[med-svn] [mira] 02/05: Imported Debian patch 3.4.0-2
Michael Crusoe
misterc-guest at moszumanska.debian.org
Tue Feb 2 15:37:43 UTC 2016
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository mira.
commit ff795a85058b829e0ca2c0a2a0327bf52938e77d
Merge: 4aa59e0 536f766
Author: Steffen Moeller <moeller at debian.org>
Date: Mon Aug 29 22:54:53 2011 +0200
Imported Debian patch 3.4.0-2
.tarball-version | 1 -
.version | 1 -
GETTING_STARTED | 13 +-
HELP_WANTED | 14 +-
INSTALL | 706 +-
Makefile.am | 65 +-
Makefile.in | 197 +-
README | 56 +-
README_build.html | 482 -
THANKS | 8 +-
aclocal.m4 | 8705 +--------
build-aux/git-version-gen | 181 -
config.guess | 258 +-
config.sub | 209 +-
{m4 => config/m4}/ax_boost_base.m4 | 25 +-
{m4 => config/m4}/ax_boost_regex.m4 | 19 +-
{m4 => config/m4}/ax_boost_thread.m4 | 33 +-
{m4 => config/m4}/ax_check_zlib.m4 | 13 +-
config/m4/ax_cxx_have_std.m4 | 46 +
config/m4/ax_cxx_have_stl.m4 | 44 +
config/m4/ax_cxx_namespaces.m4 | 40 +
{m4 => config/m4}/ax_lib_expat.m4 | 18 +-
config/m4/ax_with_perl.m4 | 35 +
config/m4/ax_with_prog.m4 | 70 +
aclocal.m4 => config/m4/libtool.m4 | 3881 +---
config/m4/ltoptions.m4 | 368 +
config/m4/ltsugar.m4 | 123 +
config/m4/ltversion.m4 | 23 +
config/m4/lt~obsolete.m4 | 92 +
configure | 9105 ++++-----
configure.ac => configure.in | 943 +-
debian/README.source | 27 +
debian/TODO | 3 +
debian/changelog | 172 +-
debian/clean | 1 -
debian/compat | 2 +-
debian/control | 75 +-
debian/copyright | 110 +-
debian/mans/convert_project.1 | 302 -
debian/mans/fasta2frag.1 | 95 -
debian/mans/fastaselect.1 | 47 -
debian/mans/fastatool.1 | 49 -
debian/mans/fastqselect.1 | 47 -
debian/mans/fixACE4consed.1 | 32 -
debian/mans/mira.1 | 53 -
debian/mans/miraSearchESTSNPs.1 | 43 -
debian/mans/mirabait.1 | 131 -
debian/mans/miraconvert.1 | 327 -
debian/mans/miradiff.1 | 36 -
debian/mans/miramem.1 | 33 -
debian/mans/miramer.1 | 36 -
debian/mans/scftool.1 | 50 -
debian/mira-assembler.install | 8 +
debian/mira-assembler.lintian-overrides | 2 -
debian/mira-assembler.manpages | 1 -
debian/mira-doc.README.Debian | 2 +-
debian/mira-doc.doc-base | 12 -
debian/mira-examples.lintian-overrides | 3 -
debian/patches/add_shebang_lines | 27 +
debian/patches/fix_strange_link_issue.patch | 16 -
debian/patches/read_default_constructor.patch | 15 +
debian/patches/series | 5 +-
debian/patches/spelling.patch | 396 -
debian/patches/xsltproc_nonet_for_doc_build | 21 +
debian/rules | 86 +-
debian/stamp-autotools-files | 0
debian/stamp-makefile-build | 0
debian/stamp-makefile-check | 0
debian/upstream-metadata.yaml | 18 +
debian/upstream/metadata | 15 -
debian/watch | 2 +-
depcomp | 563 +-
distribution/Makefile | 170 +-
distribution/Makefile.am | 64 +-
distribution/Makefile.in | 116 +-
distribution/README | 84 +-
doc/Makefile | 109 +-
doc/Makefile.in | 55 +-
doc/docbook/Makefile | 179 +-
doc/docbook/Makefile.am | 45 +-
doc/docbook/Makefile.in | 125 +-
doc/docbook/attic/README.txt | 266 -
doc/docbook/attic/chap_pacbio_part.xml | 549 -
doc/docbook/attic/chap_solexa_part.xml | 1512 --
doc/docbook/attic/pb_misc.xml | 839 -
doc/docbook/attic/solexa_lenski.xml | 499 -
doc/docbook/book.xsl | 7 +-
doc/docbook/book_3rdparty.xml | 28 -
doc/docbook/book_definitiveguide.xml | 87 +-
doc/docbook/bookfigures/ion_dh10bcovB13_12kb.png | Bin 0 -> 28874 bytes
doc/docbook/bookfigures/ion_dh10bcovB13_320kb.png | Bin 0 -> 40689 bytes
doc/docbook/bookfigures/results_mira2other.png | Bin 80496 -> 0 bytes
doc/docbook/bookfigures/results_miraconvert.png | Bin 60664 -> 0 bytes
doc/docbook/chap_3p_ghbambus_part.xml | 409 -
doc/docbook/{attic => }/chap_454_part.xml | 433 +-
doc/docbook/chap_bitsandpieces_part.xml | 83 -
doc/docbook/chap_bonus_part.xml | 5 +-
.../{chap_bonus_part.xml => chap_bonus_part.xml~} | 392 +-
doc/docbook/chap_dataprep_part.xml | 160 -
doc/docbook/chap_denovo_part.xml | 473 -
doc/docbook/chap_est_part.xml | 328 +-
doc/docbook/chap_faq_part.xml | 139 +-
doc/docbook/chap_hard_part.xml | 121 +-
doc/docbook/chap_installation_part.xml | 640 +-
doc/docbook/chap_intro_part.xml | 179 +-
doc/docbook/{attic => }/chap_iontor_part.xml | 712 +-
doc/docbook/chap_logfiles_part.xml | 28 +-
doc/docbook/chap_maf_part.xml | 55 +-
doc/docbook/chap_mapping_part.xml | 776 -
doc/docbook/chap_mirautils_part.xml | 651 +-
doc/docbook/chap_pacbio_part.xml | 1786 ++
