[med-svn] [fastaq] branch upstream updated (3817361 -> e83fffb)
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a change to branch upstream
in repository fastaq.
from 3817361 Imported Upstream version 3.10.1
new e83fffb Imported Upstream version 3.11.0
The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
pyfastaq/common.py | 2 +-
pyfastaq/runners/interleave.py | 10 +-
pyfastaq/tasks.py | 9 -
..._bad_1.fa => sequences_test_deinterleaved_no_suffixes_1.fa} | 2 +-
...aved_2.fa => sequences_test_deinterleaved_no_suffixes_2.fa} | 2 +-
...erleaved.fa => sequences_test_interleaved_with_suffixes.fa} | 0
pyfastaq/tests/tasks_test.py | 5 +
setup.py | 2 +-
8 files changed, 26 insertions(+), 6 deletions(-)
copy pyfastaq/tests/data/{sequences_test_deinterleaved_bad_1.fa =>
sequences_test_deinterleaved_no_suffixes_1.fa} (72%)
copy pyfastaq/tests/data/{sequences_test_deinterleaved_2.fa =>
sequences_test_deinterleaved_no_suffixes_2.fa} (72%)
copy pyfastaq/tests/data/{sequences_test_interleaved.fa =>
sequences_test_interleaved_with_suffixes.fa} (100%)
--
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/srv/git.debian.org/git/debian-med/fastaq.git
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[med-svn] [fastaq] 02/03: Imported Upstream version 3.11.0
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository fastaq.
commit e83fffbce611f881bbb5f63af44e71a99dc936c0
Author: Sascha Steinbiss
Date: Mon Nov 30 19:09:05 2015 +
Imported Upstream version 3.11.0
---
pyfastaq/common.py | 2 +-
pyfastaq/runners/interleave.py | 10 +-
pyfastaq/tasks.py | 9 -
.../tests/data/sequences_test_deinterleaved_no_suffixes_1.fa | 4
.../tests/data/sequences_test_deinterleaved_no_suffixes_2.fa | 4
.../tests/data/sequences_test_interleaved_with_suffixes.fa | 8
pyfastaq/tests/tasks_test.py | 5 +
setup.py | 2 +-
8 files changed, 40 insertions(+), 4 deletions(-)
diff --git a/pyfastaq/common.py b/pyfastaq/common.py
index b951f1c..aa6eaf2 100644
--- a/pyfastaq/common.py
+++ b/pyfastaq/common.py
@@ -1 +1 @@
-version = '3.10.1'
+version = '3.11.0'
diff --git a/pyfastaq/runners/interleave.py b/pyfastaq/runners/interleave.py
index 60f2782..4732820 100644
--- a/pyfastaq/runners/interleave.py
+++ b/pyfastaq/runners/interleave.py
@@ -5,8 +5,16 @@ def run(description):
parser = argparse.ArgumentParser(
description = description,
usage = 'fastaq interleave ')
+parser.add_argument('--suffix1', help='Suffix to add to all names from
infile_1 (if suffix not already present)')
+parser.add_argument('--suffix2', help='Suffix to add to all names from
infile_2 (if suffix not already present)')
parser.add_argument('infile_1', help='Name of first input file')
parser.add_argument('infile_2', help='Name of second input file')
parser.add_argument('outfile', help='Name of output file of interleaved
reads')
options = parser.parse_args()
-tasks.interleave(options.infile_1, options.infile_2, options.outfile)
+tasks.interleave(
+options.infile_1,
+options.infile_2,
+options.outfile,
+suffix1=options.suffix1,
+suffix2=options.suffix2
+)
diff --git a/pyfastaq/tasks.py b/pyfastaq/tasks.py
index e5e1b42..0085b83 100644
--- a/pyfastaq/tasks.py
+++ b/pyfastaq/tasks.py
@@ -354,7 +354,9 @@ def get_seqs_flanking_gaps(infile, outfile, left, right):
utils.close(fout)
-def interleave(infile_1, infile_2, outfile):
+def interleave(infile_1, infile_2, outfile, suffix1=None, suffix2=None):
+'''Makes interleaved file from two sequence files. If used, will append
suffix1 onto end
+of every sequence name in infile_1, unless it already ends with suffix1.
Similar for sufffix2.'''
seq_reader_1 = sequences.file_reader(infile_1)
seq_reader_2 = sequences.file_reader(infile_2)
f_out = utils.open_file_write(outfile)
@@ -366,6 +368,11 @@ def interleave(infile_1, infile_2, outfile):
utils.close(f_out)
raise Error('Error getting mate for sequence', seq_1.id, ' ...
cannot continue')
+if suffix1 is not None and not seq_1.id.endswith(suffix1):
+seq_1.id += suffix1
+if suffix2 is not None and not seq_2.id.endswith(suffix2):
+seq_2.id += suffix2
+
print(seq_1, file=f_out)
print(seq_2, file=f_out)
diff --git a/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_1.fa
b/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_1.fa
new file mode 100644
index 000..d79df33
--- /dev/null
+++ b/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_1.fa
@@ -0,0 +1,4 @@
+>1/1
+ACGTA
+>2
+A
diff --git a/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_2.fa
b/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_2.fa
new file mode 100644
index 000..dfe47cd
--- /dev/null
+++ b/pyfastaq/tests/data/sequences_test_deinterleaved_no_suffixes_2.fa
@@ -0,0 +1,4 @@
+>1
+ACGTA
+>2/2
+C
diff --git a/pyfastaq/tests/data/sequences_test_interleaved_with_suffixes.fa
b/pyfastaq/tests/data/sequences_test_interleaved_with_suffixes.fa
new file mode 100644
index 000..3692716
--- /dev/null
+++ b/pyfastaq/tests/data/sequences_test_interleaved_with_suffixes.fa
@@ -0,0 +1,8 @@
+>1/1
+ACGTA
+>1/2
+ACGTA
+>2/1
+A
+>2/2
+C
diff --git a/pyfastaq/tests/tasks_test.py b/pyfastaq/tests/tasks_test.py
index 3d157ea..e8688b9 100644
--- a/pyfastaq/tests/tasks_test.py
+++ b/pyfastaq/tests/tasks_test.py
@@ -224,6 +224,11 @@ class TestInterleave(unittest.TestCase):
tmp)
self.assertTrue(filecmp.cmp(os.path.join(data_dir,
'sequences_test_interleaved.fa'), tmp))
+tasks.interleave(os.path.join(dat
[med-svn] [fastaq] 03/03: Merge tag 'upstream/3.11.0'
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository fastaq. commit 7ce2d8cb8f190921fc8ee0804f8615eb6d67f575 Merge: bca96a6 e83fffb Author: Sascha Steinbiss Date: Mon Nov 30 19:09:06 2015 + Merge tag 'upstream/3.11.0' Upstream version 3.11.0 pyfastaq/common.py | 2 +- pyfastaq/runners/interleave.py | 10 +- pyfastaq/tasks.py | 9 - .../tests/data/sequences_test_deinterleaved_no_suffixes_1.fa | 4 .../tests/data/sequences_test_deinterleaved_no_suffixes_2.fa | 4 .../tests/data/sequences_test_interleaved_with_suffixes.fa | 8 pyfastaq/tests/tasks_test.py | 5 + setup.py | 2 +- 8 files changed, 40 insertions(+), 4 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/fastaq.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r20593 - in trunk/packages/aragorn/trunk/debian: . tests
Author: sascha-guest Date: 2015-12-01 23:39:02 + (Tue, 01 Dec 2015) New Revision: 20593 Added: trunk/packages/aragorn/trunk/debian/tests/ trunk/packages/aragorn/trunk/debian/tests/control trunk/packages/aragorn/trunk/debian/tests/testseq.fasta Modified: trunk/packages/aragorn/trunk/debian/changelog trunk/packages/aragorn/trunk/debian/control trunk/packages/aragorn/trunk/debian/rules Log: fix freeze, housekeeping Modified: trunk/packages/aragorn/trunk/debian/changelog === --- trunk/packages/aragorn/trunk/debian/changelog 2015-12-01 21:28:33 UTC (rev 20592) +++ trunk/packages/aragorn/trunk/debian/changelog 2015-12-01 23:39:02 UTC (rev 20593) @@ -1,3 +1,11 @@ +aragorn (1.2.36-5) unstable; urgency=medium + + * Fix freeze with -O2/3. + * Add simple autopkgtest. + * Bump standards version. + + -- Sascha Steinbiss Tue, 01 Dec 2015 23:32:50 + + aragorn (1.2.36-4) unstable; urgency=low * Fix hardening flags Modified: trunk/packages/aragorn/trunk/debian/control === --- trunk/packages/aragorn/trunk/debian/control 2015-12-01 21:28:33 UTC (rev 20592) +++ trunk/packages/aragorn/trunk/debian/control 2015-12-01 23:39:02 UTC (rev 20593) @@ -4,7 +4,7 @@ Maintainer: Debian Med Packaging Team Uploaders: Sascha Steinbiss Build-Depends: debhelper (>= 9) -Standards-Version: 3.9.5 +Standards-Version: 3.9.6 Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/aragorn/trunk/ Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/aragorn/trunk/ Modified: trunk/packages/aragorn/trunk/debian/rules === --- trunk/packages/aragorn/trunk/debian/rules 2015-12-01 21:28:33 UTC (rev 20592) +++ trunk/packages/aragorn/trunk/debian/rules 2015-12-01 23:39:02 UTC (rev 20593) @@ -13,10 +13,10 @@ dh $@ override_dh_auto_clean: - rm -f aragorn + rm -f aragorn override_dh_auto_build: - $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -O3 -ffast-math -finline-functions -o aragorn *.c + $(CC) $(CPPFLAGS) $(CFLAGS) $(LDFLAGS) -Os -o aragorn *.c override_dh_auto_install: mkdir -p $(DESTDIR)/usr/bin Added: trunk/packages/aragorn/trunk/debian/tests/control === --- trunk/packages/aragorn/trunk/debian/tests/control (rev 0) +++ trunk/packages/aragorn/trunk/debian/tests/control 2015-12-01 23:39:02 UTC (rev 20593) @@ -0,0 +1,3 @@ +Test-Command: aragorn debian/tests/testseq.fasta +Depends: @ + Added: trunk/packages/aragorn/trunk/debian/tests/testseq.fasta === --- trunk/packages/aragorn/trunk/debian/tests/testseq.fasta (rev 0) +++ trunk/packages/aragorn/trunk/debian/tests/testseq.fasta 2015-12-01 23:39:02 UTC (rev 20593) @@ -0,0 +1,261 @@ +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Ile-GAT-1-1 (chr.trna1-IleGAT) chr:225381-225457 (+) Ile (GAT) 77 bp Sc: 80.6 +AGGCTTGTAGCTCAGGTGGTtAGAGCGCATGATAAGGGTGAGGtCGGTGGTTCAAG +TCCACTCAGGCCTACCA +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Lys-TTT-1-2 (chr.trna10-LysTTT) chr:780843-780918 (+) Lys (TTT) 76 bp Sc: 96.2 +GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACAATCAATTGGtCGCAGGTTCGAAT +CCTGCACGACCCACCA +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Val-TAC-1-2 (chr.trna11-ValTAC) chr:781068-781143 (+) Val (TAC) 76 bp Sc: 86.6 +GGGTGATTAGCTCAGCTGGGAGAGCACCTCCCTTACAAGGAGtCGGCGGTTCGATC +CCGTCATCACCCACCA +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Lys-TTT-1-3 (chr.trna12-LysTTT) chr:781147-781222 (+) Lys (TTT) 76 bp Sc: 96.2 +GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACAATCAATTGGtCGCAGGTTCGAAT +CCTGCACGACCCACCA +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Lys-TTT-1-4 (chr.trna13-LysTTT) chr:781369-781444 (+) Lys (TTT) 76 bp Sc: 96.2 +GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACAATCAATTGGtCGCAGGTTCGAAT +CCTGCACGACCCACCA +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Lys-TTT-1-5 (chr.trna14-LysTTT) chr:781577-781652 (+) Lys (TTT) 76 bp Sc: 96.2 +GGGTCGTTAGCTCAGTTGGTAGAGCAGTTGACAATCAATTGGtCGCAGGTTCGAAT +CCTGCACGACCCACCA +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Val-GAC-2-1 (chr.trna15-ValGAC) chr:1746435-1746511 (+) Val (GAC) 77 bp Sc: 84.4 +GCGTTCATAGCTCAGTTGGTtAGAGCACCACCTTGACATGGTGtCGTTGGTTCGAG +TCCAATTGAACGCACCA +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Val-GAC-1-1 (chr.trna16-ValGAC) chr:1746516-1746592 (+) Val (GAC) 77 bp Sc: 88.6 +GCGTCCGTAGCTCAGTTGGTtAGAGCACCACCTTGACATGGTGtCGGTGGTTCGAG +TCCACTCGGACGCACCA +>Escherichia_coli_str_K-12_substr_MG1655_tRNA-Asn-GTT-1-1 (chr.trna17-AsnGTT) chr:2044549-2044624 (+) Asn (GTT) 76 bp Sc: 84.0 +TCCTCTGTAGTTCAGTCGGTAGAACGGCGGACTGTTAATCCGTATGtCACTGGTTCGAGT +CCAGTCAGAGG
[med-svn] r20594 - in trunk/packages/aragorn/tags: . 1.2.36-5/debian
Author: sascha-guest
Date: 2015-12-01 23:41:18 + (Tue, 01 Dec 2015)
New Revision: 20594
Added:
trunk/packages/aragorn/tags/1.2.36-5/
trunk/packages/aragorn/tags/1.2.36-5/debian/changelog
trunk/packages/aragorn/tags/1.2.36-5/debian/control
trunk/packages/aragorn/tags/1.2.36-5/debian/rules
trunk/packages/aragorn/tags/1.2.36-5/debian/tests/
Removed:
trunk/packages/aragorn/tags/1.2.36-5/debian/changelog
trunk/packages/aragorn/tags/1.2.36-5/debian/control
trunk/packages/aragorn/tags/1.2.36-5/debian/rules
Log:
[svn-buildpackage] Tagging aragorn 1.2.36-5
Deleted: trunk/packages/aragorn/tags/1.2.36-5/debian/changelog
===
--- trunk/packages/aragorn/trunk/debian/changelog 2015-11-27 23:44:12 UTC
(rev 20570)
+++ trunk/packages/aragorn/tags/1.2.36-5/debian/changelog 2015-12-01
23:41:18 UTC (rev 20594)
@@ -1,27 +0,0 @@
-aragorn (1.2.36-4) unstable; urgency=low
-
- * Fix hardening flags
- * Add patch description
-
- -- Sascha Steinbiss Wed, 16 Jul 2014 23:29:34 +0100
-
-aragorn (1.2.36-3) unstable; urgency=low
-
- * hardening-includes => use dpkg-buildflags instead
- * debian/control: Update vcs field
- * debian/control: Update standards version
-
- -- Sascha Steinbiss Wed, 16 Jul 2014 21:56:49 +0100
-
-aragorn (1.2.36-2) unstable; urgency=low
-
- * Adjust weekday in changelog (fixes lintian warning)
- * Fix spelling error in manpage
-
- -- Sascha Steinbiss Tue, 05 Nov 2013 15:22:41
+0100
-
-aragorn (1.2.36-1) unstable; urgency=low
-
- * Initial release (Closes: #701571)
-
- -- Sascha Steinbiss Sat, 16 Feb 2013 10:02:30
+0100
Copied: trunk/packages/aragorn/tags/1.2.36-5/debian/changelog (from rev 20593,
trunk/packages/aragorn/trunk/debian/changelog)
===
--- trunk/packages/aragorn/tags/1.2.36-5/debian/changelog
(rev 0)
+++ trunk/packages/aragorn/tags/1.2.36-5/debian/changelog 2015-12-01
23:41:18 UTC (rev 20594)
@@ -0,0 +1,35 @@
+aragorn (1.2.36-5) unstable; urgency=medium
+
+ * Fix freeze with -O2/3.
+ * Add simple autopkgtest.
+ * Bump standards version.
+
+ -- Sascha Steinbiss Tue, 01 Dec 2015 23:32:50 +
+
+aragorn (1.2.36-4) unstable; urgency=low
+
+ * Fix hardening flags
+ * Add patch description
+
+ -- Sascha Steinbiss Wed, 16 Jul 2014 23:29:34 +0100
+
+aragorn (1.2.36-3) unstable; urgency=low
+
+ * hardening-includes => use dpkg-buildflags instead
+ * debian/control: Update vcs field
+ * debian/control: Update standards version
+
+ -- Sascha Steinbiss Wed, 16 Jul 2014 21:56:49 +0100
+
+aragorn (1.2.36-2) unstable; urgency=low
+
+ * Adjust weekday in changelog (fixes lintian warning)
+ * Fix spelling error in manpage
+
+ -- Sascha Steinbiss Tue, 05 Nov 2013 15:22:41
+0100
+
+aragorn (1.2.36-1) unstable; urgency=low
+
+ * Initial release (Closes: #701571)
+
+ -- Sascha Steinbiss Sat, 16 Feb 2013 10:02:30
+0100
Deleted: trunk/packages/aragorn/tags/1.2.36-5/debian/control
===
--- trunk/packages/aragorn/trunk/debian/control 2015-11-27 23:44:12 UTC (rev
20570)
+++ trunk/packages/aragorn/tags/1.2.36-5/debian/control 2015-12-01 23:41:18 UTC
(rev 20594)
@@ -1,19 +0,0 @@
-Source: aragorn
-Section: science
-Priority: optional
-Maintainer: Debian Med Packaging Team
-Uploaders: Sascha Steinbiss
-Build-Depends: debhelper (>= 9)
-Standards-Version: 3.9.5
-Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
-Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/aragorn/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/aragorn/trunk/
-
-Package: aragorn
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Description: tRNA and tmRNA detection in nucleotide sequences
- The program employs heuristic algorithms to predict tRNA secondary structure,
- based on homology with recognized tRNA consensus sequences and ability to form
- a base-paired cloverleaf. tmRNA genes are identified using a modified version
- of the BRUCE program.
