ obj/gthdata:
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,2 @@
debian-gt-libs.patch
gt-path-fix.patch
-skip-human-bssm-tests.patch
=====================================
debian/patches/skip-human-bssm-tests.patch deleted
=====================================
@@ -1,191 +0,0 @@
---- a/testsuite/gth_include.rb
-+++ b/testsuite/gth_include.rb
-@@ -111,28 +111,28 @@
- Name "gth regression test (-exondistri)"
- Keywords "gth"
- Test do
-- run_test "#{$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
View it on GitLab: https://salsa.debian.org/med-team/genomethreader/compare/39f0fcff61e685f1a55919cd872de5baf8b537c3...3eb9fa4892fb404eb2a1bfca5cc647fabea8c561
--
View it on GitLab: https://salsa.debian.org/med-team/genomethreader/compare/39f0fcff61e685f1a55919cd872de5baf8b537c3...3eb9fa4892fb404eb2a1bfca5cc647fabea8c561
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