doc/docbook/chap_preface_part.xml | 21 +-
..._definitiveguide.xml => chap_preface_part.xml~} | 87 +-
doc/docbook/chap_reference_part.xml | 5645 +++---
doc/docbook/chap_results_part.xml | 860 +-
doc/docbook/{attic => }/chap_sanger_part.xml | 74 +-
doc/docbook/chap_seqadvice_part.xml | 820 +-
doc/docbook/chap_seqtechdesc_part.xml | 891 -
doc/docbook/chap_solexa_part.xml | 1995 ++
doc/docbook/chap_specialparams_part.xml | 79 -
doc/docbook/chap_sra_part.xml | 145 -
doc/docbook/copyrightfile | 4 -
doc/docbook/doccss/miradocstyle.css | 10 +-
doc/docbook/replace_all.sh | 9 -
doc/docbook/{version.stub => versionfile} | 1 +
doc/docbook/warning_frontofchapter.xml | 12 -
doccss/miradocstyle.css | 34 -
ltmain.sh | 4026 ++--
m4/ax_boost_filesystem.m4 | 118 -
m4/ax_boost_iostreams.m4 | 116 -
m4/ax_boost_system.m4 | 120 -
minidemo/bbdemo2/runme.sh | 14 +-
minidemo/estdemo2/README | 6 +-
minidemo/solexa1/runme.sh | 3 +-
minidemo/solexa2/runme.sh | 3 +-
missing | 53 +-
src/EdIt/Makefile.am | 10 +
src/{caf => EdIt}/Makefile.in | 141 +-
src/EdIt/faultRegion.C | 1222 ++
src/EdIt/hypothesen.C | 2305 +++
src/EdIt/hypothesen.H | 281 +
src/EdIt/parameters.C | 563 +
src/EdIt/parameters.H | 307 +
src/EdIt/parameters_flexer.cc | 2106 +++
src/EdIt/parameters_flexer.ll | 160 +
src/EdIt/parameters_tokens.h | 74 +
src/Makefile.am | 38 +-
src/Makefile.in | 114 +-
src/caf/Makefile.am | 7 +-
src/caf/Makefile.in | 95 +-
src/caf/caf.C | 974 +-
src/caf/caf.H | 149 +-
src/caf/caf_flexer.cc | 2250 +--
src/caf/caf_flexer.ll | 55 +-
src/debuggersupport/Makefile.am | 5 -
src/debuggersupport/dbgsupport.C | 59 -
src/debuggersupport/dbgsupport.H | 33 -
src/errorhandling/Makefile.am | 3 +-
src/errorhandling/Makefile.in | 59 +-
src/errorhandling/errorhandling.C | 107 +-
src/errorhandling/errorhandling.H | 49 +-
src/examine/Makefile.am | 7 +
src/{debuggersupport => examine}/Makefile.in | 101 +-
src/examine/afh_info.C | 541 +
src/examine/buffer.C | 296 +
src/examine/buffer.H | 84 +
src/examine/calc.C | 754 +
src/examine/cfh.C | 420 +
src/examine/globals.H | 239 +
src/examine/misc.C | 398 +
src/examine/misc.H | 76 +
src/examine/prescan.C | 261 +
src/examine/prescan.H | 102 +
src/examine/ranges.C | 591 +
src/examine/scf_look.C | 2655 +++
src/examine/scf_look.H | 406 +
src/examine/scfbuffer.H | 70 +
src/examples_programming/Makefile.am | 25 +
src/{modules => examples_programming}/Makefile.in | 157 +-
src/examples_programming/README | 6 +
src/examples_programming/mira_101.C | 114 +
src/examples_programming/read_101.C | 155 +
src/examples_programming/readpool_101.C | 142 +
src/io/Makefile.am | 49 +-
src/io/Makefile.in | 166 +-
src/io/annotationmappings.C | 348 -
src/io/annotationmappings.H | 170 -
src/io/exp.C | 43 +-
src/io/exp.H | 160 +-
src/io/fasta.C | 107 +-
src/io/fasta.H | 63 +-
src/io/fastq-lh.H | 164 +-
src/io/fastq-mira.C | 278 +-
src/io/fastq-mira.H | 82 +-
src/io/gap4_ft_so_map.xxd | 99 -
src/{mira/gbf_parse.C => io/gbf.C} | 641 +-
src/io/gbf.H | 128 +
src/io/generalio.C | 26 +-
src/io/generalio.H | 17 +-
src/io/mira_ft_set.xxd | 54 -
src/io/ncbiinfoxml.C | 99 +-
src/io/ncbiinfoxml.H | 36 +-
src/io/oldso2so.xxd | 2 -
src/io/phd.C | 31 +-
src/io/phd.H | 38 +-
src/io/scf.C | 205 +-
src/io/scf.H | 58 +-
src/io/so.obo | 18725 -------------------
src/io/so2xgap4map.xxd | 2068 --
src/knn_abi373/Makefile.am | 6 +
src/{debuggersupport => knn_abi373}/Makefile.in | 160 +-
src/knn_abi373/add.c | 224 +
src/knn_abi373/add.h | 14 +
src/knn_abi373/missing.c | 238 +
src/knn_abi373/missing.h | 14 +
src/knn_abi373/ncall.c | 176 +
src/knn_abi373/ncall.h | 14 +
src/knn_abi373/nplus.c | 159 +
src/knn_abi373/nplus.h | 14 +
src/knn_abi373/over.c | 224 +
src/knn_abi373/over.h | 14 +
src/knn_abi373/under.c | 224 +
src/knn_abi373/under.h | 14 +
src/knn_abi373/wrong.c | 176 +
src/knn_abi373/wrong.h | 14 +
src/knn_alf/Makefile.am | 6 +
src/{debuggersupport => knn_alf}/Makefile.in | 160 +-
src/knn_alf/add.c | 224 +
src/knn_alf/add.h | 14 +
src/knn_alf/missing.c | 238 +
src/knn_alf/missing.h | 14 +
src/knn_alf/ncall.c | 176 +
src/knn_alf/ncall.h | 14 +
src/knn_alf/nplus.c | 159 +
src/knn_alf/nplus.h | 14 +
src/knn_alf/over.c | 224 +
src/knn_alf/over.h | 14 +
src/knn_alf/under.c | 224 +
src/knn_alf/under.h | 14 +
src/knn_alf/wrong.c | 176 +
src/knn_alf/wrong.h | 14 +
src/lec/Makefile.am | 6 +