Copied: trunk/packages/aragorn/tags/1.2.36-5/debian/control (from rev 20593,
trunk/packages/aragorn/trunk/debian/control)
===
--- trunk/packages/aragorn/tags/1.2.36-5/debian/control
(rev 0)
+++ trunk/packages/aragorn/tags/1.2.36-5/debian/control 2015-12-01 23:41:18 UTC
(rev 20594)
@@ -0,0 +1,19 @@
+Source: aragorn
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team
+Uploaders: Sascha Steinbiss
+Build-Depends: debhelper (>= 9)
+Standards-Version: 3.9.6
+Homepage: http://mbio-serv2.mbioekol.lu.se/ARAGORN/
+Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/aragorn/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/aragorn/trunk/
+
+Package: aragorn
+Architecture:
[med-svn] r20634 - in trunk/packages/genometools/trunk/debian: . patches strip-nondeterminism tests
Author: sascha-guest
Date: 2015-12-04 22:47:42 + (Fri, 04 Dec 2015)
New Revision: 20634
Added:
trunk/packages/genometools/trunk/debian/patches/sort-inputs
trunk/packages/genometools/trunk/debian/patches/use-mx32
trunk/packages/genometools/trunk/debian/tests/
trunk/packages/genometools/trunk/debian/tests/build-lib
trunk/packages/genometools/trunk/debian/tests/control
trunk/packages/genometools/trunk/debian/tests/eden.gff3
trunk/packages/genometools/trunk/debian/tests/gff3validator.c
trunk/packages/genometools/trunk/debian/tests/python-lib
Modified:
trunk/packages/genometools/trunk/debian/changelog
trunk/packages/genometools/trunk/debian/patches/series
trunk/packages/genometools/trunk/debian/rules
trunk/packages/genometools/trunk/debian/strip-nondeterminism/a2x
trunk/packages/genometools/trunk/debian/strip-nondeterminism/pdflatex
Log:
fix builds, work on reproducibility, add tests
Modified: trunk/packages/genometools/trunk/debian/changelog
===
--- trunk/packages/genometools/trunk/debian/changelog 2015-12-04 18:16:43 UTC
(rev 20633)
+++ trunk/packages/genometools/trunk/debian/changelog 2015-12-04 22:47:42 UTC
(rev 20634)
@@ -1,3 +1,14 @@
+genometools (1.5.7-4) unstable; urgency=medium
+
+ * Fix builds on less popular platforms
+- Check if faketime works
+- Do no use -m32/-m64 on x32
+ * Improve reproducibility
+- sort files to compile by name
+ * Add autopkgtests
+
+ -- Sascha Steinbiss Fri, 04 Dec 2015 22:18:11 +
+
genometools (1.5.7-3) unstable; urgency=low
* d/control: remove obsolete dependency on libncurses5
Modified: trunk/packages/genometools/trunk/debian/patches/series
===
--- trunk/packages/genometools/trunk/debian/patches/series 2015-12-04
18:16:43 UTC (rev 20633)
+++ trunk/packages/genometools/trunk/debian/patches/series 2015-12-04
22:47:42 UTC (rev 20634)
@@ -3,3 +3,5 @@
remove-gitignores
fix-exports
split-manuals
+use-mx32
+sort-inputs
Added: trunk/packages/genometools/trunk/debian/patches/sort-inputs
===
--- trunk/packages/genometools/trunk/debian/patches/sort-inputs
(rev 0)
+++ trunk/packages/genometools/trunk/debian/patches/sort-inputs 2015-12-04
22:47:42 UTC (rev 20634)
@@ -0,0 +1,40 @@
+--- a/Makefile
b/Makefile
+@@ -115,7 +115,7 @@
+ EXAMPLES_SRC:=src/example.c
+ EXAMPLES_DEP:=$(EXAMPLES_SRC:%.c=obj/%.d)
+
+-TOOLS_SRC:=$(wildcard src/tools/*.c)
++TOOLS_SRC:=$(sort $(wildcard src/tools/*.c))
+ TOOLS_OBJ:=$(TOOLS_SRC:%.c=obj/%.o)
+ TOOLS_DEP:=$(TOOLS_SRC:%.c=obj/%.d)
+
+@@ -449,7 +449,7 @@
+ endif
+
+ # the GenomeTools library
+-LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard
$(DIR)/*.c))
++LIBGENOMETOOLS_PRESRC:=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard
$(DIR)/*.c)))
+ # remove AnnotationSketch-only bindings
+ LIBGENOMETOOLS_PRESRC:=$(filter-out $(CAIRO_FILTER_OUT),\
+ $(LIBGENOMETOOLS_PRESRC))
+@@ -664,7 +664,7 @@
+ @test -d $(@D) || mkdir -p $(@D)
+ @$(CC) $(EXP_LDFLAGS) $(GT_LDFLAGS) $^ -lm $(LUA_LDLIB) -o $@
+
+-API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(wildcard $(DIR)/*_api.h))
++API_HEADERS=$(foreach DIR,$(LIBGENOMETOOLS_DIRS),$(sort $(wildcard
$(DIR)/*_api.h)))
+
+ obj/public_symbols.lst: $(API_HEADERS) $(LIBGENOMETOOLS_SRC)
+ @echo '[gathering public API symbols to $@]'
+@@ -995,8 +995,8 @@
+ ABTOOLS=${shell grep -l Blaufelder src/tools/*.c}
+
+ ALLSPLINT=${addprefix obj/,${notdir ${subst .c,.splint,\
+- ${filter-out ${EISFILES},${wildcard ${CURDIR}/src/match/*.c}}\
+- ${wildcard ${CURDIR}/src/ltr/*.c}\
++ ${filter-out ${EISFILES},${sort ${wildcard
${CURDIR}/src/match/*.c}}}\
++ ${sort ${wildcard ${CURDIR}/src/ltr/*.c}}\
+ ${SKTOOLS} ${SKCORE} ${SKEXT} \
+${DWTOOLS} ${DWCORE} ${DWEXT} \
+ ${GGTOOLS} ${GGCORE} ${GGEXT} \
Added: trunk/packages/genometools/trunk/debian/patches/use-mx32
===
--- trunk/packages/genometools/trunk/debian/patches/use-mx32
(rev 0)
+++ trunk/packages/genometools/trunk/debian/patches/use-mx322015-12-04
22:47:42 UTC (rev 20634)
@@ -0,0 +1,32 @@
+--- a/Makefile
b/Makefile
+@@ -327,17 +327,19 @@
+ endif
+ endif
+
+-ifeq ($(m32),yes)
+- GT_CFLAGS += -m32
+- GT_LDFLAGS += -m32
+- SQLITE_CFLAGS += -m32
+-endif
++ifneq ($(x32),yes)
++ ifeq ($(m32),yes)
++GT_CFLAGS += -m32
++GT_LDFLAGS += -m32
++SQLITE_CFLAGS += -m32
++ endif
+
+-ifeq ($(m64),yes)
+- ifeq (,$(filter $(MACHINE),ia64 alpha mips64 mips64el aarch64))
+-GT_CFLAGS += -m64
+-GT_LDFLAGS += -m64
+-SQLITE_CFLAGS += -m64
++ ifeq (
[med-svn] r20635 - trunk/packages/genometools/trunk/debian/patches
Author: sascha-guest Date: 2015-12-04 22:48:45 + (Fri, 04 Dec 2015) New Revision: 20635 Modified: trunk/packages/genometools/trunk/debian/patches/sort-inputs trunk/packages/genometools/trunk/debian/patches/use-mx32 Log: cme fix dpkg Modified: trunk/packages/genometools/trunk/debian/patches/sort-inputs === --- trunk/packages/genometools/trunk/debian/patches/sort-inputs 2015-12-04 22:47:42 UTC (rev 20634) +++ trunk/packages/genometools/trunk/debian/patches/sort-inputs 2015-12-04 22:48:45 UTC (rev 20635) @@ -1,3 +1,4 @@ +Description: Sort inputs --- a/Makefile +++ b/Makefile @@ -115,7 +115,7 @@ Modified: trunk/packages/genometools/trunk/debian/patches/use-mx32 === --- trunk/packages/genometools/trunk/debian/patches/use-mx322015-12-04 22:47:42 UTC (rev 20634) +++ trunk/packages/genometools/trunk/debian/patches/use-mx322015-12-04 22:48:45 UTC (rev 20635) @@ -1,3 +1,4 @@ +Description: Use mx32 --- a/Makefile +++ b/Makefile @@ -327,17 +327,19 @@ ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r20636 - in trunk/packages/genometools/tags: . 1.5.7-4/debian 1.5.7-4/debian/patches 1.5.7-4/debian/strip-nondeterminism
Author: sascha-guest Date: 2015-12-04 23:06:34 + (Fri, 04 Dec 2015) New Revision: 20636 Added: trunk/packages/genometools/tags/1.5.7-4/ trunk/packages/genometools/tags/1.5.7-4/debian/changelog trunk/packages/genometools/tags/1.5.7-4/debian/patches/series trunk/packages/genometools/tags/1.5.7-4/debian/patches/sort-inputs trunk/packages/genometools/tags/1.5.7-4/debian/patches/use-mx32 trunk/packages/genometools/tags/1.5.7-4/debian/rules trunk/packages/genometools/tags/1.5.7-4/debian/strip-nondeterminism/a2x trunk/packages/genometools/tags/1.5.7-4/debian/strip-nondeterminism/pdflatex trunk/packages/genometools/tags/1.5.7-4/debian/tests/ Removed: trunk/packages/genometools/tags/1.5.7-4/debian/changelog trunk/packages/genometools/tags/1.5.7-4/debian/patches/series trunk/packages/genometools/tags/1.5.7-4/debian/rules trunk/packages/genometools/tags/1.5.7-4/debian/strip-nondeterminism/a2x trunk/packages/genometools/tags/1.5.7-4/debian/strip-nondeterminism/pdflatex Log: [svn-buildpackage] Tagging genometools 1.5.7-4 Deleted: trunk/packages/genometools/tags/1.5.7-4/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2015-12-04 18:16:43 UTC (rev 20633) +++ trunk/packages/genometools/tags/1.5.7-4/debian/changelog2015-12-04 23:06:34 UTC (rev 20636) @@ -1,193 +0,0 @@ -genometools (1.5.7-3) unstable; urgency=low - - * d/control: remove obsolete dependency on libncurses5 -Closes: #804576 - - -- Sascha Steinbiss Mon, 09 Nov 2015 19:15:29 + - -genometools (1.5.7-2) unstable; urgency=low - - * disable parallel building - - -- Sascha Steinbiss Sat, 10 Oct 2015 12:04:37 + - -genometools (1.5.7-1) unstable; urgency=low - - * New upstream release. - * d/rules: try ro improve reproducibility - - -- Sascha Steinbiss Sun, 13 Sep 2015 08:22:39 + - -genometools (1.5.6-1) unstable; urgency=low - - * New upstream release. - - -- Sascha Steinbiss Mon, 22 Jun 2015 19:26:35 + - -genometools (1.5.5-2) unstable; urgency=low - - * Disable faketime on hurd-i386 to fix FTBFS on that arch. - - -- Sascha Steinbiss Wed, 10 Jun 2015 10:03:22 + - -genometools (1.5.5-1) unstable; urgency=low - - * New upstream release. - - -- Sascha Steinbiss Sat, 06 Jun 2015 09:49:49 + - -genometools (1.5.4-2) experimental; urgency=low - - * Work towards reproducibility. - - -- Sascha Steinbiss Sun, 22 Mar 2015 08:09:07 + - -genometools (1.5.4-1) experimental; urgency=low - - * New upstream release. - - -- Sascha Steinbiss Fri, 12 Dec 2014 12:06:42 + - -genometools (1.5.3-2) unstable; urgency=low - - * Reactivate missing patch. - - -- Sascha Steinbiss Fri, 05 Sep 2014 14:23:31 +0100 - -genometools (1.5.3-1) unstable; urgency=low - - * New upstream release. - - -- Sascha Steinbiss Wed, 16 Jul 2014 20:32:19 +0100 - -genometools (1.5.2-4) unstable; urgency=low - - * Incorporate patches addressing type conversion errors (thanks to -Michael Tautschnig). -Closes: #748305 - - -- Sascha Steinbiss Sat, 24 May 2014 18:57:45 + - -genometools (1.5.2-3) unstable; urgency=low - - * Address building issues on s390x, powerpc and armhf - * Don't use -m64 for arm64 (thanks to Logan Rosen) -Closes: #748708 - * Build-depend on docbook-xsl to fix FTBFS while offline (thanks to -Logan Rosen) -Closes: #748709 - - -- Sascha Steinbiss Mon, 19 May 2014 23:06:34 + - -genometools (1.5.2-2) unstable; urgency=low - - * Split manuals into separate documents to avoid strange LaTeX build issues. - - -- Sascha Steinbiss Thu, 15 May 2014 23:23:20 + - -genometools (1.5.2-1) unstable; urgency=low - - * New upstream release. - * Remove symbols file because private symbols are exported (next upstream -version will properly control exported symbols and a new symbols file -will be created and maintained) - * Remove manpages from debian directory as they are now autogenerated on -build - * Fix some missing symbols problems - - -- Sascha Steinbiss Thu, 15 May 2014 10:51:41 + - -genometools (1.5.1-3) unstable; urgency=low - - * debian/rules - - Add basic tests to check whether cairo/pango linking works - - Clean up indices created by tests to make repeated builds possible - - Make sure bin/examples/sketch_parsed_with_* are built - - Enable compiler optimization - * debian/control - - Move libgenometools0 package into libs section - - Switch pango deps to new package - - Add ruby builddep, required for the testsuite - - -- Sascha Steinbiss Wed, 06 Nov 2013 14:28:41 +0100 - -genometools (1.5.1-2) unstable; urgency=low - - * debian/control - - Add myself to Uploaders - - cme fix dpkg-control - - Follow liblua package name transition - Closes: #728017 - - Remove depends from virtual package python-ctypes which is provided - by python - * provide symbols
[med-svn] r20637 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2015-12-05 01:52:09 + (Sat, 05 Dec 2015) New Revision: 20637 Modified: trunk/packages/genometools/trunk/debian/rules Log: use target arch Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2015-12-04 23:06:34 UTC (rev 20636) +++ trunk/packages/genometools/trunk/debian/rules 2015-12-05 01:52:09 UTC (rev 20637) @@ -7,8 +7,8 @@ export PATH := $(CURDIR)/debian/strip-nondeterminism:$(PATH) export SOURCE_DATE_EPOCH = $(shell date -d "$$(dpkg-parsechangelog -SDate)" +%s) -DARCH:=$(shell dpkg-architecture | grep DEB_BUILD_ARCH | cut -f 2 -d'=') -BITS:=$(shell dpkg-architecture | grep DEB_BUILD_ARCH_BITS | cut -f 2 -d'=') +DARCH:=$(shell dpkg-architecture | grep DEB_TARGET_ARCH | cut -f 2 -d'=') +BITS:=$(shell dpkg-architecture | grep DEB_TARGET_ARCH_BITS | cut -f 2 -d'=') ifeq ($(DARCH),x32) X32:=yes ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch master created (now 0ffb158)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository ariba. at 0ffb158 fix runtime depends This branch includes the following new commits: new a8ce3c5 Imported Upstream version 0.6.0 new 9cfc50f add debian dir new afa737f flesh out first package new 8cb3871 add manpages new 9ef44d9 fix spelling new 0ffb158 fix runtime depends The 6 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch upstream created (now a8ce3c5)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch upstream in repository ariba. at a8ce3c5 Imported Upstream version 0.6.0 No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 05/06: fix spelling
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository ariba.
commit 9ef44d9c06a8d068ef99b344c806f94e22a5f539
Author: Sascha Steinbiss
Date: Sat Dec 5 10:55:36 2015 +
fix spelling
---
debian/patches/series | 1 +
debian/patches/spelling | 12
2 files changed, 13 insertions(+)
diff --git a/debian/patches/series b/debian/patches/series
new file mode 100644
index 000..e057d52
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+spelling
diff --git a/debian/patches/spelling b/debian/patches/spelling
new file mode 100644
index 000..3ed170a
--- /dev/null
+++ b/debian/patches/spelling
@@ -0,0 +1,12 @@
+Description: Spelling
+--- a/ariba/tasks/summary.py
b/ariba/tasks/summary.py
+@@ -8,7 +8,7 @@
+ epilog = 'Files must be listed after the output file and/or the
option --fofn must be used. If both used, all files in the filename specified
by --fofn AND the files listed after the output file will be used as input. The
input report files must be in tsv format, not xls.')
+ parser.add_argument('-f', '--fofn', help='File of filenames of ariba
reports in tsv format (not xls) to be summarised. Must be used if no input
files listed after the outfile.', metavar='FILENAME')
+ parser.add_argument('--min_id', type=float, help='Minimum percent
identity cutoff to count as assembled [%(default)s]', default=90,
metavar='FLOAT')
+-parser.add_argument('--no_filter', action='store_true', help='Do not
filter rows or columns of output that are all 0 (by deafult, they are removed
from the output)')
++parser.add_argument('--no_filter', action='store_true', help='Do not
filter rows or columns of output that are all 0 (by default, they are removed
from the output)')
+ parser.add_argument('outfile', help='Name of output file. If file ends
with ".xls", then an excel spreadsheet is written. Otherwise a tsv file is
written')
+ parser.add_argument('infiles', nargs='*', help='Files to be summarised')
+ options = parser.parse_args()
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[med-svn] [ariba] 04/06: add manpages
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sascha-guest pushed a commit to branch master
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commit 8cb38711c036a61a871a45be74c1ee66e1cdc0e2
Author: Sascha Steinbiss
Date: Sat Dec 5 10:55:19 2015 +
add manpages
---
debian/ariba.manpages | 1 +
debian/control| 38 ++
debian/make_man | 12
debian/rules | 12
4 files changed, 51 insertions(+), 12 deletions(-)
diff --git a/debian/ariba.manpages b/debian/ariba.manpages
new file mode 100644
index 000..d2c65e3
--- /dev/null
+++ b/debian/ariba.manpages
@@ -0,0 +1 @@
+debian/man/*
\ No newline at end of file
diff --git a/debian/control b/debian/control
index e5a8354..90bbb5d 100644
--- a/debian/control
+++ b/debian/control
@@ -3,26 +3,40 @@ Maintainer: Debian Med Packaging Team
Section: science
Priority: optional
-Testsuite: autopkgtest
-Build-Depends: debhelper (>= 9), python3, python3-setuptools, python3-pymummer,
- python3-pysam, python3-openpyxl, fastaq (>= 3.10.0),
- python3-nose, python3-lxml
+Build-Depends: debhelper (>= 9),
+ python3,
+ python3-setuptools,
+ python3-pymummer,
+ python3-pysam,
+ python3-openpyxl,
+ fastaq (>= 3.10.0),
+ python3-nose,
+ python3-lxml,
+ help2man
Standards-Version: 3.9.6
-Homepage: https://github.com/sanger-pathogens/ariba
-Vcs-Git: git://anonscm.debian.org/debian-med/ariba.git
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ariba.git
+Vcs-Git: git://anonscm.debian.org/debian-med/ariba.git
+Homepage: https://github.com/sanger-pathogens/ariba
Package: ariba
Architecture: all
-Depends: ${misc:Depends}, ${python3:Depends}, bowtie2 (>= 2.1.0),
- cd-hit (>= 4.6), samtools (>= 1.2),
- mummer, velvet (>= 1.2.07), python3-pymummer, python3-pysam,
- python3-openpyxl, fastaq (>= 3.10.0), python3-lxml
+Depends: ${misc:Depends},
+ ${python3:Depends},
+ bowtie2 (>= 2.1.0),
+ cd-hit,
+ samtools (>= 1.2),
+ bcftools (>= 1.2)
+ mummer,
+ velvet (>= 1.2.07),
+ python3-pymummer,
+ python3-pysam,
+ python3-openpyxl,
+ fastaq (>= 3.10.0),
+ python3-lxml
Description: Antibiotic Resistance Identification By Assembly
ARIBA is a tool that identifies antibiotic resistance genes by running local
assemblies.
The input is a FASTA file of reference genes and paired sequencing reads.
ARIBA
reports which of the reference genes were found, plus detailed information on
the quality of the assemblies and any variants between the sequencing reads
- and the reference genes. bcftools (>= 1.2),
-
+ and the reference genes.
diff --git a/debian/make_man b/debian/make_man
new file mode 100755
index 000..e80eeca
--- /dev/null
+++ b/debian/make_man
@@ -0,0 +1,12 @@
+#!/usr/bin/perl
+
+my $v = `PYTHONPATH=. scripts/ariba version`;
+
+while(<>) {
+ chomp;
+ my ($name, $desc) = split(/\s{2,}/);
+ my $uname = uc($name);
+ `PYTHONPATH=. help2man -N -o ./debian/man/ariba-$name.1 -n '$desc'
--version-string='$v' 'scripts/ariba $name'`;
+ `sed -i 's/.TH ARIBA /.TH ARIBA-$uname /' debian/man/ariba-$name.1`;
+ `sed -i 's/ariba $name/ariba_$name/' debian/man/ariba-$name.1`;
+}
\ No newline at end of file
diff --git a/debian/rules b/debian/rules
index 04fc69b..afb1b23 100755
--- a/debian/rules
+++ b/debian/rules
@@ -2,6 +2,18 @@
export PYBUILD_NAME=ariba
+mandir := $(CURDIR)/debian/man
+debfolder := $(CURDIR)/debian
+
%:
dh $@ --with python3 --buildsystem=pybuild
+override_dh_installman:
+ mkdir -p $(mandir)
+ PYTHONPATH=. help2man -N -o debian/man/ariba.1 \
+ -n 'Antibiotic Resistance Identification by Assembly' \
+ --no-discard-stderr \
+ --version-string=`PYTHONPATH=. scripts/ariba version` scripts/ariba
+ sed -i 's/.SH DESCRIPTION/.SH DESCRIPTION\\n.nf/' $(mandir)/ariba.1
+ scripts/ariba 2>&1 | tail -n +13 | debian/make_man
+ dh_installman --
\ No newline at end of file
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[med-svn] [ariba] 01/01: pristine-tar data for ariba_0.6.0.orig.tar.gz
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch pristine-tar in repository ariba. commit f973dd87b863680dc28934d976beab3c03a833f4 Author: Sascha Steinbiss Date: Sat Dec 5 07:43:07 2015 + pristine-tar data for ariba_0.6.0.orig.tar.gz --- ariba_0.6.0.orig.tar.gz.delta | Bin 0 -> 7255 bytes ariba_0.6.0.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/ariba_0.6.0.orig.tar.gz.delta b/ariba_0.6.0.orig.tar.gz.delta new file mode 100644 index 000..a948419 Binary files /dev/null and b/ariba_0.6.0.orig.tar.gz.delta differ diff --git a/ariba_0.6.0.orig.tar.gz.id b/ariba_0.6.0.orig.tar.gz.id new file mode 100644 index 000..8e7a75f --- /dev/null +++ b/ariba_0.6.0.orig.tar.gz.id @@ -0,0 +1 @@ +92a18003f30fd83568fbc9d04414fc25e3a198b9 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 06/06: fix runtime depends
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository ariba.
commit 0ffb1584f554b382e944ab4b967f7e5c682341e3
Author: Sascha Steinbiss
Date: Sat Dec 5 10:57:22 2015 +
fix runtime depends
---
debian/control | 2 +-
1 file changed, 1 insertion(+), 1 deletion(-)
diff --git a/debian/control b/debian/control
index 90bbb5d..598849b 100644
--- a/debian/control
+++ b/debian/control
@@ -25,7 +25,7 @@ Depends: ${misc:Depends},
bowtie2 (>= 2.1.0),
cd-hit,
samtools (>= 1.2),
- bcftools (>= 1.2)
+ bcftools (>= 1.2),
mummer,
velvet (>= 1.2.07),
python3-pymummer,
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[med-svn] [ariba] 02/06: add debian dir
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository ariba.
commit 9cfc50f1b54ed35488b5f14fd31795088a87967b
Author: Sascha Steinbiss
Date: Sat Dec 5 07:55:31 2015 +
add debian dir
---
debian/changelog | 5 +
debian/compat| 1 +
debian/control | 26 ++
debian/rules | 8
debian/source/format | 1 +
5 files changed, 41 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 000..7a755f6
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+ariba (0.6.0-1) unstable; urgency=low
+
+ * source package automatically created by stdeb 0.8.2
+
+ -- Martin Hunt Sat, 05 Dec 2015 07:44:21 +
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 000..e9a20df
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,26 @@
+Source: ariba
+Maintainer: Debian Med Packaging Team
+Uploaders: Sascha Steinbiss
+Section: science
+Priority: optional
+X-Python3-Version: >= 3.4.2
+Testsuite: autopkgtest
+Build-Depends: debhelper (>= 9), python3, python3-setuptools
+Standards-Version: 3.9.6
+Homepage: https://github.com/sanger-pathogens/ariba
+Vcs-Git: git://anonscm.debian.org/debian-med/ariba.git
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ariba.git
+
+Package: ariba
+Architecture: all
+Depends: ${misc:Depends}, ${python3:Depends}, bowtie2 (>= 2.1.0),
+ cd-hit (>= 4.6), samtools (>= 1.2), bcftools (>= 1.2),
+ mummer (>= 3.23), velvet (>= 1.2.07)
+Description: Antibiotic Resistance Identification By Assembly
+ ARIBA is a tool that identifies antibiotic resistance genes by running local
+ assemblies.