src/{scripts => lec}/Makefile.in | 100 +-
src/memorc/Makefile.am | 23 -
src/memorc/Makefile.in | 535 -
src/memorc/main.C | 101 -
src/memorc/memorc.C | 566 -
src/memorc/memorc.H | 91 -
src/mira/CHANGES.txt | 737 +-
src/mira/CHANGES_old.txt | 57 -
src/mira/Makefile.am | 112 +-
src/mira/Makefile.in | 285 +-
src/mira/TODO | 335 +-
src/mira/adaptorsforclip.454.xxd | 6 +-
src/mira/adaptorsforclip.iontor.xxd | 13 +-
src/mira/adaptorsforclip.solexa.xxd | 93 +-
src/mira/adaptorsregex.iontor.xxd | 8 +-
src/mira/adaptorsregex.solexa.xxd | 5 +-
src/mira/ads.C | 623 +-
src/mira/ads.H | 106 +-
src/mira/adsfacts.C | 166 +-
src/mira/adsfacts.H | 93 +-
src/mira/align.C | 681 +-
src/mira/align.H | 85 +-
src/mira/assembly.C | 4559 +++--
src/mira/assembly.H | 1539 +-
src/mira/assembly_buildcontigs.C | 2260 ---
src/mira/assembly_info.C | 223 +-
src/mira/assembly_info.H | 51 +-
src/mira/assembly_io.C | 2183 ++-
src/mira/assembly_misc.C | 2373 ---
src/mira/assembly_output.C | 5258 +++---
src/mira/assembly_output.H | 358 +-
src/mira/assembly_pbcorrect.C | 2126 ---
src/mira/assembly_reduceskimhits.C | 1238 +-
src/mira/assembly_repeatresolve.C | 532 +
src/mira/assembly_swalign.C | 828 +-
src/mira/contig.C | 9225 +++++----
src/mira/contig.H | 1988 +-
src/mira/contig_analysis.C | 3805 ++--
src/mira/contig_consensus.C | 2774 ---
src/mira/contig_covanalysis.C | 287 -
src/mira/contig_edit.C | 2026 +-
src/mira/contig_featureinfo.C | 623 -
src/mira/contig_output.C | 1924 +-
src/mira/contig_pairconsistency.C | 398 -
src/mira/dataprocessing.C | 4475 +++--
src/mira/dataprocessing.H | 324 -
src/mira/dynamic.C | 750 +-
src/mira/dynamic.H | 76 +-
src/mira/enums.H | 22 +-
src/mira/estassembly.C | 89 +-
src/mira/gbf_parse.H | 138 -
src/mira/gff_parse.C | 620 +-
src/mira/gff_parse.H | 87 +-
src/mira/gff_save.C | 304 -
src/mira/gff_save.H | 79 -
src/mira/hashstats.C | 2894 ---
src/mira/hashstats.H | 616 -
src/mira/hashstats_sdbg.C | 693 -
src/mira/hdeque.H | 666 -
src/mira/indexed_deque.H | 541 +
src/mira/maf_parse.C | 1578 +-
src/mira/maf_parse.H | 210 +-
src/mira/manifest.C | 590 -
src/mira/manifest.H | 99 -
src/mira/multitag.C | 408 +-
src/mira/multitag.H | 207 +-
src/mira/newpathfinder.C | 5018 +++++
src/mira/newpathfinder.H | 405 +
src/mira/overlapedges.H | 143 -
src/mira/parameters.C | 4543 ++---
src/mira/parameters.H | 486 +-
src/mira/parameters_flexer.cc | 10877 ++++++-----
src/mira/parameters_flexer.ll | 474 +-
src/mira/parameters_tokens.h | 192 +-
src/mira/pcrcontainer.C | 890 -
src/mira/pcrcontainer.H | 435 -
src/mira/ppathfinder.C | 2492 ---
src/mira/ppathfinder.H | 472 -
src/mira/preventinitfiasco.C | 372 -
src/mira/read.C | 4520 +++--
src/mira/read.H | 722 +-
src/mira/readgrouplib.C | 824 -
src/mira/readgrouplib.H | 475 -
src/mira/readlotstat.C | 51 -
src/mira/readlotstat.H | 64 -
src/mira/readpool.C | 2421 ++-
src/mira/readpool.H | 296 +-
src/mira/readpool_io.C | 1005 -
src/mira/readpool_io.H | 172 -
src/mira/readseqtypes.H | 47 -
src/mira/sam_collect.C | 542 -
src/mira/sam_collect.H | 136 -
src/mira/scaffolder.C | 183 +-
src/mira/scaffolder.H | 77 +-
src/mira/seqforfilter_phix174.solexa.xxd | 2 -
src/mira/seqtohash.C | 46 -
src/mira/seqtohash.H | 102 -
src/mira/simple_2Dsignalprocessing.H | 96 -
src/mira/simplebloomfilter.C | 85 -
src/mira/simplebloomfilter.H | 221 -
src/mira/skim.C | 3558 ++--
src/mira/skim.H | 729 +-
src/mira/skim_lowbph.C | 621 -
src/mira/stringcontainer.H | 106 +-
src/mira/structs.H | 378 +-
src/mira/timerestrict.H | 10 +-
src/mira/types_basic.H | 10 -
src/mira/vhash.H | 133 -
src/mira/vluint.H | 388 -
src/mira/warnings.C | 171 -
src/mira/warnings.H | 117 -
src/modules/Makefile.am | 5 -
src/modules/misc.C | 165 -
src/modules/misc.H | 52 -
src/modules/mod_bait.C | 868 -
src/modules/mod_bait.H | 145 -
src/modules/mod_convert.C | 2130 ---
src/modules/mod_convert.H | 154 -
src/modules/mod_dbgreplay.C | 90 -
src/modules/mod_diff.C | 305 -
src/modules/mod_diff.H | 55 -
src/modules/mod_memestim.C | 438 -
src/modules/mod_memestim.H | 27 -
src/modules/mod_mer.C | 524 -
src/modules/mod_mer.H | 67 -
src/modules/mod_mira.C | 480 -
src/modules/mod_mira.H | 10 -
src/modules/mod_scaffold.C | 101 -
src/modules/mod_scaffold.H | 50 -
src/modules/mod_sigconex.C | 253 -
src/modules/mod_sigconex.H | 51 -
src/modules/mod_tagsnp.C | 254 -
src/modules/mod_tagsnp.H | 54 -
src/progs/Makefile.am | 113 +-
src/progs/Makefile.in | 215 +-
src/progs/convert_project.C | 2518 +++
src/progs/dbgreplay.C | 124 +
src/progs/fastatool.C | 338 +
src/progs/me_step1.par | 27 +
src/progs/me_step2.par | 140 +
src/progs/me_step3.par | 152 +
src/progs/mira.C | 1716 +-
src/progs/miratest.C | 677 +-
src/progs/par2c.pl | 7 +
src/progs/quirks.C | 71 -
src/progs/quirks.H | 34 -
src/progs/scftool.C | 510 +
src/progs/sw.C | 140 +
src/progs/version.H | 30 +
src/scripts/Makefile.am | 8 +-
src/scripts/Makefile.in | 63 +-
src/scripts/fasta2frag.tcl | 274 +-
src/scripts/fastaselect.tcl | 125 +
src/scripts/fastqselect.tcl | 170 +
src/stdinc/Makefile.in | 55 +-
src/stdinc/defines.H | 80 +-
src/stdinc/stlincludes.H | 78 +-
src/stdinc/template.C | 22 +-
src/stdinc/template.H | 14 +-
src/stdinc/types.H | 6 +-
src/support/GTAGDB | 52 +-
src/support/Makefile.in | 65 +-
src/test/Makefile.am | 3 +
{doc => src/test}/Makefile.in | 63 +-
src/test/io/Makefile.am | 3 +
{doc => src/test/io}/Makefile.in | 63 +-
src/test/io/fasta/Makefile.am | 19 +
src/{errorhandling => test/io/fasta}/Makefile.in | 122 +-
src/test/io/fasta/tstFASTA.C | 181 +
src/test/io/generalio/Makefile.am | 18 +
src/{modules => test/io/generalio}/Makefile.in | 135 +-
src/test/io/generalio/tstgeneralio.C | 67 +
src/test/io/scf/Makefile.am | 19 +
src/{debuggersupport => test/io/scf}/Makefile.in | 123 +-
src/test/io/scf/tstSCF.C | 30 +
src/test/mira/Makefile.am | 4 +
{doc => src/test/mira}/Makefile.in | 65 +-
src/test/mira/align/Makefile.am | 20 +
.../mira/align}/Makefile.in | 123 +-
src/test/mira/align/tstAlign.C | 72 +
src/test/mira/read/Makefile.am | 10 +
src/{errorhandling => test/mira/read}/Makefile.in | 115 +-
src/test/mira/read/tstRead.C | 117 +
src/test/mira/readpool/Makefile.am | 10 +
.../mira/readpool}/Makefile.in | 115 +-
src/test/mira/readpool/tstReadPool.C | 107 +
src/util/Makefile.am | 10 +-
src/util/Makefile.in | 88 +-
src/util/boostiostrutil.H | 81 -
src/util/dptools.C | 236 +-
src/util/dptools.H | 111 +-
src/util/fileanddisk.C | 1009 -
src/util/fileanddisk.H | 200 -
src/util/fmttext.C | 115 -
src/util/fmttext.H | 49 -
src/util/machineinfo.C | 218 -
src/util/machineinfo.H | 70 -
src/util/memusage.H | 126 +-
src/util/misc.C | 369 +-
src/util/misc.H | 70 +-
src/util/progressindic.H | 64 +-
src/util/stlimprove.H | 40 -
src/util/timer.H | 111 -
src/version.H | 18 -
src/version.stub | 15 -
447 files changed, 91453 insertions(+), 141111 deletions(-)
diff --cc debian/README.source
index 0000000,0000000..fd71d46
new file mode 100644
--- /dev/null
+++ b/debian/README.source
@@@ -1,0 -1,0 +1,27 @@@
++mira for Debian
++---------------
++
++debian/patches/read_default_constructor.patch:
++
++ adding default constructor to class to circumvent error
++ read.C:45:28: error: uninitialized const ‘Read::REA_bposhashstat_default’ [-fpermissive]
++ ../../src/mira/read.H:159:10: note: ‘const struct Read::bposhashstat_t’ has no user-provided default constructor
++
++mira-3.4.0/doc/3rdparty/scaffolding_MIRA_BAMBUS.pdf
++was removed by a request from upstream.
++
++ -- Steffen Moeller <moeller at debian.org> Tue, 23 Aug 2011 22:56:50 +0200
++
++Basic packaging seems fine. There are issues with the location of
++Google's tcmalloc library.
++
++ -- Charles Plessy <charles-debian-nospam at plessy.org> Sun, 5 Aug 2007 14:01:14 +0900
++ Steffen Moeller <moeller at debian.org> Fri, 04 Mar 2011 17:39:07 +0100
++
++Further to the above, on Sid right now it looks like this should build fine with a
++build dependency on libgoogle-perftools-dev and a runtime dependency on
++libtcmalloc-minimal0. However, backporting this package to Lucid is a non-starter
++so instead I've made it build against the runtime.
++
++ -- Tim Booth <tbooth at ceh.ac.uk> Thu, 18 Aug 2011 11:34:11 +0100
++
diff --cc debian/TODO
index 0000000,0000000..7c86cbd
new file mode 100644
--- /dev/null
+++ b/debian/TODO
@@@ -1,0 -1,0 +1,3 @@@
++Maybe the mira package should be renamed mira-assembler, as there are other
++software called Mira around, such as http://www.mirametrics.com/ (proprietary,
++but...)
diff --cc debian/changelog
index 36d84f3,0000000..cec164f
mode 100644,000000..100644
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,205 -1,0 +1,35 @@@
- mira (4.9.5-4) UNRELEASED; urgency=medium
-
- * Loosen boost dependencies.