+ The input is a FASTA file of reference genes and paired sequencing reads.
ARIBA
+ reports which of the reference genes were found, plus detailed information on
+ the quality of the assemblies and any variants between the sequencing reads
+ and the reference genes.
+
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 000..55e66bd
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,8 @@
+#!/usr/bin/make -f
+
+# This file was automatically generated by stdeb 0.8.2 at
+# Sat, 05 Dec 2015 07:44:21 +
+export PYBUILD_NAME=ariba
+%:
+ dh $@ --with python2 --buildsystem=pybuild
+
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 000..163aaf8
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
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[med-svn] [ariba] branch pristine-tar created (now f973dd8)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch pristine-tar in repository ariba. at f973dd8 pristine-tar data for ariba_0.6.0.orig.tar.gz This branch includes the following new commits: new f973dd8 pristine-tar data for ariba_0.6.0.orig.tar.gz The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 03/06: flesh out first package
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
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commit afa737f1c23c933751dc63be04fc166bcf973e1e
Author: Sascha Steinbiss
Date: Sat Dec 5 08:29:01 2015 +
flesh out first package
---
debian/changelog | 4 ++--
debian/control | 12 +++-
debian/copyright | 29 +
debian/rules | 5 ++---
debian/watch | 3 +++
5 files changed, 43 insertions(+), 10 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 7a755f6..58f9abd 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
ariba (0.6.0-1) unstable; urgency=low
- * source package automatically created by stdeb 0.8.2
+ * Initial packaging (Closes: #12345678904)
- -- Martin Hunt Sat, 05 Dec 2015 07:44:21 +
+ -- Sascha Steinbiss Sat, 05 Dec 2015 07:44:21 +
diff --git a/debian/control b/debian/control
index e9a20df..e5a8354 100644
--- a/debian/control
+++ b/debian/control
@@ -3,9 +3,10 @@ Maintainer: Debian Med Packaging Team
Section: science
Priority: optional
-X-Python3-Version: >= 3.4.2
Testsuite: autopkgtest
-Build-Depends: debhelper (>= 9), python3, python3-setuptools
+Build-Depends: debhelper (>= 9), python3, python3-setuptools, python3-pymummer,
+ python3-pysam, python3-openpyxl, fastaq (>= 3.10.0),
+ python3-nose, python3-lxml
Standards-Version: 3.9.6
Homepage: https://github.com/sanger-pathogens/ariba
Vcs-Git: git://anonscm.debian.org/debian-med/ariba.git
@@ -14,13 +15,14 @@ Vcs-Browser:
https://anonscm.debian.org/cgit/debian-med/ariba.git
Package: ariba
Architecture: all
Depends: ${misc:Depends}, ${python3:Depends}, bowtie2 (>= 2.1.0),
- cd-hit (>= 4.6), samtools (>= 1.2), bcftools (>= 1.2),
- mummer (>= 3.23), velvet (>= 1.2.07)
+ cd-hit (>= 4.6), samtools (>= 1.2),
+ mummer, velvet (>= 1.2.07), python3-pymummer, python3-pysam,
+ python3-openpyxl, fastaq (>= 3.10.0), python3-lxml
Description: Antibiotic Resistance Identification By Assembly
ARIBA is a tool that identifies antibiotic resistance genes by running local
assemblies.
The input is a FASTA file of reference genes and paired sequencing reads.
ARIBA
reports which of the reference genes were found, plus detailed information on
the quality of the assemblies and any variants between the sequencing reads
- and the reference genes.
+ and the reference genes. bcftools (>= 1.2),
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 000..7d86de7
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: ariba
+Source: https://github.com/sanger-pathogens/ariba
+
+Files: *
+Copyright: © 2014-2015 Martin Hunt
+License: GPL-3+
+
+Files: debian/*
+Copyright: © 2015 Debian Med Packaging Team
+License: GPL-3+
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+
diff --git a/debian/rules b/debian/rules
index 55e66bd..04fc69b 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,8 +1,7 @@
#!/usr/bin/make -f
-# This file was automatically generated by stdeb 0.8.2 at
-# Sat, 05 Dec 2015 07:44:21 +
export PYBUILD_NAME=ariba
+
%:
- dh $@ --with python2 --buildsystem=pybuild
+ dh $@ --with python3 --buildsystem=pybuild
diff --git a/debian/watch b/debian/watch
new file mode 100644
index 000..fbb491d
--- /dev/null
+++ b/debian/watch
@@ -0,0 +1,3 @@
+version=3
+https://github.com/sanger-pathogens/ariba/releases
.*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz)
+
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[med-svn] [ariba] annotated tag upstream/0.6.0 created (now 577f82d)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to annotated tag upstream/0.6.0 in repository ariba. at 577f82d (tag) tagging a8ce3c5113b2d265aadb5a4c91a668bdb9cf5cd0 (commit) tagged by Sascha Steinbiss on Sat Dec 5 07:43:07 2015 + - Log - Upstream version 0.6.0 Sascha Steinbiss (1): Imported Upstream version 0.6.0 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch master updated (0ffb158 -> 03d63f6)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository ariba. from 0ffb158 fix runtime depends new 66abfe4 remove unavailable tests, adjust binary names new 03d63f6 cme fix dpkg The 2 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/patches/rename_cdhit_binary| 41 +++ debian/patches/series | 2 ++ debian/patches/skip_unavailable_tests | 30 + 3 files changed, 73 insertions(+) create mode 100644 debian/patches/rename_cdhit_binary create mode 100644 debian/patches/skip_unavailable_tests -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 02/02: cme fix dpkg
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository ariba. commit 03d63f6f87637577d7e5a8908ee18a54d86eb2b0 Author: Sascha Steinbiss Date: Sat Dec 5 12:49:38 2015 + cme fix dpkg --- debian/patches/rename_cdhit_binary| 1 + debian/patches/skip_unavailable_tests | 1 + 2 files changed, 2 insertions(+) diff --git a/debian/patches/rename_cdhit_binary b/debian/patches/rename_cdhit_binary index 28078ab..a89223d 100644 --- a/debian/patches/rename_cdhit_binary +++ b/debian/patches/rename_cdhit_binary @@ -1,3 +1,4 @@ +Description: Rename_cdhit_binary --- a/ariba/cdhit.py +++ b/ariba/cdhit.py @@ -61,7 +61,7 @@ diff --git a/debian/patches/skip_unavailable_tests b/debian/patches/skip_unavailable_tests index 1831ac3..e07652f 100644 --- a/debian/patches/skip_unavailable_tests +++ b/debian/patches/skip_unavailable_tests @@ -1,3 +1,4 @@ +Description: Skip_unavailable_tests --- a/ariba/tests/cluster_test.py +++ b/ariba/tests/cluster_test.py @@ -134,7 +134,7 @@ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 01/02: remove unavailable tests, adjust binary names
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository ariba.
commit 66abfe45301b166c3e07f81c20b7380ad717719a
Author: Sascha Steinbiss
Date: Sat Dec 5 12:49:10 2015 +
remove unavailable tests, adjust binary names
---
debian/patches/rename_cdhit_binary| 40 +++
debian/patches/series | 2 ++
debian/patches/skip_unavailable_tests | 29 +
3 files changed, 71 insertions(+)
diff --git a/debian/patches/rename_cdhit_binary
b/debian/patches/rename_cdhit_binary
new file mode 100644
index 000..28078ab
--- /dev/null
+++ b/debian/patches/rename_cdhit_binary
@@ -0,0 +1,40 @@
+--- a/ariba/cdhit.py
b/ariba/cdhit.py
+@@ -61,7 +61,7 @@
+ new_to_old_name = self._enumerate_fasta(self.infile, infile_renamed)
+
+ cmd = ' '.join([
+-'cd-hit-est',
++'cdhit-est',
+ '-i', infile_renamed,
+ '-o', cdhit_fasta,
+ '-c', str(self.seq_identity_threshold),
+--- a/ariba/external_progs.py
b/ariba/external_progs.py
+@@ -16,7 +16,7 @@
+ prog_to_default = {
+ 'bcftools': 'bcftools',
+ 'bowtie2': 'bowtie2',
+-'cdhit': 'cd-hit-est',
++'cdhit': 'cdhit-est',
+ 'gapfiller': 'GapFiller.pl',
+ 'nucmer' : 'nucmer',
+ 'samtools': 'samtools',
+@@ -31,7 +31,7 @@
+ prog_to_env_var = {
+ 'bcftools': 'ARIBA_BCFTOOLS',
+ 'samtools': 'ARIBA_SAMTOOLS',
+-'spades': 'ARIBA_SPADES',
++'spades': 'ARIBA_SPADES',
+ }
+
+
+@@ -123,7 +123,7 @@
+ 'sspace',
+ 'gapfiller',
+ ]
+-
++
+ if opts.assembler == 'spades':
+ to_check.append('spades')
+ elif opts.assembler == 'velvet':
diff --git a/debian/patches/series b/debian/patches/series
index e057d52..4fa99be 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
+rename_cdhit_binary
+skip_unavailable_tests
spelling
diff --git a/debian/patches/skip_unavailable_tests
b/debian/patches/skip_unavailable_tests
new file mode 100644
index 000..1831ac3
--- /dev/null
+++ b/debian/patches/skip_unavailable_tests
@@ -0,0 +1,29 @@
+--- a/ariba/tests/cluster_test.py
b/ariba/tests/cluster_test.py
+@@ -134,7 +134,7 @@
+ clean_cluster_dir(cluster_dir)
+
+
+-def test_assemble_with_spades(self):
++def _test_assemble_with_spades(self):
+ '''test _assemble_with_spades'''
+ cluster_dir = os.path.join(data_dir,
'cluster_test_assemble_with_spades')
+ clean_cluster_dir(cluster_dir)
+@@ -145,7 +145,7 @@
+ clean_cluster_dir(cluster_dir)
+
+
+-def test_assemble_with_spades_fail(self):
++def _test_assemble_with_spades_fail(self):
+ '''test _assemble_with_spades handles spades fail'''
+ cluster_dir = os.path.join(data_dir,
'cluster_test_assemble_with_spades')
+ clean_cluster_dir(cluster_dir)
+@@ -630,7 +630,7 @@
+ clean_cluster_dir(cluster_dir)
+
+
+-def test_make_assembly_vcf(self):
++def _test_make_assembly_vcf(self):
+ '''test _make_assembly_vcf'''
+ cluster_dir = os.path.join(data_dir, 'cluster_test_generic')
+ clean_cluster_dir(cluster_dir)
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[med-svn] [ariba] 01/01: use patch
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository ariba. commit 3181da68dcd00f58cae15365ce27eb5a12db6219 Author: Sascha Steinbiss Date: Sat Dec 5 12:57:10 2015 + use patch --- debian/patches/series | 1 + 1 file changed, 1 insertion(+) diff --git a/debian/patches/series b/debian/patches/series index 4fa99be..d240e23 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,3 +1,4 @@ rename_cdhit_binary skip_unavailable_tests spelling +make_velvet_default -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 02/02: make velvet the default assembler
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository ariba.
commit df6a4815f84c2c84293841f55663f7d1c6722b4c
Author: Sascha Steinbiss
Date: Sat Dec 5 12:56:37 2015 +
make velvet the default assembler
spades is not yet packaged...
---
debian/patches/make_velvet_default | 11 +++
1 file changed, 11 insertions(+)
diff --git a/debian/patches/make_velvet_default
b/debian/patches/make_velvet_default
new file mode 100644
index 000..e2d68ca
--- /dev/null
+++ b/debian/patches/make_velvet_default
@@ -0,0 +1,11 @@
+--- a/ariba/tasks/run.py
b/ariba/tasks/run.py
+@@ -24,7 +24,7 @@
+
+ assembly_group = parser.add_argument_group('Assembly options')
+ allowed_assemblers = ['velvet', 'spades']
+-assembly_group.add_argument('--assembler', help='Assembler to use.
Available options: ' + ','.join(allowed_assemblers) + ' [%(default)s]',
choices=allowed_assemblers, default='spades', metavar='Assembler')
++assembly_group.add_argument('--assembler', help='Assembler to use.
Available options: ' + ','.join(allowed_assemblers) + ' [%(default)s]',
choices=allowed_assemblers, default='velvet', metavar='Assembler')
+ assembly_group.add_argument('--min_scaff_depth', type=int, help='Minimum
number of read pairs needed as evidence for scaffold link between two contigs.
This is also the value used for sspace -k when scaffolding [%(default)s]',
default=10, metavar='INT')
+ assembly_group.add_argument('--assembler_k', type=int, help='kmer size to
use with assembler. You can use 0 to set kmer to 2/3 of the read length.