-
- -- Michael R. Crusoe <crusoe at ucdavis.edu> Tue, 02 Feb 2016 00:45:21 -0800
-
- mira (4.9.5-3) unstable; urgency=medium
-
- * Remove *.cc files that are created by old flex version which breaks
- build otherwise
- Closes: #812681
-
- -- Andreas Tille <tille at debian.org> Wed, 27 Jan 2016 13:19:53 +0100
-
- mira (4.9.5-2) unstable; urgency=medium
-
- * Verify that package builds without problems with gcc-5
- Closes: #793261
- * override false lintian positives
- * Fix spelling
- * wrote missing manpage and moved manpages to separate dir
-
- -- Andreas Tille <tille at debian.org> Fri, 04 Dec 2015 12:56:09 +0100
-
- mira (4.9.5-1) unstable; urgency=medium
-
- * New upstream version
- * Moved debian/upstream to debian/upstream/metadata
- * cme fix dpkg-control
-
- -- Andreas Tille <tille at debian.org> Wed, 01 Jul 2015 22:09:47 +0200
-
- mira (4.0.2-1) unstable; urgency=low
-
- * new upstream version
-
- -- Thorsten Alteholz <debian at alteholz.de> Sat, 26 Apr 2014 19:00:35 +0200
-
- mira (4.0-1) unstable; urgency=low
-
- [ Thorsten Alteholz ]
- * New upstream version
- * debian/rules: add boost dir in auto_configure (Closes: #735798)
-
- [ Andreas Tille ]
- * cme fix dpkg-control
- * debian/patches/{make.patch,spelling.patch}: applied upstream (thus removed)
-
- -- Thorsten Alteholz <debian at alteholz.de> Sun, 02 Feb 2014 22:51:35 +0100
-
- mira (3.9.18-1) unstable; urgency=low
-
- * New upstream version (most patches applied by upstream)
- * debian/copyright: Add Upstream-Contact
- * debian/control: cme fix dpkg-control
- * debian/mira-assembler.lintian-overrides: deleted unused override
- * debian/rules: Prevent installing duplicated data, rather
- create symlink
- * debian/mirabait.1: wrote missing manpage
-
- -- Andreas Tille <tille at debian.org> Fri, 09 Aug 2013 13:59:24 +0200
-
- mira (3.9.17-1) unstable; urgency=low
-
- [ Thorsten Alteholz ]
- * new upstream version
- * debian/control: Standards-Version set to 3.9.4 (no changes)
- * debian/control: DM-Upload-Allowed: removed
- * debian/control: use dh 9
- * debian/control: add dependency to libboost-iostreams-dev
- * debian/control: improve extended descriptions
- * debian/control: change VCS-tags according to new lintian
- * debian/rules: get-orig-source added
- * debian/watch: do not look at dev-versions
- * debian/mira-doc.README.Debian: correct path to documentation
-
- [ Dmitrijs Ledkovs ]
- * Build depend on libboost-all-dev and libbz2-dev.
- * Add boost-minimal patch, to add boost-libraries in final linking,
- fixing FTBFS (Closes: #701322)
- * Enable parallel builds, to speed up compilation.
-
- [ Andreas Tille ]
- * delete debian/README.source which is outdated / wrong
- * debian/*.1: Wrote / reviewed manpages for all installed programs
- * debian/miraSearchESTSNPs.1: Wrote manpage but mention that this
- functionality is deactivated in version 3.9.17
- * debian/mira-assembler.manpages: Simply install all manpages that can be
- found
- * Removed debian/obsolete.mira-assembler.install
- * debian/control: The actual scripts do not contain the .tcl suffix
- in our installation
- * debian/rules:
- - Currently miraSearchESTSNPs and miraclip claim to be deactivated so
- why bothering installing these?
- - Use xz compression for binaries
-
- -- Andreas Tille <tille at debian.org> Fri, 07 Jun 2013 08:34:21 +0200
-
- mira (3.4.0.1-3) unstable; urgency=low
-
- [ Charles Plessy ]
- * Build-depend on libgoogle-perftools-dev instead of libtcmalloc-minimal0
- (debian/control, debian/README.source, debian/rules).
- Closes: #673527, #674822
- * Conforms to Policy 3.9.3 (debian/control, no other changes needed).
- * Rely on dpkg source format 3.0 (quilt) for the patches, and remove
- build dependance on quilt (debian/control, debian/rules).
- * Verbose Debhelper (debian/rules).
-
- [ Andreas Tille ]
- * debian/upstream: very small fix to prevent bibcheck warning
-
- -- Charles Plessy <plessy at debian.org> Mon, 28 May 2012 10:51:01 +0900
-
- mira (3.4.0.1-2) unstable; urgency=low
-
- [ Andreas Tille ]
- * Remove two patches:
- - read_default_constructor.patch which introduces a duplicate
- bposhashstat_t() definition
- - fix_duplicate_bposhashstat_t_definition.patch which removes
- this duplicate afterwards
-
- [ Charles Plessy ]
- * Removed unconditional dependency on libtcmalloc-minimal0 (debian/control).
- Closes: #654884
- * Machine-readable debian/copyright file.
-
- -- Charles Plessy <plessy at debian.org> Sat, 07 Jan 2012 13:24:48 +0900
-
- mira (3.4.0.1-1) unstable; urgency=low
-
- * New upstream version
- Closes: #648762 (at least if I'm not mislead - feel free to reopen)
- * debian/control:
- - Added myself to Uploaders
- - Depends: libtcmalloc-minimal0 [i386 amd64]
- Thanks for the patch to Michael Terry <michael.terry at canonical.com>
- however I left out powerpc where libtcmalloc-minimal0 is not
- available
- Closes: #649093
- - Fixed Vcs fields
- * debian/patches/fix_duplicate_bposhashstat_t_definition.patch
- Remove duplicate definition of bposhashstat_t()
-
- -- Andreas Tille <tille at debian.org> Thu, 08 Dec 2011 08:50:19 +0100
-
- mira (3.4.0-3ubuntu1) lucid; urgency=low
-
- * Small fix to dependencies - there is no "mira" binary package
-
- -- Tim Booth <tbooth at ceh.ac.uk> Fri, 02 Dec 2011 15:00:35 +0000
-
- mira (3.4.0-3) unstable; urgency=low
-
- * Rendering Tim's additions available for Debian
-
- -- Steffen Moeller <moeller at debian.org> Sat, 03 Sep 2011 01:02:10 +0200
-
- mira (3.4.0-2ubuntu5) lucid; urgency=low
-
- * Small fix to clean target and suppress warnings
- on Lucid backport.
- * Fixed missing dependency which caused misleading configure
- failure.
- * Yet another missing build dep - flex and xxd
-
- -- Tim Booth <tbooth at ceh.ac.uk> Tue, 30 Aug 2011 17:17:11 +0100
-
+mira (3.4.0-2) unstable; urgency=low
+
+ * Fixing source tree (removed PDF with no source)
+
+ -- Steffen Moeller <moeller at debian.org> Mon, 29 Aug 2011 22:54:53 +0200
+
+mira (3.4.0-1) UNRELEASED; urgency=low
+
+ * New upstream version.
+ - added default constructor to avoid FTBFS
- * Sponsoring Tim's work for Debian
++ * Sposoring Tim's work for Debian
+ * Using 3.0 (quilt) source format for bz2 upstream
+
+ -- Steffen Moeller <moeller at debian.org> Tue, 23 Aug 2011 20:46:32 +0200
+
+mira (3.4rc3-2) lucid; urgency=low
+
+ * Version 3.2.1.8 has been removed from SF.net. Packaging the
+ latest RC instead.
+ * Fixed linking against tcmalloc (see README)
+ * Fixed build of docs - HTML is installed in mira-doc
+
+ -- Tim Booth <tbooth at ceh.ac.uk> Fri, 19 Aug 2011 12:35:12 +0100
+
+mira (3.2.1.8-1) UNRELEASED; urgency=low
+
+ * Initial release (Closes: #435915)
+
+ -- Steffen Moeller <moeller at debian.org> Fri, 04 Mar 2011 11:55:25 +0100
+
+mira (3~rc2-1) UNRELEASED; urgency=low
+
+ * Initial packaging.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 08 Sep 2009 13:35:31 +0900
diff --cc debian/compat
index ec63514,0000000..7f8f011
mode 100644,000000..100644
--- a/debian/compat
+++ b/debian/compat
@@@ -1,1 -1,0 +1,1 @@@
- 9
++7
diff --cc debian/control
index 19cc4f9,0000000..9061702
mode 100644,000000..100644
--- a/debian/control
+++ b/debian/control
@@@ -1,99 -1,0 +1,72 @@@
+Source: mira
- Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
- Uploaders: Charles Plessy <plessy at debian.org>,
- Steffen Moeller <moeller at debian.org>,
- Tim Booth <tbooth at ceh.ac.uk>,
- Andreas Tille <tille at debian.org>,
- Thorsten Alteholz <debian at alteholz.de>,
- Michael R. Crusoe <crusoe at ucdavis.edu>
+Section: science
+Priority: optional
- Build-Depends: debhelper (>= 9),
- dblatex,
- dh-autoreconf,
- autoconf-archive,
- docbook-xsl,
- libbz2-dev,
- libexpat1-dev,
- libgoogle-perftools-dev [i386 amd64],
- perl,
- flex,
- vim-common,
- zlib1g-dev,
- libboost-thread-dev,
- libboost-regex-dev,
- libboost-filesystem-dev,
- libboost-system-dev,
- libboost-iostreams-dev
- Standards-Version: 3.9.6
- Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/mira/trunk/
- Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/mira/trunk/
++Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
++DM-Upload-Allowed: yes
++Uploaders: Charles Plessy <plessy at debian.org>, Steffen Moeller <moeller at debian.org>,
++ Tim Booth <tbooth at ceh.ac.uk>
++Build-Depends: debhelper (>= 7.0.50~), autotools-dev, dblatex, docbook-xsl,
++ libboost-thread-dev, libexpat1-dev, libtcmalloc-minimal0, perl,
++ quilt,
++ zlib1g-dev
++Standards-Version: 3.9.2
+Homepage: http://chevreux.org/projects_mira.html
++Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mira/trunk/?rev=0&sc=0
++Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mira/trunk/
+
+Package: mira-assembler
+Architecture: any
- Depends: ${shlibs:Depends},
- ${misc:Depends}
- Suggests: mira-examples,
- mira-doc
++Depends: ${shlibs:Depends}, ${misc:Depends}, libtcmalloc-minimal0
++Suggests: mira-examples, mira-doc
+Description: Whole Genome Shotgun and EST Sequence Assembler
+ The mira genome fragment assembler is a specialised assembler for
+ sequencing projects classified as 'hard' due to high number of similar
+ repeats. For expressed sequence tags (ESTs) transcripts, miraEST is
+ specialised on reconstructing pristine mRNA transcripts while
+ detecting and classifying single nucleotide polymorphisms (SNP)
- occurring in different variations thereof.
++ occuring in different variations thereof.
+ .
+ The assembler is routinely used for such various tasks as mutation
+ detection in different cell types, similarity analysis of transcripts
+ between organisms, and pristine assembly of sequences from various
+ sources for oligo design in clinical microarray experiments.
+ .
+ The package provides the following executables:
+ Binaries provided:
+ * mira: for assembly of genome sequences
+ * miramem: estimating memory needed to assemble projects. Realised through
+ link to mira.
+ * convert_project: for converting project file types into other types
+ * caf2fasta, caf2gbf, caf2text, caf2html, gbf2caf and gbf2fasta are some
+ frequently used file converters (realised through links to convert_project)
+ * scftool: set of tools useful when working with SCF trace files
+ * fastatool: set of tools useful when working with FASTA trace files
+ .
+ Scripts provided:
- * fasta2frag: fragmenting sequences into smaller, overlapping
++ * fasta2frag.tcl: fragmenting sequences into smaller, overlapping
+ subsequences. Useful for simulating shotgun sequences. Can create
+ subsequences in both directions (/default) and also paired-end sequences.
- * fastaselect: given a FASTA file (and possibly a FASTA quality file) and
++ * fastaselect.tcl: given a FASTA file (and possibly a FASTA quality file) and
+ a file with names of reads, select the sequences from the input FASTA (and
+ quality file) and writes them to an output FASTA
- * fastqselect: like fastaselect, only for FASTQ
- * fixACE4consed: Consed has a bug which incapacitates it from reading
++ * fastqselect.tcl: like fastaselect.tcl, only for FASTQ
++ * fixACE4consed.tcl: Consed has a bug which incapacitates it from reading
+ consensus tags in ACE files written by the MIRA assembler (and possibly
+ other programs). This script massages an ACE file so that consed can read
+ the consensus tags.
+
++
+Package: mira-examples
+Architecture: all
+Depends: ${misc:Depends}
- Suggests: mira-assembler,
- mira-doc
++Suggests: mira
+Description: files to experiment with the mira assembler
- The mira genome fragment assembler is a specialised assembler for
- sequencing projects classified as 'hard' due to high number of similar
- repeats.