Warning - lower kmers are usually better. [%(default)s]', metavar='INT',
default=21)
+ assembly_group.add_argument('--spades_other', help='Put options string to
be used with spades in quotes. This will NOT be sanity checked. Do not use -k
or -t: for these options you should use the ariba run options --assembler_k and
--threads [%(default)s]', default="--only-assembler", metavar="OPTIONS")
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[med-svn] [ariba] branch master updated (df6a481 -> 3181da6)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository ariba. from df6a481 make velvet the default assembler new 3181da6 use patch The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/patches/series | 1 + 1 file changed, 1 insertion(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 01/02: add README with time delay
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository ariba. commit f6b88a94413e28d4ea3b1cdc4cc2c1c6da1d2dc0 Author: Sascha Steinbiss Date: Sat Dec 5 12:51:55 2015 + add README with time delay --- debian/README.package | 1 + 1 file changed, 1 insertion(+) diff --git a/debian/README.package b/debian/README.package new file mode 100644 index 000..a748d25 --- /dev/null +++ b/debian/README.package @@ -0,0 +1 @@ +Please do not upload until bcftools has entered the archive. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch master updated (03d63f6 -> df6a481)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository ariba. from 03d63f6 cme fix dpkg new f6b88a9 add README with time delay new df6a481 make velvet the default assembler The 2 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/README.package | 1 + debian/patches/make_velvet_default | 11 +++ 2 files changed, 12 insertions(+) create mode 100644 debian/README.package create mode 100644 debian/patches/make_velvet_default -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 01/01: cme fix dpkg
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository ariba. commit 246694a80bc6d2355e7b9e46c6e97ff1cc626136 Author: Sascha Steinbiss Date: Sat Dec 5 13:01:12 2015 + cme fix dpkg --- debian/patches/make_velvet_default | 1 + 1 file changed, 1 insertion(+) diff --git a/debian/patches/make_velvet_default b/debian/patches/make_velvet_default index e2d68ca..5419cb5 100644 --- a/debian/patches/make_velvet_default +++ b/debian/patches/make_velvet_default @@ -1,3 +1,4 @@ +Description: Make_velvet_default --- a/ariba/tasks/run.py +++ b/ariba/tasks/run.py @@ -24,7 +24,7 @@ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch master updated (3181da6 -> 246694a)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository ariba. from 3181da6 use patch new 246694a cme fix dpkg The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/patches/make_velvet_default | 1 + 1 file changed, 1 insertion(+) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] 01/01: add nose tests
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository ariba. commit 922a7a70ccf1218ea5688020ff584b8bd99214bb Author: Sascha Steinbiss Date: Sat Dec 5 13:45:27 2015 + add nose tests --- debian/control | 9 - debian/rules | 6 +- 2 files changed, 13 insertions(+), 2 deletions(-) diff --git a/debian/control b/debian/control index 598849b..e18dd41 100644 --- a/debian/control +++ b/debian/control @@ -9,11 +9,18 @@ Build-Depends: debhelper (>= 9), python3-pymummer, python3-pysam, python3-openpyxl, - fastaq (>= 3.10.0), python3-nose, python3-lxml, + bowtie2 (>= 2.1.0), + cd-hit, + samtools (>= 1.2), + bcftools (>= 1.2), + mummer, + velvet (>= 1.2.07), + fastaq (>= 3.10.0), help2man Standards-Version: 3.9.6 +Testsuite: autopkgtest Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/ariba.git Vcs-Git: git://anonscm.debian.org/debian-med/ariba.git Homepage: https://github.com/sanger-pathogens/ariba diff --git a/debian/rules b/debian/rules index afb1b23..8992bd9 100755 --- a/debian/rules +++ b/debian/rules @@ -16,4 +16,8 @@ override_dh_installman: --version-string=`PYTHONPATH=. scripts/ariba version` scripts/ariba sed -i 's/.SH DESCRIPTION/.SH DESCRIPTION\\n.nf/' $(mandir)/ariba.1 scripts/ariba 2>&1 | tail -n +13 | debian/make_man - dh_installman -- \ No newline at end of file + dh_installman -- + +override_dh_auto_test: + python3 setup.py nosetests + dh_auto_test -- \ No newline at end of file -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [ariba] branch master updated (246694a -> 922a7a7)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository ariba. from 246694a cme fix dpkg new 922a7a7 add nose tests The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/control | 9 - debian/rules | 6 +- 2 files changed, 13 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/ariba.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [libtabixpp] branch master updated (58408e0 -> 457e505)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository libtabixpp. from 58408e0 Stumbled upon this one at the end of the chain of dependencies of free-bayes; just fix the build for the moment new 8af1d9f Imported Upstream version 0.0.20151117 new e17342b Merge tag 'upstream/0.0.20151117' new 457e505 flesh out package a bit The 3 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .gitmodules | 3 + ChangeLog | 593 --- Makefile | 90 +-- NEWS | 126 README| 6 - README.md | 5 + TabixReader.java | 395 -- bam_endian.h | 42 -- bedidx.c | 156 bgzf.c| 714 -- bgzf.h| 157 bgzip.c | 206 -- debian/README.license | 3 + debian/changelog | 4 +- debian/control| 32 +- debian/libtabixpp-dev.links | 1 + debian/patches/build_with_debian_htslib.patch | 58 ++ debian/patches/series | 1 + debian/rules | 22 +- example.gtf.gz| Bin 3778 -> 0 bytes example.gtf.gz.tbi| Bin 259 -> 0 bytes index.c | 998 -- khash.h | 486 - knetfile.c| 632 knetfile.h| 75 -- kseq.h| 227 -- ksort.h | 271 --- kstring.c | 165 - kstring.h | 68 -- main.c| 290 perl/MANIFEST | 8 - perl/Makefile.PL | 8 - perl/Tabix.pm | 76 -- perl/Tabix.xs | 71 -- perl/TabixIterator.pm | 41 -- perl/t/01local.t | 28 - perl/t/02remote.t | 28 - perl/typemap | 3 - python/setup.py | 55 -- python/tabixmodule.c | 408 --- python/test.py| 91 --- tabix.1 | 132 tabix.cpp | 85 ++- tabix.h | 145 tabix.hpp | 17 +- tabix.py | 87 --- tabix.tex | 121 47 files changed, 202 insertions(+), 7028 deletions(-) create mode 100644 .gitmodules delete mode 100644 ChangeLog delete mode 100644 NEWS delete mode 100644 README create mode 100644 README.md delete mode 100644 TabixReader.java delete mode 100644 bam_endian.h delete mode 100644 bedidx.c delete mode 100644 bgzf.c delete mode 100644 bgzf.h delete mode 100644 bgzip.c create mode 100644 debian/README.license create mode 100644 debian/libtabixpp-dev.links create mode 100644 debian/patches/build_with_debian_htslib.patch create mode 100644 debian/patches/series delete mode 100644 example.gtf.gz delete mode 100644 example.gtf.gz.tbi delete mode 100644 index.c delete mode 100644 khash.h delete mode 100644 knetfile.c delete mode 100644 knetfile.h delete mode 100644 kseq.h delete mode 100644 ksort.h delete mode 100644 kstring.c delete mode 100644 kstring.h delete mode 100644 main.c delete mode 100644 perl/MANIFEST delete mode 100644 perl/Makefile.PL delete mode 100644 perl/Tabix.pm delete mode 100644 perl/Tabix.xs delete mode 100644 perl/TabixIterator.pm delete mode 100644 perl/t/01local.t delete mode 100644 perl/t/02remote.t delete mode 100644 perl/typemap delete mode 100644 python/setup.py delete mode 100644 python/tabixmodule.c delete mode 100755 python/test.py delete mode 100644 tabix.1 delete mode 100644 tabix.h delete mode 100755 tabix.py delete mode 100644 tabix.tex -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.g
[med-svn] [libtabixpp] annotated tag upstream/0.0.20151117 created (now f95d18c)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to annotated tag upstream/0.0.20151117 in repository libtabixpp. at f95d18c (tag) tagging 8af1d9f1ff7610b84993e85c293b1bc7b173026c (commit) replaces upstream/0.0.20141119 tagged by Sascha Steinbiss on Sun Dec 6 12:48:03 2015 + - Log - Upstream version 0.0.20151117 Sascha Steinbiss (1): Imported Upstream version 0.0.20151117 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [libtabixpp] 01/01: pristine-tar data for libtabixpp_0.0.20151117.orig.tar.bz2
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch pristine-tar in repository libtabixpp. commit 99b410ac85e32ae81762c7c1b429055dc750f1b2 Author: Sascha Steinbiss Date: Sun Dec 6 12:48:03 2015 + pristine-tar data for libtabixpp_0.0.20151117.orig.tar.bz2 --- libtabixpp_0.0.20151117.orig.tar.bz2.delta | Bin 0 -> 848 bytes libtabixpp_0.0.20151117.orig.tar.bz2.id| 1 + 2 files changed, 1 insertion(+) diff --git a/libtabixpp_0.0.20151117.orig.tar.bz2.delta b/libtabixpp_0.0.20151117.orig.tar.bz2.delta new file mode 100644 index 000..d59dabe Binary files /dev/null and b/libtabixpp_0.0.20151117.orig.tar.bz2.delta differ diff --git a/libtabixpp_0.0.20151117.orig.tar.bz2.id b/libtabixpp_0.0.20151117.orig.tar.bz2.id new file mode 100644 index 000..a0f390c --- /dev/null +++ b/libtabixpp_0.0.20151117.orig.tar.bz2.id @@ -0,0 +1 @@ +d2a99d9d94dbad6d42cbe6c5f2d73d42b8481c7d -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [libtabixpp] branch upstream updated (f6dfb9c -> 8af1d9f)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch upstream in repository libtabixpp. from f6dfb9c Imported Upstream version 0.0.20141119 new 8af1d9f Imported Upstream version 0.0.20151117 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: .gitmodules | 3 + ChangeLog | 593 -- Makefile | 90 ++--- NEWS | 126 --- README| 6 - README.md | 5 + TabixReader.java | 395 bam_endian.h | 42 --- bedidx.c | 156 bgzf.c| 714 bgzf.h| 157 bgzip.c | 206 --- example.gtf.gz| Bin 3778 -> 0 bytes example.gtf.gz.tbi| Bin 259 -> 0 bytes index.c | 998 -- khash.h | 486 knetfile.c| 632 knetfile.h| 75 kseq.h| 227 ksort.h | 271 -- kstring.c | 165 - kstring.h | 68 main.c| 290 --- perl/MANIFEST | 8 - perl/Makefile.PL | 8 - perl/Tabix.pm | 76 perl/Tabix.xs | 71 perl/TabixIterator.pm | 41 --- perl/t/01local.t | 28 -- perl/t/02remote.t | 28 -- perl/typemap | 3 - python/setup.py | 55 --- python/tabixmodule.c | 408 - python/test.py| 91 - tabix.1 | 132 --- tabix.cpp | 85 +++-- tabix.h | 145 tabix.hpp | 17 +- tabix.py | 87 - tabix.tex | 121 -- 40 files changed, 107 insertions(+), 7002 deletions(-) create mode 100644 .gitmodules delete mode 100644 ChangeLog delete mode 100644 NEWS delete mode 100644 README create mode 100644 README.md delete mode 100644 TabixReader.java delete mode 100644 bam_endian.h delete mode 100644 bedidx.c delete mode 100644 bgzf.c delete mode 100644 bgzf.h delete mode 100644 bgzip.c delete mode 100644 example.gtf.gz delete mode 100644 example.gtf.gz.tbi delete mode 100644 index.c delete mode 100644 khash.h delete mode 100644 knetfile.c delete mode 100644 knetfile.h delete mode 100644 kseq.h delete mode 100644 ksort.h delete mode 100644 kstring.c delete mode 100644 kstring.h delete mode 100644 main.c delete mode 100644 perl/MANIFEST delete mode 100644 perl/Makefile.PL delete mode 100644 perl/Tabix.pm delete mode 100644 perl/Tabix.xs delete mode 100644 perl/TabixIterator.pm delete mode 100644 perl/t/01local.t delete mode 100644 perl/t/02remote.t delete mode 100644 perl/typemap delete mode 100644 python/setup.py delete mode 100644 python/tabixmodule.c delete mode 100755 python/test.py delete mode 100644 tabix.1 delete mode 100644 tabix.h delete mode 100755 tabix.py delete mode 100644 tabix.tex -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [libtabixpp] 02/03: Merge tag 'upstream/0.0.20151117'
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository libtabixpp. commit e17342b6b8d98ff4e05746a863294e620caf7136 Merge: 58408e0 8af1d9f Author: Sascha Steinbiss Date: Sun Dec 6 12:48:03 2015 + Merge tag 'upstream/0.0.20151117' Upstream version 0.0.20151117 .gitmodules | 3 + ChangeLog | 593 -- Makefile | 90 ++--- NEWS | 126 --- README| 6 - README.md | 5 + TabixReader.java | 395 bam_endian.h | 42 --- bedidx.c | 156 bgzf.c| 714 bgzf.h| 157 bgzip.c | 206 --- example.gtf.gz| Bin 3778 -> 0 bytes example.gtf.gz.tbi| Bin 259 -> 0 bytes index.c | 998 -- khash.h | 486 knetfile.c| 632 knetfile.h| 75 kseq.h| 227 ksort.h | 271 -- kstring.c | 165 - kstring.h | 68 main.c| 290 --- perl/MANIFEST | 8 - perl/Makefile.PL | 8 - perl/Tabix.pm | 76 perl/Tabix.xs | 71 perl/TabixIterator.pm | 41 --- perl/t/01local.t | 28 -- perl/t/02remote.t | 28 -- perl/typemap | 3 - python/setup.py | 55 --- python/tabixmodule.c | 408 - python/test.py| 91 - tabix.1 | 132 --- tabix.cpp | 85 +++-- tabix.h | 145 tabix.hpp | 17 +- tabix.py | 87 - tabix.tex | 121 -- 40 files changed, 107 insertions(+), 7002 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [libtabixpp] 03/03: flesh out package a bit
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository libtabixpp.
commit 457e505cc279d76a16b62fc7557a5ad3059f2133
Author: Sascha Steinbiss
Date: Sun Dec 6 18:59:23 2015 +
flesh out package a bit
---
debian/README.license | 3 ++
debian/changelog | 4 +-
debian/control| 32 +++
debian/libtabixpp-dev.links | 1 +
debian/patches/build_with_debian_htslib.patch | 58 +++
debian/patches/series | 1 +
debian/rules | 22 +++---
7 files changed, 95 insertions(+), 26 deletions(-)
diff --git a/debian/README.license b/debian/README.license
new file mode 100644
index 000..dde526c
--- /dev/null
+++ b/debian/README.license
@@ -0,0 +1,3 @@
+This package does not yet have a license defined by upstream.
+
+ss34, 20151206
diff --git a/debian/changelog b/debian/changelog
index 5125bdd..37d71b5 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,5 +1,5 @@
-libtabixpp (0.0.20141119-1) UNRELEASED; urgency=low
+libtabixpp (0.0.20151117-1) UNRELEASED; urgency=low
* Initial release (Closes: #)
- -- Andreas Tille Sun, 01 Feb 2015 14:56:48 +0100
+ -- Sascha Steinbiss Sun, 06 Dec 2015 18:22:18 +
diff --git a/debian/control b/debian/control
index 309e806..4a7d1b7 100644
--- a/debian/control
+++ b/debian/control
@@ -2,24 +2,40 @@ Source: libtabixpp
Section: science
Priority: optional
Maintainer: Debian Med Packaging Team
-Uploaders: Andreas Tille
+Uploaders: Andreas Tille ,
+ Sascha Steinbiss
Build-Depends: debhelper (>= 9),
- python-markdown,
+ libhts-dev,
+ libhts1,
+ zlib1g,
zlib1g-dev
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libtabixpp.git
Vcs-Git: git://anonscm.debian.org/debian-med/libtabixpp.git
Homepage: https://github.com/ekg/tabixpp
-Package: libtabixpp
+Package: libtabixpp0
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Section: libs
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
Description: C++ wrapper to tabix indexer
Tabix indexes files where some columns indicate sequence coordinates: name
- (usually a chromosme), start and stop. The input data file must be position
+ (usually a chromosome), start and stop. The input data file must be position
sorted and compressed by bgzip (provided in this package), which has a gzip
- like interface. After indexing, tabix is able to quickly retrieve data lines
by
- chromosomal coordinates. Fast data retrieval also works over network if an URI
- is given as a file name.
+ like interface. After indexing, tabix is able to quickly retrieve data lines
+ by chromosomal coordinates. Fast data retrieval also works over network if an
+ URI is given as a file name.
.
This package provides a C++ wrapper to the tabix indexer.
+
+Package: libtabixpp-dev
+Architecture: any
+Section: libdevel
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libtabixpp0 (= ${binary:Version})
+Description: C++ wrapper to tabix indexer (development files)
+ This package provides development headers and static libraries for libtabixpp,
+ a C++ interface wrapper for Tabix. Tabix is a part of htslib to index tabular
+ files in which some columns indicate sequence coordinates.
\ No newline at end of file
diff --git a/debian/libtabixpp-dev.links b/debian/libtabixpp-dev.links
new file mode 100644
index 000..35903fa
--- /dev/null
+++ b/debian/libtabixpp-dev.links
@@ -0,0 +1 @@
+usr/lib/libtabixpp.so.0 usr/lib/libtabixpp.so
\ No newline at end of file
diff --git a/debian/patches/build_with_debian_htslib.patch
b/debian/patches/build_with_debian_htslib.patch
new file mode 100644
index 000..9bcba7e
--- /dev/null
+++ b/debian/patches/build_with_debian_htslib.patch
@@ -0,0 +1,58 @@
+Description: Build_with_debian_htslib
+--- a/Makefile
b/Makefile
+@@ -3,11 +3,12 @@
+
+ CC?= gcc
+ CXX?= g++
+-CXXFLAGS?=-g -Wall -O2 -fPIC #-m64 #-arch ppc
++CXXFLAGS+= -fPIC
+ INCLUDES?=-Ihtslib
+ HTS_HEADERS?= htslib/htslib/bgzf.h htslib/htslib/tbx.h
+ HTS_LIB?= htslib/libhts.a
+ LIBPATH?= -L. -Lhtslib
++SONUMBER=0
+
+ DFLAGS= -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
+ PROG= tabix++
+@@ -18,32 +19,21 @@
+ .c.o:
+ $(CC) -c $(CXXFLAGS) $(DFLAGS) $(INCLUDES) $< -o $@
+
+-all-recur lib-recur clean-recur cleanlocal-recur install-recur:
+- @target=`echo $@ | sed s/-recur//`; \
+- wdir=`pwd`; \
+- list='$(SUBDIRS)'; for subdir in $$list; do \
+- cd $$subdir; \
+- $(MAKE) CC="$(CC)" DFLAGS="$(DFLAGS)" CXXFLAGS="$(CXXFLAGS)" \
+- INCLUDES="$(INCLUDES)" LIBPATH=&
[med-svn] [libtabixpp] branch pristine-tar updated (eda3bce -> 99b410a)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch pristine-tar in repository libtabixpp. from eda3bce pristine-tar data for libtabixpp_0.0.20141119.orig.tar.xz new 99b410a pristine-tar data for libtabixpp_0.0.20151117.orig.tar.bz2 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: libtabixpp_0.0.20151117.orig.tar.bz2.delta | Bin 0 -> 848 bytes libtabixpp_0.0.20151117.orig.tar.bz2.id| 1 + 2 files changed, 1 insertion(+) create mode 100644 libtabixpp_0.0.20151117.orig.tar.bz2.delta create mode 100644 libtabixpp_0.0.20151117.orig.tar.bz2.id -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [codonw] 02/02: version bump
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository codonw. commit 09ce48dbe5c56641a5d45cae55183a6c59f9c841 Author: Sascha Steinbiss Date: Mon Dec 7 22:52:43 2015 + version bump --- debian/changelog | 7 +++ 1 file changed, 7 insertions(+) diff --git a/debian/changelog b/debian/changelog index 61ed68e..fde0004 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,10 @@ +codonw (1.4.4-2) unstable; urgency=medium + + * Remove nondeterminism +- menu.c: Do not print compilation date and time + + -- Sascha Steinbiss Mon, 07 Dec 2015 22:51:58 + + codonw (1.4.4-1) unstable; urgency=low * Initial release (Closes: #805693) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/codonw.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [codonw] branch master updated (830ba33 -> 09ce48d)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository codonw. from 830ba33 rename links to codonw-* new e3140d3 do not print compilation date/time new 09ce48d version bump The 2 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/changelog | 7 +++ debian/patches/remove_nondeterminism | 21 + debian/patches/series| 1 + 3 files changed, 29 insertions(+) create mode 100644 debian/patches/remove_nondeterminism -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/codonw.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [codonw] 01/02: do not print compilation date/time
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository codonw.
commit e3140d330e17f0281498721e09ec94bf4cfe3a80
Author: Sascha Steinbiss
Date: Mon Dec 7 22:51:42 2015 +
do not print compilation date/time
---
debian/patches/remove_nondeterminism | 21 +
debian/patches/series| 1 +
2 files changed, 22 insertions(+)
diff --git a/debian/patches/remove_nondeterminism
b/debian/patches/remove_nondeterminism
new file mode 100644
index 000..3714118
--- /dev/null
+++ b/debian/patches/remove_nondeterminism
@@ -0,0 +1,21 @@
+Description: Remove_nondeterminism
+--- a/menu.c
b/menu.c
+@@ -1275,7 +1275,7 @@
+ /***/
+ int printinfo(void) {
+ # if defined (__FILE__ )
+- printf("\n\tSource : %s", __FILE__);
++ /* printf("\n\tSource : %s", __FILE__); */
+ # endif
+ # if defined (DEBUG)
+ printf("(Debug version)");
+@@ -1288,7 +1288,7 @@
+(int) strlen(Author) - 10, Author + 9);
+
+ #if defined(__DATE__ ) && defined(__TIME__)
+- printf("\n\tCompiled : %s %s\n", __DATE__, __TIME__);
++ /* printf("\n\tCompiled : %s %s\n", __DATE__, __TIME__); */
+ #endif
+
+ printf("\n\t---\n\n");
diff --git a/debian/patches/series b/debian/patches/series
index 0025e5f..cde3ec1 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -5,3 +5,4 @@ define_linux
spelling
helpfile_location
fix_link_name_clashes
+remove_nondeterminism
--
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[med-svn] [codonw] annotated tag debian/1.4.4-2 created (now 289b1ae)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to annotated tag debian/1.4.4-2 in repository codonw. at 289b1ae (tag) tagging 09ce48dbe5c56641a5d45cae55183a6c59f9c841 (commit) replaces upstream/1.4.4 tagged by Sascha Steinbiss on Mon Dec 7 23:12:38 2015 + - Log - codonw Debian release 1.4.4-2 Andreas Tille (3): The license text says "version 2 or later" which is not consistent with the name GPL-2 name and what I've found inside the code. Remove unused template Add help2man to Build-Depends Sascha Steinbiss (13): add debian directory d/control: adjust Vcs-* links d/changelog: add ITP bug number fix spelling errors install help file properly make different man pages for linked tools install docs add doc-base adjust template to fit main man page cosmetics rename links to codonw-* do not print compilation date/time version bump --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/codonw.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r20669 - in trunk/packages/genometools/trunk/debian: . patches tests
Author: sascha-guest
Date: 2015-12-08 00:44:48 + (Tue, 08 Dec 2015)
New Revision: 20669
Modified:
trunk/packages/genometools/trunk/debian/changelog
trunk/packages/genometools/trunk/debian/patches/adding_soname
trunk/packages/genometools/trunk/debian/patches/libbam-fix
trunk/packages/genometools/trunk/debian/tests/control
Log:
use correct shared lib in python bindings
Modified: trunk/packages/genometools/trunk/debian/changelog
===
--- trunk/packages/genometools/trunk/debian/changelog 2015-12-07 16:19:24 UTC
(rev 20668)
+++ trunk/packages/genometools/trunk/debian/changelog 2015-12-08 00:44:48 UTC
(rev 20669)
@@ -1,3 +1,10 @@
+genometools (1.5.7-5) unstable; urgency=medium
+
+ * Try to load correct renamed .so file in Python bindings
+ * Refresh patches
+
+ -- Sascha Steinbiss Tue, 08 Dec 2015 00:42:49 +
+
genometools (1.5.7-4) unstable; urgency=medium
* Fix builds on less popular platforms
Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname
===
--- trunk/packages/genometools/trunk/debian/patches/adding_soname
2015-12-07 16:19:24 UTC (rev 20668)
+++ trunk/packages/genometools/trunk/debian/patches/adding_soname
2015-12-08 00:44:48 UTC (rev 20669)
@@ -5,7 +5,7 @@
Author: Sascha Steinbiss
--- a/Makefile
+++ b/Makefile
-@@ -102,6 +102,7 @@
+@@ -105,6 +105,7 @@
SHARED_OBJ_NAME_EXT:=.so
SHARED:=-shared
endif
@@ -13,7 +13,7 @@
# compiled executables
GTMAIN_SRC:=src/gt.c src/gtr.c src/gtt.c src/interactive.c
-@@ -559,8 +560,9 @@
+@@ -585,8 +586,9 @@
@echo "[link $(@F)]"
@test -d $(@D) || mkdir -p $(@D)
@$(CC) $(EXP_LDFLAGS) $(VERSION_SCRIPT_PARAM) \
@@ -25,7 +25,7 @@
define PROGRAM_template
$(1): $(2)
-@@ -915,7 +917,8 @@
+@@ -940,7 +942,8 @@
$(RANLIB) $(prefix)/lib/libgenometools.a
endif
ifneq ($(sharedlib),no)
@@ -35,3 +35,19 @@
endif
@echo '[build config script $(@F)]'
sed -e 's!@CC@!$(CC)!' -e 's!@CFLAGS@!$(EXP_CFLAGS)!' \
+--- a/gtpython/gt/dlload.py
b/gtpython/gt/dlload.py
+@@ -26,8 +26,12 @@
+ soext = ".dylib"
+ else:
+ soext = ".so"
++try:
++ gtlib = CDLL("libgenometools" + soext)
++except OSError:
++ # Debian sets a version suffix
++ gtlib = CDLL("libgenometools" + soext + ".0")
+
+-gtlib = CDLL("libgenometools" + soext)
+ gtlib.gt_lib_init()
+ gtlib.gt_lib_reg_atexit_func()
+
Modified: trunk/packages/genometools/trunk/debian/patches/libbam-fix
===
--- trunk/packages/genometools/trunk/debian/patches/libbam-fix 2015-12-07
16:19:24 UTC (rev 20668)
+++ trunk/packages/genometools/trunk/debian/patches/libbam-fix 2015-12-08
00:44:48 UTC (rev 20669)
@@ -5,7 +5,7 @@
--- a/Makefile
+++ b/Makefile
-@@ -192,7 +192,7 @@
+@@ -195,7 +195,7 @@
# add necessary shared lib dependencies then not building them ourselves
ifeq ($(useshared),yes)
DEPLIBS:=-lbz2 -lz -lexpat -llua5.1-lpeg -llua5.1 -llua5.1-md5 \
@@ -14,7 +14,7 @@
else
DEPLIBS:=
endif
-@@ -538,6 +538,10 @@
+@@ -564,6 +564,10 @@
@$(RANLIB) $@
endif
@@ -25,7 +25,7 @@
lib/libgenometools.a: obj/gt_config.h $(LIBGENOMETOOLS_OBJ)
@echo "[link $(@F)]"
@test -d $(@D) || mkdir -p $(@D)
-@@ -556,13 +560,14 @@
+@@ -582,13 +586,14 @@
$(LIBGENOMETOOLS_OBJ) \
$(ADDITIONAL_SO_DEPS) \
$(ADDITIONAL_ZLIBS) \
@@ -41,7 +41,7 @@
define PROGRAM_template
$(1): $(2)
-@@ -575,46 +580,55 @@
+@@ -601,46 +606,55 @@
$(eval $(call PROGRAM_template, bin/gt, $(GTMAIN_OBJ) $(TOOLS_OBJ) \
lib/libgenometools.a \
Modified: trunk/packages/genometools/trunk/debian/tests/control
===
--- trunk/packages/genometools/trunk/debian/tests/control 2015-12-07
16:19:24 UTC (rev 20668)
+++ trunk/packages/genometools/trunk/debian/tests/control 2015-12-08
00:44:48 UTC (rev 20669)
@@ -1,5 +1,5 @@
Tests: build-lib
-Depends: @, libgenometools0-dev, libgenometools0, build-essential
+Depends: libgenometools0-dev, libgenometools0, build-essential
Tests: python-lib
-Depends: @, libgenometools0-dev, libgenometools0, python-genometools, python
\ No newline at end of file
+Depends: python-genometools, python
\ No newline at end of file
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[med-svn] r20670 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2015-12-08 00:47:33 + (Tue, 08 Dec 2015) New Revision: 20670 Modified: trunk/packages/genometools/trunk/debian/changelog Log: update changelog Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2015-12-08 00:44:48 UTC (rev 20669) +++ trunk/packages/genometools/trunk/debian/changelog 2015-12-08 00:47:33 UTC (rev 20670) @@ -2,6 +2,7 @@ * Try to load correct renamed .so file in Python bindings * Refresh patches + * Use DEB_TARGET_ARCH to determine build archs -- Sascha Steinbiss Tue, 08 Dec 2015 00:42:49 + @@ -19,13 +20,13 @@ genometools (1.5.7-3) unstable; urgency=low * d/control: remove obsolete dependency on libncurses5 -Closes: #804576 +Closes: #804576 -- Sascha Steinbiss Mon, 09 Nov 2015 19:15:29 + genometools (1.5.7-2) unstable; urgency=low - * disable parallel building + * disable parallel building -- Sascha Steinbiss Sat, 10 Oct 2015 12:04:37 + @@ -50,7 +51,7 @@ genometools (1.5.5-1) unstable; urgency=low - * New upstream release. + * New upstream release. -- Sascha Steinbiss Sat, 06 Jun 2015 09:49:49 + ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r20686 - trunk/packages/genometools/trunk/debian
Author: sascha-guest
Date: 2015-12-08 21:35:05 + (Tue, 08 Dec 2015)
New Revision: 20686
Modified:
trunk/packages/genometools/trunk/debian/control
Log:
remove architectures
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2015-12-08 20:11:18 UTC
(rev 20685)
+++ trunk/packages/genometools/trunk/debian/control 2015-12-08 21:35:05 UTC
(rev 20686)
@@ -35,7 +35,8 @@
Homepage: http://genometools.org
Package: genometools
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
+ alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
Depends: ${shlibs:Depends},
${misc:Depends},
genometools-common
@@ -66,7 +67,8 @@
executable and/or library.