- .
- This package contains a series of files to exploit the functionality
- of mira.
++ A series of files to exploit the functionality of mira.
+
+Package: mira-doc
- Architecture: all
+Section: doc
++Architecture: all
+Depends: ${misc:Depends}
- Suggests: mira-assembler
++Suggests: mira
+Description: documentation for the mira assembler
- The mira genome fragment assembler is a specialised assembler for
- sequencing projects classified as 'hard' due to high number of similar
- repeats.
- .
- This package contains an HTML book introducing to mira.
++ An HTML book introducing to mira.
diff --cc debian/copyright
index c0b728d,0000000..2510d74
mode 100644,000000..100644
--- a/debian/copyright
+++ b/debian/copyright
@@@ -1,53 -1,0 +1,63 @@@
- Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
- Upstream-Contact: Bastien Chevreux <bach at chevreux.org>
++Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
++
+Source: http://jaist.dl.sourceforge.net/project/mira-assembler/MIRA/V3rc2/mira-3rc2.tar.bz2
+
- Files: *
- Copyright: © 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas Pfisterer, Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecula Biophysics.
- © 2001-2013 for MIRA V2.x: Bastien Chevreux <bach at chevreux.org>
- License: GPL-2+
- Comment:
- Author of MIRA
- .
- Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches
- Krebsforschungsinstitut, DKFZ) in Heidelberg, DE
- Now at DSM Nutritional Products AG, Kaiseraugst, CH
- .
- .
- Author of EdIt
- .
- Thomas Pfisterer, formerly at the German Cancer Research Center (Deutsches
- Krebsforschungsinstitut, DKFZ) in Heidelberg. DE
- Now at MWG Biotech AG, Ebersberg, DE
-
- Files: src/io/scf.H
- Copyright: © Medical Research Council 1994
- License: staden
- Permission to use, copy, modify and distribute this software and its
- documentation for any purpose is hereby granted without fee, provided that
- this copyright and notice appears in all copies.
- .
- This file was written by James Bonfield, Simon Dear, Rodger Staden,
- as part of the Staden Package at the MRC Laboratory of Molecular
- Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
- .
- MRC disclaims all warranties with regard to this software.
- Comment: uses part of a file from the `Staden package'.
-
- License: GPL-2+
- 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 2 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 package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
- Comment: On Debian systems, the complete text of the GNU General Public
- License version 2 can be found in `/usr/share/common-licenses/GPL-2'.
+
++© 1997-2000 for MIRA V1.x and EdIt: Bastien Chevreux, Thomas Pfisterer,
++Deutsches Krebsforschungszentrum Heidelberg -- Dept. of Molecular
++Biophysics.
++© 2001-2007 for MIRA V2.x: Bastien Chevreux.
++
++Author of MIRA
++
++Bastien Chevreux, formerly at the German Cancer Research Center (Deutsches
++ Krebsforschungsinstitut, DKFZ) in Heidelberg, DE
++ Now at DSM Nutritional Products AG, Kaiseraugst, CH
++
++
++Author of EdIt
++
++Thomas Pfisterer, formerly at the German Cancer Research Center (Deutsches
++ Krebsforschungsinstitut, DKFZ) in Heidelberg. DE
++ Now at MWG Biotech AG, Ebersberg, DE
++
++
++MIRA, EdIt and accompanying programs of the package are licenced under the GPL
++version 2, both in source code and binaries.
++
++License:
++
++ 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 2 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 package; if not, write to the Free Software
++ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
++
++On Debian systems, the complete text of the GNU General
++Public License can be found in `/usr/share/common-licenses/GPL'.
++
++The file src/io/scf.H uses part of a file from the `Staden package', which is
++released under the following terms:
++
++ * Copyright (c) Medical Research Council 1994. All rights reserved.
++ *
++ * Permission to use, copy, modify and distribute this software and its
++ * documentation for any purpose is hereby granted without fee, provided that
++ * this copyright and notice appears in all copies.
++ *
++ * This file was written by James Bonfield, Simon Dear, Rodger Staden,
++ * as part of the Staden Package at the MRC Laboratory of Molecular
++ * Biology, Hills Road, Cambridge, CB2 2QH, United Kingdom.
++ *
++ * MRC disclaims all warranties with regard to this software.
++
++The Debian packaging is © 2007, Charles Plessy <charles-debian-nospam at plessy.org> and
++is licensed under as if it were public domain.
diff --cc debian/mira-assembler.install
index 0000000,0000000..8258f35
new file mode 100644
--- /dev/null
+++ b/debian/mira-assembler.install
@@@ -1,0 -1,0 +1,8 @@@
++src/progs/fastatool usr/bin/
++src/progs/mira usr/bin/
++src/progs/scftool usr/bin/
++src/progs/sw usr/bin/
++src/progs/convert_project usr/bin/
++src/scripts/fasta2frag.tcl usr/bin/
++src/scripts/fastaselect.tcl usr/bin/
++src/scripts/fastqselect.tcl usr/bin/
diff --cc debian/mira-doc.README.Debian
index 6c502b8,0000000..88c5ded
mode 100644,000000..100644
--- a/debian/mira-doc.README.Debian
+++ b/debian/mira-doc.README.Debian
@@@ -1,4 -1,0 +1,4 @@@
+This package provides the Definitive Guide To MIRA book, which is included with
+the default MIRA download, in HTML format.
+
- See: /usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html
++See: /usr/share/doc/mira/DefinitiveGuideToMIRA.html
diff --cc debian/patches/add_shebang_lines
index 0000000,0000000..9d4f7cb
new file mode 100644
--- /dev/null
+++ b/debian/patches/add_shebang_lines
@@@ -1,0 -1,0 +1,27 @@@
++#Add a missing #! line to 2 demo scripts just to please Lintian
++--- a/minidemo/solexa1/runme.sh
+++++ b/minidemo/solexa1/runme.sh
++@@ -1,7 +1,8 @@
+++#!/bin/sh
++
++ ln -s ../data/solexa_eco_art/ecoli_* .
++
++ mira --project=ecoli --job=mapping,genome,normal,solexa --fasta -AS:nop=1 -SB:bsn=ecoli_k12_mg1655 -SB:lsd=yes:bft=gbf SOLEXA_SETTINGS -AL:mrs=60:shme=5 | tee log_assembly.txt
++
++ echo
++-echo "Please read the README to know what is in the results."