Package: libgenometools0
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
+ alpha hppa hurd-i386 kfreebsd-amd64 kfreebsd-i386 ppc64
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -82,7 +84,8 @@
more.
Package: libgenometools0-dev
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
+ alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -107,7 +110,8 @@
access, annotation visualization, and much more.
Package: genometools-dbg
-Architecture: any
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
+ alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
Section: debug
Priority: extra
Depends: ${shlibs:Depends},
@@ -119,7 +123,7 @@
to help communication with upstream developers.
Package: python-genometools
-Architecture: any
+Architecture: all
Section: python
Depends: ${shlibs:Depends},
${misc:Depends},
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[med-svn] r20687 - trunk/packages/genometools/trunk/debian
Author: sascha-guest
Date: 2015-12-08 21:39:19 + (Tue, 08 Dec 2015)
New Revision: 20687
Modified:
trunk/packages/genometools/trunk/debian/control
Log:
add back x32
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2015-12-08 21:35:05 UTC
(rev 20686)
+++ trunk/packages/genometools/trunk/debian/control 2015-12-08 21:39:19 UTC
(rev 20687)
@@ -6,7 +6,7 @@
Priority: optional
Build-Depends: debhelper (>= 9),
liblua5.1-0-dev,
- lua-md5-dev,
+ lua-md5-dev,:
lua-filesystem-dev,
lua-lpeg-dev,
libcairo2-dev,
@@ -68,7 +68,8 @@
Package: libgenometools0
Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
- alpha hppa hurd-i386 kfreebsd-amd64 kfreebsd-i386 ppc64
+ alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
+ x32
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -86,6 +87,7 @@
Package: libgenometools0-dev
Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
+ x32
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -112,6 +114,7 @@
Package: genometools-dbg
Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
+ x32
Section: debug
Priority: extra
Depends: ${shlibs:Depends},
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[med-svn] r20688 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2015-12-08 21:39:50 + (Tue, 08 Dec 2015) New Revision: 20688 Modified: trunk/packages/genometools/trunk/debian/control Log: remove stray colon Modified: trunk/packages/genometools/trunk/debian/control === --- trunk/packages/genometools/trunk/debian/control 2015-12-08 21:39:19 UTC (rev 20687) +++ trunk/packages/genometools/trunk/debian/control 2015-12-08 21:39:50 UTC (rev 20688) @@ -6,7 +6,7 @@ Priority: optional Build-Depends: debhelper (>= 9), liblua5.1-0-dev, - lua-md5-dev,: + lua-md5-dev, lua-filesystem-dev, lua-lpeg-dev, libcairo2-dev, ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r20691 - trunk/packages/genometools/trunk/debian
Author: sascha-guest
Date: 2015-12-08 21:57:59 + (Tue, 08 Dec 2015)
New Revision: 20691
Modified:
trunk/packages/genometools/trunk/debian/control
Log:
use single line architecture definition
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2015-12-08 21:49:22 UTC
(rev 20690)
+++ trunk/packages/genometools/trunk/debian/control 2015-12-08 21:57:59 UTC
(rev 20691)
@@ -35,8 +35,7 @@
Homepage: http://genometools.org
Package: genometools
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
- alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4 x32
Depends: ${shlibs:Depends},
${misc:Depends},
genometools-common
@@ -67,9 +66,7 @@
executable and/or library.
Package: libgenometools0
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
- alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
- x32
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4 x32
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -85,9 +82,7 @@
more.
Package: libgenometools0-dev
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
- alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
- x32
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4 x32
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -112,9 +107,7 @@
access, annotation visualization, and much more.
Package: genometools-dbg
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
- alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4
- x32
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4 x32
Section: debug
Priority: extra
Depends: ${shlibs:Depends},
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[med-svn] r20692 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2015-12-09 00:54:50 + (Wed, 09 Dec 2015) New Revision: 20692 Modified: trunk/packages/genometools/trunk/debian/rules Log: extract x32 status correctly Modified: trunk/packages/genometools/trunk/debian/rules === --- trunk/packages/genometools/trunk/debian/rules 2015-12-08 21:57:59 UTC (rev 20691) +++ trunk/packages/genometools/trunk/debian/rules 2015-12-09 00:54:50 UTC (rev 20692) @@ -7,8 +7,8 @@ export PATH := $(CURDIR)/debian/strip-nondeterminism:$(PATH) export SOURCE_DATE_EPOCH = $(shell date -d "$$(dpkg-parsechangelog -SDate)" +%s) -DARCH:=$(shell dpkg-architecture | grep DEB_TARGET_ARCH | cut -f 2 -d'=') -BITS:=$(shell dpkg-architecture | grep DEB_TARGET_ARCH_BITS | cut -f 2 -d'=') +DARCH:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH= | cut -f 2 -d'=') +BITS:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH_BITS= | cut -f 2 -d'=') ifeq ($(DARCH),x32) X32:=yes ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r20693 - trunk/packages/genometools/trunk/debian
Author: sascha-guest
Date: 2015-12-09 00:55:09 + (Wed, 09 Dec 2015)
New Revision: 20693
Modified:
trunk/packages/genometools/trunk/debian/control
Log:
add back mips64el
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2015-12-09 00:54:50 UTC
(rev 20692)
+++ trunk/packages/genometools/trunk/debian/control 2015-12-09 00:55:09 UTC
(rev 20693)
@@ -35,7 +35,7 @@
Homepage: http://genometools.org
Package: genometools
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4 x32
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k mips64el kfreebsd-i386 ppc64 sh4 x32
Depends: ${shlibs:Depends},
${misc:Depends},
genometools-common
@@ -66,7 +66,7 @@
executable and/or library.
Package: libgenometools0
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4 x32
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k mips64el kfreebsd-i386 ppc64 sh4 x32
Section: libs
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -82,7 +82,7 @@
more.
Package: libgenometools0-dev
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4 x32
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k mips64el kfreebsd-i386 ppc64 sh4 x32
Section: libdevel
Depends: ${shlibs:Depends},
${misc:Depends},
@@ -107,7 +107,7 @@
access, annotation visualization, and much more.
Package: genometools-dbg
-Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k kfreebsd-i386 ppc64 sh4 x32
+Architecture: amd64 arm64 armel armhf i386 mips mipsel powerpc ppc64el s390x
alpha hppa hurd-i386 kfreebsd-amd64 m68k mips64el kfreebsd-i386 ppc64 sh4 x32
Section: debug
Priority: extra
Depends: ${shlibs:Depends},
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[med-svn] r20701 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2015-12-09 22:22:38 + (Wed, 09 Dec 2015) New Revision: 20701 Modified: trunk/packages/genometools/trunk/debian/changelog Log: version bump Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2015-12-09 21:38:08 UTC (rev 20700) +++ trunk/packages/genometools/trunk/debian/changelog 2015-12-09 22:22:38 UTC (rev 20701) @@ -1,3 +1,10 @@ +genometools (1.5.7-6) unstable; urgency=medium + + * Reintroduce mips64el which was removed my mistake. + * Fix detection of x32 build + + -- Sascha Steinbiss Wed, 09 Dec 2015 22:20:47 + + genometools (1.5.7-5) unstable; urgency=medium * Try to load correct renamed .so file in Python bindings ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r20747 - in trunk/packages/ltrsift/trunk/debian: . patches
Author: sascha-guest
Date: 2015-12-12 11:02:46 + (Sat, 12 Dec 2015)
New Revision: 20747
Modified:
trunk/packages/ltrsift/trunk/debian/control
trunk/packages/ltrsift/trunk/debian/patches/use_deterministic_file_order
Log:
cme fix dpkg
Modified: trunk/packages/ltrsift/trunk/debian/control
===
--- trunk/packages/ltrsift/trunk/debian/control 2015-12-12 10:49:56 UTC (rev
20746)
+++ trunk/packages/ltrsift/trunk/debian/control 2015-12-12 11:02:46 UTC (rev
20747)
@@ -1,20 +1,26 @@
Source: ltrsift
+Maintainer: Debian Med Packaging Team
+Uploaders: Sascha Steinbiss
Section: science
Priority: optional
-Maintainer: Debian Med Packaging Team
-Uploaders: Sascha Steinbiss
-Build-Depends: debhelper (>= 9), libgenometools0-dev (>= 1.4.2), libgtk2.0-dev,
- libglib2.0-dev
+Build-Depends: debhelper (>= 9),
+ libgenometools0-dev,
+ libgtk2.0-dev,
+ libglib2.0-dev
Standards-Version: 3.9.6
-Homepage: http://www.zbh.uni-hamburg.de/LTRsift
Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/ltrsift/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/ltrsift/trunk/
+Homepage: http://www.zbh.uni-hamburg.de/LTRsift
Package: ltrsift
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, libgenometools0 (>= 1.4.2),
- libgtk2.0-0, libglib2.0-0
-Recommends: last-align, ncbi-blast+
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libgenometools0,
+ libgtk2.0-0,
+ libglib2.0-0
+Recommends: last-align,
+ncbi-blast+
Description: postprocessing and classification of LTR retrotransposons
LTRsift is a graphical desktop tool for semi-automatic postprocessing of de
novo predicted LTR retrotransposon annotations, such as the ones generated by
@@ -26,9 +32,11 @@
Package: ltrsift-dbg
Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}, ltrsift (= ${binary:Version})
Section: debug
Priority: extra
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ ltrsift (= ${binary:Version})
Description: postprocessing and classification of LTR retrotransposons, with
debug symbols
This package contains debug information stripped from LTRsift.
You may decide to install it to help identifying issues, typically
Modified:
trunk/packages/ltrsift/trunk/debian/patches/use_deterministic_file_order
===
--- trunk/packages/ltrsift/trunk/debian/patches/use_deterministic_file_order
2015-12-12 10:49:56 UTC (rev 20746)
+++ trunk/packages/ltrsift/trunk/debian/patches/use_deterministic_file_order
2015-12-12 11:02:46 UTC (rev 20747)
@@ -1,3 +1,4 @@
+Description: Use_deterministic_file_order
--- a/Makefile
+++ b/Makefile
@@ -11,7 +11,7 @@
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[med-svn] r20746 - in trunk/packages/ltrsift/trunk/debian: . patches upstream
Author: sascha-guest Date: 2015-12-12 10:49:56 + (Sat, 12 Dec 2015) New Revision: 20746 Added: trunk/packages/ltrsift/trunk/debian/patches/use_deterministic_file_order Modified: trunk/packages/ltrsift/trunk/debian/changelog trunk/packages/ltrsift/trunk/debian/patches/build_on_64bit trunk/packages/ltrsift/trunk/debian/patches/series trunk/packages/ltrsift/trunk/debian/rules trunk/packages/ltrsift/trunk/debian/upstream/metadata Log: work on compatibility and reproducibility Modified: trunk/packages/ltrsift/trunk/debian/changelog === --- trunk/packages/ltrsift/trunk/debian/changelog 2015-12-12 07:05:13 UTC (rev 20745) +++ trunk/packages/ltrsift/trunk/debian/changelog 2015-12-12 10:49:56 UTC (rev 20746) @@ -1,26 +1,34 @@ +ltrsift (1.0.2-5) unstable; urgency=low + + * use deterministic file order for build + * fix Metadata-Screenshots + * fix build on x32 + + -- Sascha Steinbiss Sat, 12 Dec 2015 09:38:35 + + ltrsift (1.0.2-4) unstable; urgency=low * remove menu file - * remove timestamp from example .gz + * remove timestamp from example .gz -- Sascha Steinbiss Sat, 17 Oct 2015 15:24:49 + ltrsift (1.0.2-3) unstable; urgency=low - * include patches + * include patches -- Sascha Steinbiss Tue, 18 Nov 2014 20:12:45 + ltrsift (1.0.2-2) unstable; urgency=low - * fix FTBFS on 64bit archs + * fix FTBFS on 64bit archs * lintian cleanups -- Sascha Steinbiss Tue, 18 Nov 2014 19:36:18 + ltrsift (1.0.2-1) unstable; urgency=low - * New upstream release + * New upstream release -- Sascha Steinbiss Mon, 11 Mar 2013 13:39:05 +0100 Modified: trunk/packages/ltrsift/trunk/debian/patches/build_on_64bit === --- trunk/packages/ltrsift/trunk/debian/patches/build_on_64bit 2015-12-12 07:05:13 UTC (rev 20745) +++ trunk/packages/ltrsift/trunk/debian/patches/build_on_64bit 2015-12-12 10:49:56 UTC (rev 20746) @@ -9,14 +9,28 @@ ifeq ($(64bit),yes) ifneq ($(MACHINE),x86_64) m64=yes -@@ -41,7 +42,9 @@ +@@ -36,14 +37,19 @@ + STATICBIN := bin/ltrsift_static bin/ltrsift_encode_static endif - ifeq ($(m64),yes) +-ifeq ($(m32),yes) +- CFLAGS += -m32 +-endif ++ifneq ($(x32),yes) ++ ifeq ($(m32),yes) ++CFLAGS += -m32 ++ endif + +-ifeq ($(m64),yes) - CFLAGS += -m64 -+ ifeq (,$(filter $(MACHINE),arm64 ia64 alpha mips64 mips64el aarch64)) -+CFLAGS += -m64 ++ ifeq ($(m64),yes) ++ifeq (,$(filter $(MACHINE),arm64 ia64 alpha mips64 mips64el aarch64)) ++ CFLAGS += -m64 ++endif + endif endif ++ ifneq ($(errorcheck),no) + CFLAGS += -Werror + endif Modified: trunk/packages/ltrsift/trunk/debian/patches/series === --- trunk/packages/ltrsift/trunk/debian/patches/series 2015-12-12 07:05:13 UTC (rev 20745) +++ trunk/packages/ltrsift/trunk/debian/patches/series 2015-12-12 10:49:56 UTC (rev 20746) @@ -1 +1,2 @@ build_on_64bit +use_deterministic_file_order Added: trunk/packages/ltrsift/trunk/debian/patches/use_deterministic_file_order === --- trunk/packages/ltrsift/trunk/debian/patches/use_deterministic_file_order (rev 0) +++ trunk/packages/ltrsift/trunk/debian/patches/use_deterministic_file_order 2015-12-12 10:49:56 UTC (rev 20746) @@ -0,0 +1,11 @@ +--- a/Makefile b/Makefile +@@ -11,7 +11,7 @@ + GT_FLAGS_STATIC := $(GT_FLAGS) `pkg-config --cflags --libs pango pangocairo` + GT_FLAGS += -lgenometools -L$(gt_prefix)/lib $(LDFLAGS) + GTK_FLAGS = `pkg-config --cflags --libs gtk+-2.0 gthread-2.0` +-SOURCES := $(wildcard src/*.c) ++SOURCES := $(sort $(wildcard src/*.c)) + OBJECTS := $(filter-out obj/src/ltrsift.o obj/src/ltrsift_encode.o, $(SOURCES:%.c=obj/%.o)) + + # system specific stuff (concerning 64bit compilation) Modified: trunk/packages/ltrsift/trunk/debian/rules === --- trunk/packages/ltrsift/trunk/debian/rules 2015-12-12 07:05:13 UTC (rev 20745) +++ trunk/packages/ltrsift/trunk/debian/rules 2015-12-12 10:49:56 UTC (rev 20746) @@ -5,7 +5,15 @@ export DESTDIR=$(CURDIR)/debian/tmp export gt_prefix=/usr -BITS:=$(shell dpkg-architecture | grep DEB_BUILD_ARCH_BITS | cut -f 2 -d'=') +DARCH:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH= | cut -f 2 -d'=') +BITS:=$(shell dpkg-architecture | fgrep DEB_TARGET_ARCH_BITS= | cut -f 2 -d'=') + +ifeq ($(DARCH),x32) + X32:=yes +else + X32:=no +endif + ifeq ($(BITS),64) 64BIT:=yes else @@ -19,10 +27,10 @@ $(MAKE) cleanup override_dh_auto_build: - dh_auto_build --parallel -- 64bit=$(64BIT) errorcheck=no + dh_auto_build --parallel -- x32=$(X32) 64bit=$(64BIT) errorcheck=no override_dh_auto_test: - #dh_au
[med-svn] r20748 - trunk/packages/genometools/trunk/debian
Author: sascha-guest Date: 2015-12-12 19:15:59 + (Sat, 12 Dec 2015) New Revision: 20748 Modified: trunk/packages/genometools/trunk/debian/changelog Log: UNRELEASED -> unstable Modified: trunk/packages/genometools/trunk/debian/changelog === --- trunk/packages/genometools/trunk/debian/changelog 2015-12-12 11:02:46 UTC (rev 20747) +++ trunk/packages/genometools/trunk/debian/changelog 2015-12-12 19:15:59 UTC (rev 20748) @@ -1,3 +1,9 @@ +genometools (1.5.7-7) unstable; urgency=medium + + * build API documentation reproducibly + + -- Sascha Steinbiss Sat, 12 Dec 2015 19:13:40 + + genometools (1.5.7-6) unstable; urgency=medium * Reintroduce mips64el which was removed my mistake. ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] r20749 - in trunk/packages/genometools/trunk/debian: . patches
Author: sascha-guest
Date: 2015-12-12 19:16:41 + (Sat, 12 Dec 2015)
New Revision: 20749
Added:
trunk/packages/genometools/trunk/debian/patches/remove_png_timestamps
Modified:
trunk/packages/genometools/trunk/debian/control
trunk/packages/genometools/trunk/debian/patches/adding_soname
trunk/packages/genometools/trunk/debian/patches/fix-exports
trunk/packages/genometools/trunk/debian/patches/series
trunk/packages/genometools/trunk/debian/patches/sort-inputs
Log:
work on reproducibility of API documentation building
Modified: trunk/packages/genometools/trunk/debian/control
===
--- trunk/packages/genometools/trunk/debian/control 2015-12-12 19:15:59 UTC
(rev 20748)
+++ trunk/packages/genometools/trunk/debian/control 2015-12-12 19:16:41 UTC
(rev 20749)
@@ -28,7 +28,8 @@
xsltproc,
ruby,
docbook-xsl,
- faketime
+ faketime,
+ imagemagick
Standards-Version: 3.9.6
Vcs-Browser:
http://anonscm.debian.org/viewvc/debian-med/trunk/packages/genometools/trunk/
Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/genometools/trunk/
Modified: trunk/packages/genometools/trunk/debian/patches/adding_soname
===
--- trunk/packages/genometools/trunk/debian/patches/adding_soname
2015-12-12 19:15:59 UTC (rev 20748)
+++ trunk/packages/genometools/trunk/debian/patches/adding_soname
2015-12-12 19:16:41 UTC (rev 20749)
@@ -25,7 +25,7 @@
define PROGRAM_template
$(1): $(2)
-@@ -940,7 +942,8 @@
+@@ -944,7 +946,8 @@
$(RANLIB) $(prefix)/lib/libgenometools.a
endif
ifneq ($(sharedlib),no)
Modified: trunk/packages/genometools/trunk/debian/patches/fix-exports
===
--- trunk/packages/genometools/trunk/debian/patches/fix-exports 2015-12-12
19:15:59 UTC (rev 20748)
+++ trunk/packages/genometools/trunk/debian/patches/fix-exports 2015-12-12
19:16:41 UTC (rev 20749)
@@ -5,7 +5,7 @@
@@ -113,6 +113,12 @@
gt_option_parser_register_hook(op, determine_outfp, ofi);
}
-
+
+/* wrapper for ABI compatibility */
+void gt_output_file_register_options(GtOutputFileInfo *ofi,
+ GtOptionParser *op, GtFile **outfp) {
Added: trunk/packages/genometools/trunk/debian/patches/remove_png_timestamps
===
--- trunk/packages/genometools/trunk/debian/patches/remove_png_timestamps
(rev 0)
+++ trunk/packages/genometools/trunk/debian/patches/remove_png_timestamps
2015-12-12 19:16:41 UTC (rev 20749)
@@ -0,0 +1,61 @@
+Description: Remove_png_timestamps
+--- a/Makefile
b/Makefile
+@@ -865,6 +865,10 @@
+ bin/examples/sketch_constructed gtdata/sketch/default.style \
+ www/genometools.org/htdocs/images/constructed.png
+ endif
++ mogrify -format jpg +set date:create +set date:modify \
++-define png:exclude-chunk=time \
++www/genometools.org/htdocs/images/*.png && \
++rm -rf www/genometools.org/htdocs/images/*.png
+ sed -nf scripts/incl.sed \
+ www/genometools.org/htdocs/examples_tmpl.html | \
+ sed 'N;N;s/\n//' > /tmp/tmp.sed. && \
+--- a/doc/manuals/annotationsketch.tex
b/doc/manuals/annotationsketch.tex
+@@ -240,7 +240,7 @@
+ We will call the second part (after the ``\texttt{|}'') of these track titles
\emph{track identifier strings} in the rest of this document.
+
+ \begin{figure}[ht]
+-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect.png}}
++\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_nocollapse_noselect}}
+ \caption{Default AnnotationSketch output for a simple GFF3 file with simple
\emph{exon}$\to$\emph{mRNA} collapsing.}
+ \label{tsexample1}
+ \end{figure}
+@@ -270,7 +270,7 @@
+ Using this track selector function would produce the desired result of
separate tracks for the \emph{mRNA} features for each strand (see Fig.
\ref{tsexample2}).
+
+ \begin{figure}[ht]
+-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect.png}}
++\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_strandselect}}
+ \caption{AnnotationSketch output with \texttt{strand\_track\_se\-lector()}
track selector function. This image now shows separate tracks for plus and
minus strand features.}
+ \label{tsexample2}
+ \end{figure}
+@@ -312,7 +312,7 @@
+ This code results in the image shown in Fig.~\ref{tsexample3} :
+
+ \begin{figure}[ht]
+-\centering{\includegraphics[width=.7\textwidth]{../../www/genometools.org/htdocs/images/example_filterselect.png}}
++\centering{\includegraphics[width=.7\textwidth]{../../www/
[med-svn] [snpomatic] branch master created (now 849e1c8)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository snpomatic. at 849e1c8 add ITP# This branch includes the following new commits: new 662e5b7 Imported Upstream version 0.0.20151015 new dc7c4d9 add debian dir new f08bc83 override install rule new c9e917f add manpage sources new 0bdbb81 man page building new 5744ec6 correct package name for ronn new b91e82f fix man page building new d0e4a22 add patches new 5801feb add hardening, build all binaries new e57d341 add documentation new 21c5c71 complete hardening new 413cbc5 cme fix dpkg new 5beff3c adjust Vcs-Browser new 150c100 add upstream metadata reference new 849e1c8 add ITP# The 15 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 02/15: add debian dir
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository snpomatic.
commit dc7c4d927bafee104de56cb673a8576118f28999
Author: Sascha Steinbiss
Date: Sat Dec 12 20:26:37 2015 +
add debian dir
---
debian/changelog | 5 +
debian/compat| 1 +
debian/control | 25 +
debian/copyright | 28
debian/rules | 9 +
debian/source/format | 1 +
6 files changed, 69 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 000..0848f56
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+snpomatic (0.0.20151015-1) unstable; urgency=medium
+
+ * Initial release. (Closes: #XX)
+
+ -- Sascha Steinbiss Sat, 12 Dec 2015 20:17:45 +
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 000..5da0837
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,25 @@
+Source: snpomatic
+Maintainer: Debian Med Packaging Team
+Uploaders: Sascha Steinbiss
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ help2man
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastaq.git
+Vcs-Git: git://anonscm.debian.org/debian-med/snpomatic.git
+Homepage: https://github.com/magnusmanske/snpomatic
+
+Package: snpomatic
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends}
+Description: fast, stringent short-read mapping software
+ High throughput sequencing technologies generate large amounts of short reads.
+ Mapping these to a reference sequence consumes large amounts of processing
+ time and memory, and read mapping errors can lead to noisy or incorrect
+ alignments.
+ .
+ SNP-o-matic is a fast, stringent short-read mapping software. It supports a
+ multitude of output types and formats, for uses in filtering reads,
alignments,
+ sequence-based genotyping calls, assisted reassembly of contigs etc.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 000..e38d9f3
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,28 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: snpomatic
+Source: https://github.com/magnusmanske/snpomatic
+
+Files: *
+Copyright: © 2009-2015 Magnus Manske
+License: GPL-3+
+
+Files: debian/*
+Copyright: © 2015 Sascha Steinbiss
+License: GPL-3+
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/rules b/debian/rules
new file mode 100755
index 000..18d6d31
--- /dev/null
+++ b/debian/rules
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+export DH_VERBOSE := 1
+
+mandir := $(CURDIR)/debian/man
+debfolder := $(CURDIR)/debian
+
+%:
+ dh $@
\ No newline at end of file
diff --git a/debian/source/format b/debian/source/format
new file mode 100644
index 000..46ebe02
--- /dev/null
+++ b/debian/source/format
@@ -0,0 +1 @@
+3.0 (quilt)
\ No newline at end of file
--
Alioth's /usr/local/bin/git-commit-notice on
/srv/git.debian.org/git/debian-med/snpomatic.git
___
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[med-svn] [snpomatic] 03/15: override install rule
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit f08bc8316d72555d46fd52d1c3a122cb2a9f7f69 Author: Sascha Steinbiss Date: Sat Dec 12 20:33:45 2015 + override install rule --- debian/rules | 6 +- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/debian/rules b/debian/rules index 18d6d31..7564f78 100755 --- a/debian/rules +++ b/debian/rules @@ -6,4 +6,8 @@ mandir := $(CURDIR)/debian/man debfolder := $(CURDIR)/debian %: - dh $@ \ No newline at end of file + dh $@ + +override_dh_auto_install: + mkdir -p $(debfolder)/snpomatic/usr/bin + cp findknownsnps $(debfolder)/snpomatic/usr/bin \ No newline at end of file -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 04/15: add manpage sources
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit c9e917f53a57ea14e214dd5f24a5b4f394133cdf Author: Sascha Steinbiss Date: Sat Dec 12 21:09:00 2015 + add manpage sources --- debian/findknownsnps.1.ronn | 167 debian/snpomatic.manpages | 1 + 2 files changed, 168 insertions(+) diff --git a/debian/findknownsnps.1.ronn b/debian/findknownsnps.1.ronn new file mode 100644 index 000..43e6507 --- /dev/null +++ b/debian/findknownsnps.1.ronn @@ -0,0 +1,167 @@ +findknownsnps(1) -- main executable for snpomatic += + +## SYNOPSIS + +`findknownsnps` + +## DESCRIPTION + +findknownsnps is the main executable for the **snpomatic** software. + +## OPTIONS + +These options control whether output is written to file(s), standard output, or +directly to a man pager. + + * `--genome=GENOME_FILE`: +FASTA file with chromosomes (mandatory) + + * `--fasta=FASTA_FILE`: +FASTA file with Solexa reads (mandatory, except when --fastq or --index is +used) + + * `--fasta=FASTA_FILE`: +FASTA file with Solexa reads (mandatory, except when --fastq or --index is +used) + + * `--fastq=FASTQ_FILE`: +FASTQ file with Solexa reads (mandatory, except when --fasta or --index is +used) + + * `--fastq2=FASTQ_FILE2`: +FASTQ file with Solexa reads (optional; read mate) + + * `--nono=FILENAME`: +File with list of read names (!) to ignore (optional) + + * `--regions=REGION_FILE`: +Region file for finding new SNPs (optional) [DEPRECATED] + + * `--snps=SNP_FILE`: +Simple SNP file (optional) + + * `--gff=GFF_FILE`: +GFF file with SNPs (optional) + + * `--uniqueness=FILE`: +Output a uniqueness data file for the reference; no Solexa reads needed; +implies `--noshortcuts` (optional) + + * `--pileup=FILE`: +Outputs complete pileup into that file (optional) + + * `--cigar=FILE`: +Outputs alignment in CIGAR format (optional) + + * `--gffout=FILE`: +Outputs reads in GFF format (optional) + + * `--coverage=FILENAME`: +Outputs (high depth) coverage data (optional) + + * `--wobble=FILENAME`: +Outputs a list of possible variations (optional; paired reads only) +[UNDER CONSTRUCTION] + + * `--fragmentplot=FILENAME`: +Outputs a plot of fragment size distribution to a file (optional) + + * `--snpsinreads=FILENAME`: +Outputs a list of reads containing known SNPs to a file (optional) + + * `--indelplot=FILENAME`: +Outputs indel data to a file (optional) + + * `--inversions=FILENAME`: +For paired reads, writes read matches indicating inversions into a file (optional) + + * `--faceaway=FILENAME`: +For paired reads, writes read matches that "face away" from each other into a file (optional) + + * `--sqlite=FILENAME`: +Creates a sqlite text file with alignment data [EXPERIMENTAL] (optional) + + * `--sam=FILENAME`: +Creates a SAM alignment file (optional) + + * `--spancontigs=FILENAME`: +Outputs read pairs where "half" reads map uniquely to different +contigs (optional) + + * `--bins=FILE_PREFIX`: +Outputs no-match, single-match and multi-match Solexa reads into prefixed +files (optional) + + * `--binmask=MASK`: +Mask of 1s and 0s to turn off individual bins. Order: No match, single +match, multi-match, IUPAC. Example: 0100 creates only single-match bin. +(optional; default:) + + * `--pair=NUMBER`: +For paired reads, the length of the first part of the read (mandatory for +paired reads) + + * `--fragment=NUMBER`: +For paired reads, the average fragment length (mandatory for paired reads) + + * `--variance=NUMBER`: +For paired reads, the variance of the fragment length to either side (optional; default: 1/4 of fragment size) + + * `--wobblemax=NUMBER`: +Maximum number of mismatches for wobble (optional; default 2; see --wobble) + + * `--mspi=NUMBER`: +Maximum number of SNPs per chromosomal index (optional; default:8) + + * `--index=FILENAME`: +Index filename (index will be created if it does not exist; optional) + + * `--noshortcuts`: +Will process all chrososomal regions, even those with lots'o'repeats (optional; +no value) + + * `--snpsonly`: +Only lists found SNPs in the pileup (optional; no value) + + * `--chromosome=NAME`: +Discards all chromosomes but NAME prior to run (optional) + + * `--index_from=NUMBER`: +Starts indexing at this position on all chromosomes (optional) + + * `--index_to=NUMBER`: +Stops indexing at this position on all chromosomes (optional) + + * `--chop=NUMBER`: +For paired reads, if one but not the other matches, shorten the other by +`NUMBER` bases (optional) + + * `--index1=NUMBER` : +Length of internal index 1 (optional; default:10) + + * `--index2=NUMBER`: +Length
[med-svn] [snpomatic] 05/15: man page building
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 0bdbb8174c0ca36f32f87161c1fb7fc8a5ecba45 Author: Sascha Steinbiss Date: Sat Dec 12 21:10:03 2015 + man page building --- debian/control | 2 +- debian/rules | 9 - 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/debian/control b/debian/control index 5da0837..27723e7 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,7 @@ Uploaders: Sascha Steinbiss Section: science Priority: optional Build-Depends: debhelper (>= 9), - help2man + ronn Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastaq.git Vcs-Git: git://anonscm.debian.org/debian-med/snpomatic.git diff --git a/debian/rules b/debian/rules index 7564f78..ed62603 100755 --- a/debian/rules +++ b/debian/rules @@ -8,6 +8,13 @@ debfolder := $(CURDIR)/debian %: dh $@ +override_dh_auto_clean: + rm -rf debian/findknownsnps.1 + rm -rf debian/findknownsnps.1.html + override_dh_auto_install: mkdir -p $(debfolder)/snpomatic/usr/bin - cp findknownsnps $(debfolder)/snpomatic/usr/bin \ No newline at end of file + cp findknownsnps $(debfolder)/snpomatic/usr/bin + +override_dh_auto_installman: + ronn debian/findknownsnps.1.ronn -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 06/15: correct package name for ronn
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 5744ec6cf1d52153e3146970574448b703b816a8 Author: Sascha Steinbiss Date: Sat Dec 12 21:10:45 2015 + correct package name for ronn --- debian/control | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/control b/debian/control index 27723e7..4beb9aa 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,7 @@ Uploaders: Sascha Steinbiss Section: science Priority: optional Build-Depends: debhelper (>= 9), - ronn + ruby-ronn Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastaq.git Vcs-Git: git://anonscm.debian.org/debian-med/snpomatic.git -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 11/15: complete hardening
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 21c5c713d4b9fcae628b6e4de6ed24cd8413b105 Author: Sascha Steinbiss Date: Sat Dec 12 21:39:19 2015 + complete hardening --- debian/patches/hardening | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/patches/hardening b/debian/patches/hardening index 3aea285..cdc62f5 100644 --- a/debian/patches/hardening +++ b/debian/patches/hardening @@ -21,7 +21,7 @@ ungap: src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o - $(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@ -+ $(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LIBS) $^ -o $@ ++ $(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@ .cpp.o: - $(CXX) $(CXXFLAGS) -c $< -o $@ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 09/15: add hardening, build all binaries
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository snpomatic.
commit 5801febdd11d5a181efdfa24e7c86ea0b4612c73
Author: Sascha Steinbiss
Date: Sat Dec 12 21:27:57 2015 +
add hardening, build all binaries
---
debian/patches/build_all_binaries | 2 +-
debian/patches/fix_ungap | 134 ++
debian/patches/hardening | 12 ++--
debian/patches/series | 1 +
debian/rules | 4 ++
5 files changed, 146 insertions(+), 7 deletions(-)
diff --git a/debian/patches/build_all_binaries
b/debian/patches/build_all_binaries
index 83ed7d5..97b9ff0 100644
--- a/debian/patches/build_all_binaries
+++ b/debian/patches/build_all_binaries
@@ -8,4 +8,4 @@
+all: findknownsnps reassemble variety mapcontigs ungap
findknownsnps: src/findknownsnps.o src/global_functions.o src/TChromosome.o
src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o
- $(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
+ $(CXX) $(CFLAGS) $(CPPFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@
diff --git a/debian/patches/fix_ungap b/debian/patches/fix_ungap
new file mode 100644
index 000..baa91e6
--- /dev/null
+++ b/debian/patches/fix_ungap
@@ -0,0 +1,134 @@
+--- a/src/ungap.cpp
b/src/ungap.cpp
+@@ -17,7 +17,7 @@
+ TRegionScan ( chrvec &_chrs , TChromosomalIndices &_index ) :
TChromosomeAlign ( _chrs , _index ) {} ;
+ void assemble_leftovers ( int cnt ) ;
+ vector leftovers ;
+-
++
+ protected:
+ virtual uint align_solexa_paired_read ( const string &name , const
string &sequence , string quality , uint read_length_1 , uint fragment_length ,
uint range ) ;
+ int get_overlap ( TLeftovers &l1 , TLeftovers &l2 ) ;
+@@ -52,7 +52,7 @@
+ /*
+ string s1 = l1.seq.substr ( o , l1.seq.length() - o ) ;
+ string s2 = l2.seq ;
+-
++
+ if ( s1.length() < s2.length() ) s2 = s2.substr ( 0 , s1.length() ) ;
+ else if ( s2.length() < s1.length() ) s1 = s1.substr ( 0 , s2.length()
) ;
+ if ( s1 != s2 ) return -1 ; // No match
+@@ -63,9 +63,9 @@
+ void TRegionScan::assemble_leftovers ( int cnt ) {
+ uint a , b ;
+ vector lo ;
+-
++
+ cout << "Assembling, depth " << cnt << endl ;
+-
++
+ for ( a = 0 ; a+1 < leftovers.size() ; a++ ) {
+ for ( b = a+1 ; b < leftovers.size() ; b++ ) {
+ int o = get_overlap ( leftovers[a] , leftovers[b] ) ;
+@@ -77,30 +77,30 @@
+ }
+ }
+ if ( cnt <= 0 ) return ;
+-
++
+ for ( a = 0 ; a < leftovers.size() ; a++ ) {
+ if ( leftovers[a].used ) continue ;
+ lo.push_back ( leftovers[a] ) ;
+ }
+-
++
+ // Add unique sequences as new source set
+ sort ( lo.begin() , lo.end() ) ;
+ leftovers.clear() ;
+ for ( a = 0 ; a < lo.size() ; a++ ) {
+ if ( a == 0 || lo[a-1].seq != lo[a].seq ) leftovers.push_back (
lo[a] ) ;
+ }
+-
++
+ assemble_leftovers ( cnt - 1 ) ;
+ }
+
+ uint TRegionScan::align_solexa_paired_read ( const string &name , const
string &sequence , string quality , uint read_length_1 , uint fragment_length ,
uint range ) {
+ string seq1 = sequence.substr ( 0 , read_length_1 ) ;
+ string seq2 = sequence.substr ( read_length_1 , sequence.length() -
read_length_1 ) ;
+-
++
+ while ( quality.length() < sequence.length() ) quality += (char) 33+30 ;
+ string qual1 = quality.substr ( 0 , read_length_1 ) ;
+ string qual2 = quality.substr ( read_length_1 , sequence.length() -
read_length_1 ) ;
+-
++
+ pwi_vector res1 , res2 ;
+ get_align_solexa_read ( seq1.c_str() , res1 ) ;
+ get_align_solexa_read ( seq2.c_str() , res2 ) ;
+@@ -112,7 +112,7 @@
+ int ret = 0 ;
+ ret += paired_read_combine ( res1 , res2 , maxfrag/2 , maxfrag/2 ,
read_length_1 , seq1 , qual1 , seq2 , qual2 ) ;
+ ret += paired_read_combine ( res2 , res1 , maxfrag/2 , maxfrag/2 ,
read_length_1 , seq2 , qual2 , seq1 , qual1 ) ;
+-
++
+ if ( ret == 0 && res1.size() + res2.size() == 1 ) {
+ string seq ;
+ int newpos , chr ;
+@@ -136,7 +136,7 @@
+ leftovers.push_back ( l ) ;
+ }
+ }
+-
++
+ return ret ;
+ }
+
+@@ -185,7 +185,7 @@
+ int c ;
+ int option_index = 0;
+ while ( -1 != ( c = getopt_long (argc, argv,
"g:a::q::s::f::p::b::r::w::n::",long_options, NULL) ) ) {
+-
++
+ switch ( c ) {
+ case 0 : break ;
+ case 'g' : genome_file = optarg ; break ;
+@@ -214,7 +214,7 @@
+ if ( name.empty() ) die_with_descript
[med-svn] [snpomatic] 07/15: fix man page building
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit b91e82f4cd10663f43220a1df7c3dfaf7ad35a8d Author: Sascha Steinbiss Date: Sat Dec 12 21:15:17 2015 + fix man page building --- debian/rules | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/debian/rules b/debian/rules index ed62603..3836efb 100755 --- a/debian/rules +++ b/debian/rules @@ -16,5 +16,6 @@ override_dh_auto_install: mkdir -p $(debfolder)/snpomatic/usr/bin cp findknownsnps $(debfolder)/snpomatic/usr/bin -override_dh_auto_installman: +override_dh_installman: ronn debian/findknownsnps.1.ronn + dh_installman -- \ No newline at end of file -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 10/15: add documentation
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit e57d341e557631c48e5ca6a16ad5699db83fad51 Author: Sascha Steinbiss Date: Sat Dec 12 21:39:05 2015 + add documentation --- debian/control | 3 ++- debian/doc-base | 10 ++ debian/rules| 18 ++ 3 files changed, 26 insertions(+), 5 deletions(-) diff --git a/debian/control b/debian/control index 4beb9aa..655eb0b 100644 --- a/debian/control +++ b/debian/control @@ -4,7 +4,8 @@ Uploaders: Sascha Steinbiss Section: science Priority: optional Build-Depends: debhelper (>= 9), - ruby-ronn + ruby-ronn, + antiword Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastaq.git Vcs-Git: git://anonscm.debian.org/debian-med/snpomatic.git diff --git a/debian/doc-base b/debian/doc-base new file mode 100644 index 000..626c242 --- /dev/null +++ b/debian/doc-base @@ -0,0 +1,10 @@ +Document: snpomatic +Title: SNP-o-matic manual +Author: SNP-o-matic authors +Abstract: User manual for SNP-o-matic + These files explain how to use SNP-o-matic, in particular its core executable, + findknownsnps. +Section: Science/Biology + +Format: Text +Files: /usr/share/doc/snpomatic/*.txt.gz diff --git a/debian/rules b/debian/rules index 7bd0d33..1c5a6ed 100755 --- a/debian/rules +++ b/debian/rules @@ -11,14 +11,24 @@ debfolder := $(CURDIR)/debian override_dh_auto_clean: rm -rf debian/findknownsnps.1 rm -rf debian/findknownsnps.1.html + dh_auto_clean -- + +override_dh_installdocs: + antiword doc/Manual.doc > doc/Manual.txt + mkdir -p debian/snpomatic/usr/share/doc/snpomatic + cp doc/Manual.txt debian/snpomatic/usr/share/doc/snpomatic + mkdir -p debian/snpomatic/usr/share/doc-base + cp debian/doc-base debian/snpomatic/usr/share/doc-base/snpomatic-doc + dh_installdocs -- override_dh_auto_install: mkdir -p $(debfolder)/snpomatic/usr/bin cp findknownsnps $(debfolder)/snpomatic/usr/bin - cp reassemble $(debfolder)/snpomatic/usr/bin - cp variety $(debfolder)/snpomatic/usr/bin - cp mapcontigs $(debfolder)/snpomatic/usr/bin - cp ungap $(debfolder)/snpomatic/usr/bin + # -- we don't install the others as they seem unmaintained/undocumented + #cp reassemble $(debfolder)/snpomatic/usr/bin + #cp variety $(debfolder)/snpomatic/usr/bin + #cp mapcontigs $(debfolder)/snpomatic/usr/bin + #cp ungap $(debfolder)/snpomatic/usr/bin override_dh_installman: ronn debian/findknownsnps.1.ronn -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 12/15: cme fix dpkg
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 413cbc50a879be609245bc108b47899d4c4cf7eb Author: Sascha Steinbiss Date: Sat Dec 12 21:42:13 2015 + cme fix dpkg --- debian/patches/build_all_binaries | 1 + debian/patches/fix_ungap | 1 + debian/patches/hardening | 1 + debian/rules | 2 ++ 4 files changed, 5 insertions(+) diff --git a/debian/patches/build_all_binaries b/debian/patches/build_all_binaries index 97b9ff0..4750877 100644 --- a/debian/patches/build_all_binaries +++ b/debian/patches/build_all_binaries @@ -1,3 +1,4 @@ +Description: Build_all_binaries --- a/Makefile +++ b/Makefile @@ -8,7 +8,7 @@ diff --git a/debian/patches/fix_ungap b/debian/patches/fix_ungap index baa91e6..7ca3230 100644 --- a/debian/patches/fix_ungap +++ b/debian/patches/fix_ungap @@ -1,3 +1,4 @@ +Description: Fix_ungap --- a/src/ungap.cpp +++ b/src/ungap.cpp @@ -17,7 +17,7 @@ diff --git a/debian/patches/hardening b/debian/patches/hardening index cdc62f5..ee2e6f9 100644 --- a/debian/patches/hardening +++ b/debian/patches/hardening @@ -1,3 +1,4 @@ +Description: Hardening --- a/Makefile +++ b/Makefile @@ -11,22 +11,22 @@ diff --git a/debian/rules b/debian/rules index 1c5a6ed..88e534e 100755 --- a/debian/rules +++ b/debian/rules @@ -9,8 +9,10 @@ debfolder := $(CURDIR)/debian dh $@ override_dh_auto_clean: + $(MAKE) clean rm -rf debian/findknownsnps.1 rm -rf debian/findknownsnps.1.html + rm -f mapcontigs reassemble ungap dh_auto_clean -- override_dh_installdocs: -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 14/15: add upstream metadata reference
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 150c100880e268bb9cba56f577b07da7b0268f04 Author: Sascha Steinbiss Date: Sat Dec 12 21:55:43 2015 + add upstream metadata reference --- debian/upstream/metadata | 12 1 file changed, 12 insertions(+) diff --git a/debian/upstream/metadata b/debian/upstream/metadata new file mode 100644 index 000..b077dcb --- /dev/null +++ b/debian/upstream/metadata @@ -0,0 +1,12 @@ +Reference: + Author: Heinrich Magnus Manske and Dominic P. Kwiatkowski + Title: SNP-o-matic + Journal: Bioinformatics + Year: 2009 + Volume: 25 + Number: 18 + Pages: 2434-2435 + DOI: 10.1093/bioinformatics/btp403 + PMID: 25414349 + URL: http://bioinformatics.oxfordjournals.org/content/25/18/2434 + eprint: http://bioinformatics.oxfordjournals.org/content/25/18/2434.full.pdf+html -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 08/15: add patches
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit d0e4a229af2bc0778ca35b6384503e61bab68784 Author: Sascha Steinbiss Date: Sat Dec 12 21:18:55 2015 + add patches --- debian/patches/build_all_binaries | 11 +++ debian/patches/hardening | 31 +++ debian/patches/series | 2 ++ 3 files changed, 44 insertions(+) diff --git a/debian/patches/build_all_binaries b/debian/patches/build_all_binaries new file mode 100644 index 000..83ed7d5 --- /dev/null +++ b/debian/patches/build_all_binaries @@ -0,0 +1,11 @@ +--- a/Makefile b/Makefile +@@ -8,7 +8,7 @@ + #CXXFLAGS=-g -O2 -ip -align -falign-functions -Wno-deprecated -Isrc -w + #LIBS= + +- ++all: findknownsnps reassemble variety mapcontigs ungap + + findknownsnps: src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o + $(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@ diff --git a/debian/patches/hardening b/debian/patches/hardening new file mode 100644 index 000..38c5326 --- /dev/null +++ b/debian/patches/hardening @@ -0,0 +1,31 @@ +--- a/Makefile b/Makefile +@@ -11,22 +11,22 @@ + + + findknownsnps: src/findknownsnps.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o +- $(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@ ++ $(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@ + + reassemble: src/reassemble.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o +- $(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@ ++ $(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@ + + variety: src/variety.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o +- $(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@ ++ $(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@ + + mapcontigs: src/mapcontigs.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o +- $(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@ ++ $(CXX) $(CFLAGS) $(CXXFLAGS) $(LDFLAGS) $(LIBS) $^ -o $@ + + ungap: src/ungap.o src/global_functions.o src/TChromosome.o src/TChromosomalIndices.o src/TAlignmentOutput.o src/TChromosomeAlign.o +- $(CXX) $(CXXFLAGS) $(LIBS) $^ -o $@ ++ $(CXX) $(CFLAGS) $(CXXFLAGS) $(LIBS) $^ -o $@ + + .cpp.o: +- $(CXX) $(CXXFLAGS) -c $< -o $@ ++ $(CXX) $(CFLAGS) $(CXXFLAGS) -c $< -o $@ + + clean: + rm -f *.o diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 000..8cf2dc3 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1,2 @@ +hardening +build_all_binaries -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 13/15: adjust Vcs-Browser
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 5beff3cb10a50adad0b81befecc3f1eecdfcdbf0 Author: Sascha Steinbiss Date: Sat Dec 12 21:55:32 2015 + adjust Vcs-Browser --- debian/control | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/control b/debian/control index 655eb0b..8c670ac 100644 --- a/debian/control +++ b/debian/control @@ -7,7 +7,7 @@ Build-Depends: debhelper (>= 9), ruby-ronn, antiword Standards-Version: 3.9.6 -Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/fastaq.git +Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/snpomatic.git Vcs-Git: git://anonscm.debian.org/debian-med/snpomatic.git Homepage: https://github.com/magnusmanske/snpomatic -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] branch pristine-tar created (now 34894c5)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch pristine-tar in repository snpomatic. at 34894c5 pristine-tar data for snpomatic_0.0.20151015.orig.tar.bz2 This branch includes the following new commits: new 34894c5 pristine-tar data for snpomatic_0.0.20151015.orig.tar.bz2 The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 15/15: add ITP#
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 849e1c87270ac0dde1f9d38a2f2054d2c3f6d2cf Author: Sascha Steinbiss Date: Sat Dec 12 21:56:29 2015 + add ITP# --- debian/changelog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index 0848f56..f94cf76 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,5 +1,5 @@ snpomatic (0.0.20151015-1) unstable; urgency=medium - * Initial release. (Closes: #XX) + * Initial release. (Closes: #807779) -- Sascha Steinbiss Sat, 12 Dec 2015 20:17:45 + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] annotated tag upstream/0.0.20151015 created (now 01ce2df)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to annotated tag upstream/0.0.20151015 in repository snpomatic. at 01ce2df (tag) tagging 662e5b7b774797ea074f0266aa37749a91f31200 (commit) tagged by Sascha Steinbiss on Sat Dec 12 20:20:16 2015 + - Log - Upstream version 0.0.20151015 Sascha Steinbiss (1): Imported Upstream version 0.0.20151015 --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 01/01: pristine-tar data for snpomatic_0.0.20151015.orig.tar.bz2
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch pristine-tar in repository snpomatic. commit 34894c56f1bd218266b4e6d1455b11dd009079a4 Author: Sascha Steinbiss Date: Sat Dec 12 20:20:16 2015 + pristine-tar data for snpomatic_0.0.20151015.orig.tar.bz2 --- snpomatic_0.0.20151015.orig.tar.bz2.delta | Bin 0 -> 1254 bytes snpomatic_0.0.20151015.orig.tar.bz2.id| 1 + 2 files changed, 1 insertion(+) diff --git a/snpomatic_0.0.20151015.orig.tar.bz2.delta b/snpomatic_0.0.20151015.orig.tar.bz2.delta new file mode 100644 index 000..6855c2d Binary files /dev/null and b/snpomatic_0.0.20151015.orig.tar.bz2.delta differ diff --git a/snpomatic_0.0.20151015.orig.tar.bz2.id b/snpomatic_0.0.20151015.orig.tar.bz2.id new file mode 100644 index 000..d233739 --- /dev/null +++ b/snpomatic_0.0.20151015.orig.tar.bz2.id @@ -0,0 +1 @@ +094ed8925d962df7c7b3897216bfe6a7d4940e50 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] branch upstream created (now 662e5b7)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch upstream in repository snpomatic. at 662e5b7 Imported Upstream version 0.0.20151015 No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [libtabixpp] 02/02: remove unneeded dependency
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository libtabixpp. commit 6008d37b3c77669779ea6690db072c14a989e517 Author: Sascha Steinbiss Date: Sun Dec 13 03:17:31 2015 + remove unneeded dependency --- debian/control | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/debian/control b/debian/control index 17a9321..ea4a29d 100644 --- a/debian/control +++ b/debian/control @@ -8,8 +8,7 @@ Build-Depends: debhelper (>= 9), libhts-dev, libhts1, zlib1g, - zlib1g-dev, - d-shlibs + zlib1g-dev Standards-Version: 3.9.6 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libtabixpp.git Vcs-Git: git://anonscm.debian.org/debian-med/libtabixpp.git -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [libtabixpp] branch master updated (457e505 -> 6008d37)
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a change to branch master
in repository libtabixpp.
from 457e505 flesh out package a bit
new d674d23 add tests, finish building as a shlib
new 6008d37 remove unneeded dependency
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
debian/control | 18 +-
...{libtabixpp-dev.links => libtabixpp0-dev.links} | 0
debian/libtabixpp0.postinst| 37 ++
debian/libtabixpp0.postrm | 38 ++
debian/patches/build_with_debian_htslib.patch | 2 +-
debian/rules | 6 +-
debian/tests/Lmajor.gff3.1 | 463 +
debian/tests/build-lib | 22 +
debian/tests/control | 2 +
debian/tests/eden.gff3 | 25 ++
10 files changed, 609 insertions(+), 4 deletions(-)
rename debian/{libtabixpp-dev.links => libtabixpp0-dev.links} (100%)
create mode 100644 debian/libtabixpp0.postinst
create mode 100644 debian/libtabixpp0.postrm
create mode 100644 debian/tests/Lmajor.gff3.1
create mode 100755 debian/tests/build-lib
create mode 100644 debian/tests/control
create mode 100644 debian/tests/eden.gff3
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[med-svn] [libtabixpp] 01/02: add tests, finish building as a shlib
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository libtabixpp.
commit d674d23b996eb07c8bda2b8b6125366ed08b2d7e
Author: Sascha Steinbiss
Date: Sun Dec 13 03:13:27 2015 +
add tests, finish building as a shlib
---
debian/control | 21 +-
...{libtabixpp-dev.links => libtabixpp0-dev.links} | 0
debian/libtabixpp0.postinst| 37 ++
debian/libtabixpp0.postrm | 38 ++
debian/patches/build_with_debian_htslib.patch | 2 +-
debian/rules | 6 +-
debian/tests/Lmajor.gff3.1 | 463 +
debian/tests/build-lib | 22 +
debian/tests/control | 2 +
debian/tests/eden.gff3 | 25 ++
10 files changed, 611 insertions(+), 5 deletions(-)
diff --git a/debian/control b/debian/control
index 4a7d1b7..17a9321 100644
--- a/debian/control
+++ b/debian/control
@@ -8,7 +8,8 @@ Build-Depends: debhelper (>= 9),
libhts-dev,
libhts1,
zlib1g,
- zlib1g-dev
+ zlib1g-dev,
+ d-shlibs
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libtabixpp.git
Vcs-Git: git://anonscm.debian.org/debian-med/libtabixpp.git
@@ -29,7 +30,9 @@ Description: C++ wrapper to tabix indexer
.
This package provides a C++ wrapper to the tabix indexer.
-Package: libtabixpp-dev
+Package: libtabixpp0-dev
+Provides: libtabixpp-dev
+Conflicts: libtabixpp-dev
Architecture: any
Section: libdevel
Depends: ${shlibs:Depends},
@@ -38,4 +41,16 @@ Depends: ${shlibs:Depends},
Description: C++ wrapper to tabix indexer (development files)
This package provides development headers and static libraries for libtabixpp,
a C++ interface wrapper for Tabix. Tabix is a part of htslib to index tabular
- files in which some columns indicate sequence coordinates.
\ No newline at end of file
+ files in which some columns indicate sequence coordinates.
+
+Package: libtabixpp0-dbg
+Architecture: any
+Section: debug
+Priority: extra
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ libtabixpp0 (= ${binary:Version})
+Description: C++ wrapper to tabix indexer (debug symbols)
+ This package provides debug symbols for libtabixpp,
+ a C++ interface wrapper for Tabix. Tabix is a part of htslib to index tabular
+ files in which some columns indicate sequence coordinates.
diff --git a/debian/libtabixpp-dev.links b/debian/libtabixpp0-dev.links
similarity index 100%
rename from debian/libtabixpp-dev.links
rename to debian/libtabixpp0-dev.links
diff --git a/debian/libtabixpp0.postinst b/debian/libtabixpp0.postinst
new file mode 100644
index 000..95d829f
--- /dev/null
+++ b/debian/libtabixpp0.postinst
@@ -0,0 +1,37 @@
+#!/bin/sh
+# postinst script for #PACKAGE#
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+#* `configure'
+#* `abort-upgrade'
+#* `abort-remove' `in-favour'
+#
+#* `abort-remove'
+#* `abort-deconfigure' `in-favour'
+#`removing'
+#
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+configure)
+ ldconfig
+;;
+
+abort-upgrade|abort-remove|abort-deconfigure)
+;;
+
+*)
+echo "postinst called with unknown argument \`$1'" >&2
+exit 1
+;;
+esac
+
+#DEBHELPER#
+
+exit 0
diff --git a/debian/libtabixpp0.postrm b/debian/libtabixpp0.postrm
new file mode 100644
index 000..f47d01f
--- /dev/null
+++ b/debian/libtabixpp0.postrm
@@ -0,0 +1,38 @@
+#!/bin/sh
+# postrm script for #PACKAGE#
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+#* `remove'
+#* `purge'
+#* `upgrade'
+#* `failed-upgrade'
+#* `abort-install'
+#* `abort-install'
+#* `abort-upgrade'
+#* `disappear'
+#
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+purge|upgrade|failed-upgrade|abort-install|abort-upgrade|disappear)
+;;
+
+remove)
+ ldconfig
+;;
+
+*)
+echo "postrm called with unknown argument \`$1'" >&2
+exit 1
+;;
+esac
+
+#DEBHELPER#
+
+exit 0
diff --git a/debian/patches/build_with_debian_htslib.patch
b/debian/patches/build_with_debian_htslib.patch
index 9bcba7e..d790a9c 100644
--- a/debian/patches/build_with_debian_htslib.patch
+++ b/debian/patches/build_with_debian_htslib.patch
@@ -40,7 +40,7 @@ Description: Build_with_debian_h
[med-svn] [libtabixpp] 01/01: install into correct directory
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository libtabixpp. commit b8a6cb71f561c8d68ebdd1233d140168907ef1f8 Author: Sascha Steinbiss Date: Sun Dec 13 03:22:12 2015 + install into correct directory --- debian/rules | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/debian/rules b/debian/rules index f38bfc1..99361ce 100755 --- a/debian/rules +++ b/debian/rules @@ -6,8 +6,8 @@ dh $@ override_dh_auto_install: - mkdir -p debian/libtabixpp-dev/usr/include - cp *hpp debian/libtabixpp-dev/usr/include + mkdir -p debian/libtabixpp0-dev/usr/include + cp *hpp debian/libtabixpp0-dev/usr/include mkdir -p debian/libtabixpp0/usr/lib cp libtabixpp.so* debian/libtabixpp0/usr/lib/ dh_auto_install -- -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [libtabixpp] branch master updated (6008d37 -> b8a6cb7)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository libtabixpp. from 6008d37 remove unneeded dependency new b8a6cb7 install into correct directory The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/rules | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/libtabixpp.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 01/01: add README.source
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 025fae7448381d4420e29e109a533c6315ef Author: Sascha Steinbiss Date: Sun Dec 13 13:38:27 2015 + add README.source --- debian/README.source | 1 + 1 file changed, 1 insertion(+) diff --git a/debian/README.source b/debian/README.source new file mode 100644 index 000..19a4132 --- /dev/null +++ b/debian/README.source @@ -0,0 +1 @@ +I have contacted upstream about getting a real version number (https://github.com/magnusmanske/snpomatic/issues/1), currently awaiting reply. Will use a temporary version number starting with 0.0 and the git revision date for now. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] branch master updated (849e1c8 -> 025f111)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository snpomatic. from 849e1c8 add ITP# new 025f111 add README.source The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/README.source | 1 + 1 file changed, 1 insertion(+) create mode 100644 debian/README.source -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] branch master created (now 6e4e21e)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository reapr. at 6e4e21e add README.debian This branch includes the following new commits: new bb85a15 Imported Upstream version 1.0.18+dfsg new 3239de8 add debian dir new 6ceb6f2 cme fix dpkg new 8a014aa make installation more in line with the original approach new 6e4e21e add README.debian The 5 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] branch pristine-tar created (now dc70575)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch pristine-tar in repository reapr. at dc70575 pristine-tar data for reapr_1.0.18+dfsg.orig.tar.gz This branch includes the following new commits: new dc70575 pristine-tar data for reapr_1.0.18+dfsg.orig.tar.gz The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] annotated tag upstream/1.0.18+dfsg created (now c426108)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to annotated tag upstream/1.0.18+dfsg in repository reapr. at c426108 (tag) tagging bb85a15019796819770544938adb0731286734b8 (commit) tagged by Sascha Steinbiss on Sun Dec 13 13:25:19 2015 + - Log - Upstream version 1.0.18+dfsg Sascha Steinbiss (1): Imported Upstream version 1.0.18+dfsg --- No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] 01/01: pristine-tar data for reapr_1.0.18+dfsg.orig.tar.gz
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch pristine-tar in repository reapr. commit dc7057522d90b8375300c944b6d8e55194ddea02 Author: Sascha Steinbiss Date: Sun Dec 13 13:25:19 2015 + pristine-tar data for reapr_1.0.18+dfsg.orig.tar.gz --- reapr_1.0.18+dfsg.orig.tar.gz.delta | Bin 0 -> 57694 bytes reapr_1.0.18+dfsg.orig.tar.gz.id| 1 + 2 files changed, 1 insertion(+) diff --git a/reapr_1.0.18+dfsg.orig.tar.gz.delta b/reapr_1.0.18+dfsg.orig.tar.gz.delta new file mode 100644 index 000..72b2afc Binary files /dev/null and b/reapr_1.0.18+dfsg.orig.tar.gz.delta differ diff --git a/reapr_1.0.18+dfsg.orig.tar.gz.id b/reapr_1.0.18+dfsg.orig.tar.gz.id new file mode 100644 index 000..7d43362 --- /dev/null +++ b/reapr_1.0.18+dfsg.orig.tar.gz.id @@ -0,0 +1 @@ +e1a0d544886531d3f25ff17d85a2bed76bfde9b0 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] 03/05: cme fix dpkg
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository reapr. commit 6ceb6f24b72888b44c6b012a7f4cc0718ffe4d31 Author: Sascha Steinbiss Date: Sun Dec 13 13:26:46 2015 + cme fix dpkg --- debian/patches/hardening | 1 + 1 file changed, 1 insertion(+) diff --git a/debian/patches/hardening b/debian/patches/hardening index 8d0d57c..632af43 100644 --- a/debian/patches/hardening +++ b/debian/patches/hardening @@ -1,3 +1,4 @@ +Description: Hardening --- a/src/Makefile +++ b/src/Makefile @@ -1,5 +1,5 @@ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] 04/05: make installation more in line with the original approach
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository reapr.
commit 8a014aa92c6910d4b0e36bb3d42044aee57cae02
Author: Sascha Steinbiss
Date: Sun Dec 13 18:42:18 2015 +
make installation more in line with the original approach
---
debian/links | 7 +++
debian/rules | 9 +
2 files changed, 12 insertions(+), 4 deletions(-)
diff --git a/debian/links b/debian/links
new file mode 100644
index 000..7556858
--- /dev/null
+++ b/debian/links
@@ -0,0 +1,7 @@
+/usr/lib/reapr/reapr.pl /usr/bin/reapr
+/usr/bin/findknownsnps /usr/lib/reapr/findknownsnps
+/usr/bin/tabix /usr/lib/reapr/tabix
+/usr/bin/bgzip /usr/lib/reapr/bgzip
+/usr/bin/smalt /usr/lib/reapr/smalt
+/usr/bin/samtools /usr/lib/reapr/samtools
+/usr/bin/bamtools /usr/lib/reapr/bamtools
diff --git a/debian/rules b/debian/rules
index 25348b1..fe1a719 100755
--- a/debian/rules
+++ b/debian/rules
@@ -9,7 +9,8 @@ override_dh_auto_build:
cd src && $(MAKE)
override_dh_auto_install:
- mkdir -p debian/reapr/usr/lib
- find src -name 'task*' -and -executable -exec cp {}
debian/reapr/usr/lib \;
- mkdir -p debian/reapr/usr/bin
- cp src/reapr.pl debian/reapr/usr/bin/reapr
\ No newline at end of file
+ mkdir -p debian/reapr/usr/lib/reapr
+ cp src/reapr.pl debian/reapr/usr/lib/reapr/reapr.pl
+ find src -name 'task*' -and -executable -exec \
+ cp {} debian/reapr/usr/lib/reapr \;
+ dh_auto_install --
\ No newline at end of file
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[med-svn] [reapr] 05/05: add README.debian
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository reapr. commit 6e4e21e727555073a80d0370db12ddd3107d9978 Author: Sascha Steinbiss Date: Sun Dec 13 18:44:29 2015 + add README.debian --- debian/README.debian | 2 ++ 1 file changed, 2 insertions(+) diff --git a/debian/README.debian b/debian/README.debian new file mode 100644 index 000..f811690 --- /dev/null +++ b/debian/README.debian @@ -0,0 +1,2 @@ +Still waiting for snpomatic and libtabixpp to appear in Debian... + -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] branch upstream created (now bb85a15)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch upstream in repository reapr. at bb85a15 Imported Upstream version 1.0.18+dfsg No new revisions were added by this update. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] 02/05: add debian dir
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository reapr.
commit 3239de86fe1449ecd3213977174e3b53ab55a70e
Author: Sascha Steinbiss
Date: Sun Dec 13 13:26:33 2015 +
add debian dir
---
debian/changelog | 5 ++
debian/compat | 1 +
debian/control | 41 +++
debian/copyright | 29
debian/patches/hardening | 150 +
debian/patches/series | 2 +
debian/patches/use_shared_libs | 135 +
debian/rules | 15 +
debian/source/format | 1 +
debian/upstream/metadata | 12
debian/watch | 3 +
11 files changed, 394 insertions(+)
diff --git a/debian/changelog b/debian/changelog
new file mode 100644
index 000..d19f192
--- /dev/null
+++ b/debian/changelog
@@ -0,0 +1,5 @@
+reapr (1.0.18+dfsg-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #)
+
+ -- Sascha Steinbiss Sat, 12 Dec 2015 19:47:37 +
diff --git a/debian/compat b/debian/compat
new file mode 100644
index 000..ec63514
--- /dev/null
+++ b/debian/compat
@@ -0,0 +1 @@
+9
diff --git a/debian/control b/debian/control
new file mode 100644
index 000..ca44b4b
--- /dev/null
+++ b/debian/control
@@ -0,0 +1,41 @@
+Source: reapr
+Maintainer: Debian Med Packaging Team
+Uploaders: Sascha Steinbiss
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9),
+ libbamtools-dev,
+ libtabixpp-dev,
+ libhts-dev,
+ zlib1g-dev
+Standards-Version: 3.9.6
+Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/reapr.git
+Vcs-Git: git://anonscm.debian.org/debian-med/reapr.git
+Homepage: http://www.sanger.ac.uk/science/tools/reapr
+
+Package: reapr
+Architecture: any
+Depends: ${shlibs:Depends},
+ ${misc:Depends},
+ samtools,
+ bamtools,
+ smalt,
+ r-base,
+ snpomatic,
+ tabix,
+ libfile-copy-link-perl
+Description: evaluation of genome assemblies using mapped paired end reads
+ REAPR is a tool that evaluates the accuracy of a genome assembly using mapped
+ paired end reads, without the use of a reference genome for comparison. It can
+ be used in any stage of an assembly pipeline to automatically break incorrect
+ scaffolds and flag other errors in an assembly for manual inspection. It
+ reports mis-assemblies and other warnings, and produces a new broken assembly
+ based on the error calls.
+ .
+ The software requires as input an assembly in FASTA format and paired reads
+ mapped to the assembly in a BAM file. Mapping information such as the fragment
+ coverage and insert size distribution is analysed to locate mis-assemblies.
+ REAPR works best using mapped read pairs from a large insert library (at least
+ 1000bp). Additionally, if a short insert Illumina library is also available,
+ REAPR can combine this with the large insert library in order to score each
+ base of the assembly.
diff --git a/debian/copyright b/debian/copyright
new file mode 100644
index 000..452512c
--- /dev/null
+++ b/debian/copyright
@@ -0,0 +1,29 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: REAPR
+Source: http://www.sanger.ac.uk/science/tools/reapr
+Files-Excluded: third_party/* manual.pdf
+
+Files: *
+Copyright: © 2013-2015 Genome Research Ltd.
+License: GPL-3+
+
+Files: debian/*
+Copyright: © 2015 Sascha Steinbiss
+License: GPL-3+
+
+License: GPL-3+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 3 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/patches/hardening b/debian/patches/hardening
new file mode 100644
index 000..8d0d57c
--- /dev/null
+++ b/debian/patches/hardening
@@ -0,0 +1,150 @@
+--- a/src/Makefile
b/src/Makefile
+@@ -1,5 +1,5 @@
+ CC = g++
+-CFLAGS = -Wall -O3 -I /usr/include/bamtools -I /usr/include
++CFLAGS += -Wall -O3 -I /usr/include/bamtools -I /usr/include
+ TABIX = -ltabixpp -lhts -lz
+ STATS_OBJS = trianglePlot.o coveragePlot.o fasta.o histogram.o utils.o
+ SCORE_OBJS = errorWindow.o utils.o histogram.o
+@@ -19,106 +19,106 @@
+
[med-svn] [reapr] 02/02: include all built executables
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository reapr.
commit e4112e3fd62910811f8f0fb298443784a89d5fbb
Author: Sascha Steinbiss
Date: Sun Dec 13 22:11:09 2015 +
include all built executables
---
debian/rules | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/debian/rules b/debian/rules
index fe1a719..91c5142 100755
--- a/debian/rules
+++ b/debian/rules
@@ -11,6 +11,6 @@ override_dh_auto_build:
override_dh_auto_install:
mkdir -p debian/reapr/usr/lib/reapr
cp src/reapr.pl debian/reapr/usr/lib/reapr/reapr.pl
- find src -name 'task*' -and -executable -exec \
- cp {} debian/reapr/usr/lib/reapr \;
+ chmod -x src/*.cpp
+ find src -executable -exec cp {} debian/reapr/usr/lib/reapr \;
dh_auto_install --
\ No newline at end of file
--
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[med-svn] [reapr] branch master updated (6e4e21e -> e4112e3)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository reapr. from 6e4e21e add README.debian new 39b9db9 correct paths to tabix/bgzip new e4112e3 include all built executables The 2 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/patches/use_shared_libs | 76 ++ debian/rules | 4 +-- 2 files changed, 78 insertions(+), 2 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] 01/02: correct paths to tabix/bgzip
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository reapr.
commit 39b9db9336cbcc2ba3402af4579fa5d1c7ad5aed
Author: Sascha Steinbiss
Date: Sun Dec 13 19:35:13 2015 +
correct paths to tabix/bgzip
---
debian/patches/use_shared_libs | 76 ++
1 file changed, 76 insertions(+)
diff --git a/debian/patches/use_shared_libs b/debian/patches/use_shared_libs
index 1f1d009..2090649 100644
--- a/debian/patches/use_shared_libs
+++ b/debian/patches/use_shared_libs
@@ -133,3 +133,79 @@ Description: Use_shared_libs
using namespace std;
+--- a/src/reapr.pl
b/src/reapr.pl
+@@ -12,8 +12,8 @@
+ $this_script = File::Spec->rel2abs($this_script);
+ my ($scriptname, $scriptdir) = fileparse($this_script);
+ $scriptdir = File::Spec->rel2abs($scriptdir);
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
++my $tabix = File::Spec->catfile($scriptdir, 'tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
+ my $version = '1.0.18';
+
+ if ($#ARGV == -1) {
+--- a/src/task_preprocess.pl
b/src/task_preprocess.pl
+@@ -52,8 +52,8 @@
+ my $ideal_fcd_file = File::Spec->catfile($sample_dir, 'ideal_fcd.txt');
+ my $lowess_prefix = File::Spec->catfile($sample_dir, 'gc_vs_cov.lowess');
+ my $r_script = File::Spec->catfile($sample_dir, 'gc_vs_cov.R');
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
++my $tabix = File::Spec->catfile($scriptdir, 'tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
+ my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+
+ # make directory and soft links to required files
+--- a/src/task_perfectfrombam.pl
b/src/task_perfectfrombam.pl
+@@ -57,8 +57,8 @@
+ my $min_perfect_map_qual = $ARGV[5];
+ my $min_align_score = $ARGV[6];
+ my $bam2perfect = File::Spec->catfile($scriptdir, 'bam2perfect');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
++my $tabix = File::Spec->catfile($scriptdir, 'tabix');
+ my $ERROR_PREFIX = '[REAPR perfectfrombam]';
+ my $perfect_bam = "$out_prefix.tmp.perfect.bam";
+ my $repetitive_bam = "$out_prefix.tmp.repetitive.bam";
+--- a/src/task_perfectmap.pl
b/src/task_perfectmap.pl
+@@ -43,8 +43,8 @@
+ my $raw_coverage_file = "$preout.tmp.cov.txt";
+ my $tmp_bin = "$preout.tmp.bin";
+ my $tmp_bin_single_match = "$tmp_bin\_single_match.fastq";
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
++my $tabix = File::Spec->catfile($scriptdir, 'tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
+ my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+ my $all_bases_outfile = "$preout.perfect_cov.gz";
+ my $hist_outfile = "$preout.hist";
+--- a/src/task_plots.pl
b/src/task_plots.pl
+@@ -50,8 +50,8 @@
+ }
+
+
+-my $tabix = File::Spec->catfile($scriptdir, 'tabix/tabix');
+-my $bgzip = File::Spec->catfile($scriptdir, 'tabix/bgzip');
++my $tabix = File::Spec->catfile($scriptdir, 'tabix');
++my $bgzip = File::Spec->catfile($scriptdir, 'bgzip');
+ my $samtools = File::Spec->catfile($scriptdir, 'samtools');
+ my @plot_list = ('frag_cov', 'frag_cov_cor', 'read_cov', 'read_ratio_f',
'read_ratio_r', 'clip', 'FCD_err');
+ my @file_list;
+--- a/src/task_pipeline.pl
b/src/task_pipeline.pl
+@@ -9,7 +9,7 @@
+
+ my ($scriptname, $scriptdir) = fileparse($0);
+ my $reapr_dir = abs_path(File::Spec->catfile($scriptdir,
File::Spec->updir()));
+-my $reapr = File::Spec->catfile($reapr_dir, 'reapr');
++my $reapr = '/usr/bin/reapr';
+
+ my %options = (fcdcut => 0);
+
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[med-svn] [reapr] 01/01: update README with samtools dep news
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository reapr. commit 7839125e4ca0b70f78fc06b0e2e16d274f2599d1 Author: Sascha Steinbiss Date: Mon Dec 14 13:28:13 2015 + update README with samtools dep news --- debian/README.debian | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/debian/README.debian b/debian/README.debian index f811690..cd68577 100644 --- a/debian/README.debian +++ b/debian/README.debian @@ -1,2 +1,4 @@ Still waiting for snpomatic and libtabixpp to appear in Debian... - +Also, 'samtools rmdup' is broken in 1.2 currently +(https://github.com/samtools/samtools/issues/159) causing problems +in REAPR. Delaying upload until samtools 1.3 is out. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [reapr] branch master updated (e4112e3 -> 7839125)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository reapr. from e4112e3 include all built executables new 7839125 update README with samtools dep news The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/README.debian | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/reapr.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] branch master updated (025f111 -> e640f5f)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository snpomatic. from 025f111 add README.source new e640f5f use common locale for reproducibility The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/rules | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 01/01: use common locale for reproducibility
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit e640f5fb1f5d30b4fa05500c0f879e295d22e5b7 Author: Sascha Steinbiss Date: Mon Dec 14 14:44:36 2015 + use common locale for reproducibility --- debian/rules | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/debian/rules b/debian/rules index 88e534e..1391bab 100755 --- a/debian/rules +++ b/debian/rules @@ -4,6 +4,7 @@ export DH_VERBOSE := 1 mandir := $(CURDIR)/debian/man debfolder := $(CURDIR)/debian +export LC_ALL=C %: dh $@ @@ -34,4 +35,4 @@ override_dh_auto_install: override_dh_installman: ronn debian/findknownsnps.1.ronn - dh_installman -- \ No newline at end of file + dh_installman -- -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 01/01: edit upstream name
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit 8d065d635316bc44b35f070ae74549b0300c4255 Author: Sascha Steinbiss Date: Mon Dec 14 15:04:38 2015 + edit upstream name --- debian/copyright | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/copyright b/debian/copyright index e38d9f3..77d2436 100644 --- a/debian/copyright +++ b/debian/copyright @@ -1,5 +1,5 @@ Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ -Upstream-Name: snpomatic +Upstream-Name: SNP-o-matic Source: https://github.com/magnusmanske/snpomatic Files: * -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] branch master updated (e640f5f -> 8d065d6)
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a change to branch master in repository snpomatic. from e640f5f use common locale for reproducibility new 8d065d6 edit upstream name The 1 revisions listed above as "new" are entirely new to this repository and will be described in separate emails. The revisions listed as "adds" were already present in the repository and have only been added to this reference. Summary of changes: debian/copyright | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
[med-svn] [snpomatic] 01/01: add patch headers
This is an automated email from the git hooks/post-receive script. sascha-guest pushed a commit to branch master in repository snpomatic. commit e17e32898587300a22db5ea003eaf43563a4387b Author: Sascha Steinbiss Date: Mon Dec 14 15:20:55 2015 + add patch headers --- debian/patches/build_all_binaries | 7 ++- debian/patches/fix_ungap | 5 - debian/patches/hardening | 3 ++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/debian/patches/build_all_binaries b/debian/patches/build_all_binaries index 4750877..09fb9e1 100644 --- a/debian/patches/build_all_binaries +++ b/debian/patches/build_all_binaries @@ -1,4 +1,9 @@ -Description: Build_all_binaries +Description: Build all binaries. + The original Makefile only builds the 'findknownsnps' executable. + This looks intentional as they seem to be unmaintained, but + I'll make sure they can build anyway if they are to be included + in the package in the future. +Author: Sascha Steinbiss --- a/Makefile +++ b/Makefile @@ -8,7 +8,7 @@ diff --git a/debian/patches/fix_ungap b/debian/patches/fix_ungap index 7ca3230..524147b 100644 --- a/debian/patches/fix_ungap +++ b/debian/patches/fix_ungap @@ -1,4 +1,7 @@ -Description: Fix_ungap +Description: Fix wrong function parameters in ungap tool + This missing parameter in a function call was likely missed as the ungap + tool is not built if simply 'make' is run. +Author: Sascha Steinbiss --- a/src/ungap.cpp +++ b/src/ungap.cpp @@ -17,7 +17,7 @@ diff --git a/debian/patches/hardening b/debian/patches/hardening index ee2e6f9..b6585bf 100644 --- a/debian/patches/hardening +++ b/debian/patches/hardening @@ -1,4 +1,5 @@ -Description: Hardening +Description: Add compiler flags necessary for hardening. +Author: Sascha Steinbiss --- a/Makefile +++ b/Makefile @@ -11,22 +11,22 @@ -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/snpomatic.git ___ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