++\ No newline at end of file
+++echo "Please read the README to know what is in the results."
++--- a/minidemo/solexa2/runme.sh
+++++ b/minidemo/solexa2/runme.sh
++@@ -1,7 +1,8 @@
+++#!/bin/sh
++
++ ln -s ../data/solexa_eco_art/ecoli_*fasta* .
++
++ mira --project=ecoli --job=denovo,genome,normal,solexa --fasta | tee log_assembly.txt
++
++ echo
++-echo "This was a de-novo assembly of Solexa reads."
++\ No newline at end of file
+++echo "This was a de-novo assembly of Solexa reads."
diff --cc debian/patches/read_default_constructor.patch
index 0000000,0000000..f988bc4
new file mode 100644
--- /dev/null
+++ b/debian/patches/read_default_constructor.patch
@@@ -1,0 -1,0 +1,15 @@@
++Index: mira-3.4.0/src/mira/read.H
++===================================================================
++--- mira-3.4.0.orig/src/mira/read.H 2011-08-23 21:25:23.821159194 +0200
+++++ mira-3.4.0/src/mira/read.H 2011-08-23 21:53:40.777573643 +0200
++@@ -213,6 +213,10 @@
++ ostr << "r; " << bhs.rev << ' ';
++ return ostr;
++ }
+++
+++ bposhashstat_t () {
+++ }
+++
++ };
++
++
diff --cc debian/patches/series
index 77bee94,0000000..244e68e
mode 100644,000000..100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@@ -1,2 -1,0 +1,3 @@@
- fix_strange_link_issue.patch
- spelling.patch
++add_shebang_lines
++xsltproc_nonet_for_doc_build
++read_default_constructor.patch
diff --cc debian/patches/xsltproc_nonet_for_doc_build
index 0000000,0000000..939d7a6
new file mode 100644
--- /dev/null
+++ b/debian/patches/xsltproc_nonet_for_doc_build
@@@ -1,0 -1,0 +1,21 @@@
++# Makes sure the documentation builds without needing network access.
++# This magically works if docbook-xsl is installed, otherwise it fails
++# complaining that it needs to access http://docbook.sourceforge.net/release/xsl/current/html/docbook.xsl
++
++--- a/doc/docbook/Makefile.in
+++++ b/doc/docbook/Makefile.in
++@@ -385,12 +385,12 @@
++
++ %_part.html: %_part.xml
++ @echo "Making .html out of _part.xml" $@
++- @$(SHELL) -ec 'xsltproc --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<'
+++ $(SHELL) -ec 'xsltproc --nonet --xinclude --output $@ $(top_srcdir)/doc/docbook/mira.xsl $<'
++
++ chapters: ${CHAP_HTML}
++
++ books: ${CHAP_XML} book_definitiveguide.xml
++- xsltproc --xinclude --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml
+++ xsltproc --xinclude --nonet --output DefinitiveGuideToMIRA.html $(top_srcdir)/doc/docbook/book.xsl $(top_srcdir)/doc/docbook/book_definitiveguide.xml
++ dblatex --xslt-opts=--nonet --output=DefinitiveGuideToMIRA.pdf $(top_srcdir)/doc/docbook/book_definitiveguide.xml
++
++ all: chapters books
diff --cc debian/rules
index 71d1343,0000000..720dc78
mode 100755,000000..100755
--- a/debian/rules
+++ b/debian/rules
@@@ -1,103 -1,0 +1,45 @@@
+#!/usr/bin/make -f
+
+# Uncomment this to turn on verbose mode.
- export DH_VERBOSE=1
- #Hacky thing to allow building against tcmalloc without installing
- #troublesome libbgoogle-perftools-dev, see README.Debian
- export DEB_CFLAGS_MAINT_APPEND=-L$(CURDIR)/lib
-
- pkg=mira-assembler
- exampledir=usr/share/doc/mira-examples/examples/minidemo/data/bbdataset1/
-
- include /usr/share/dpkg/default.mk
++#export DH_VERBOSE=1
+
+%:
- dh $@ --with autoreconf
++ dh $@ --with quilt
+
+override_dh_auto_install :
- make install DESTDIR=$(CURDIR)/debian/$(pkg)
++ make install DESTDIR=$(CURDIR)/debian/mira-assembler
+ #There is no installation target for the docs
- mkdir -p $(CURDIR)/debian/tmp/usr/share/doc/$(pkg)
- cp -r -t $(CURDIR)/debian/tmp/usr/share/doc/$(pkg) doc/docbook/bookfigures doc/docbook/images \
++ mkdir -p $(CURDIR)/debian/tmp/usr/share/doc/mira-assembler
++ cp -r -t $(CURDIR)/debian/tmp/usr/share/doc/mira-assembler doc/docbook/bookfigures doc/docbook/images \
+ doc/docbook/doccss doc/docbook/DefinitiveGuideToMIRA.html || true
+
- override_dh_installexamples:
- dh_installexamples
- # avoid duplicated files
- if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.fasta.qual $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual >/dev/null ; then \
- echo "removing copy of $(exampledir)/cjejuni_demo_in.fasta.qual and create symling" ; \
- rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual ; \
- ln -s cjejuni_demo_in.fasta.qual.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.qual.gz ; \
- fi
- if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.fasta $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta >/dev/null ; then \
- echo "removing copy of $(exampledir)/cjejuni_demo_in.fasta and create symling" ; \
- rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta ; \
- ln -s cjejuni_demo_in.fasta.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_in.sanger.fasta.gz ; \
- fi
- if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_NCTC11168_first40kb.gbf $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf >/dev/null ; then \
- echo "removing copy of $(exampledir)/cjejuni_NCTC11168_first40kb.gbf and create symling" ; \
- rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf ; \
- ln -s cjejuni_NCTC11168_first40kb.gbf.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_backbone_in.gbf.gz ; \
- fi
- if cmp $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.xml $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml >/dev/null ; then \
- echo "removing copy of $(exampledir)/cjejuni_demo_traceinfo_in.xml and create symling" ; \
- rm -f $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml ; \
- ln -s cjejuni_demo_traceinfo_in.xml.gz $(CURDIR)/debian/mira-examples/$(exampledir)/cjejuni_demo_traceinfo_in.sanger.xml.gz ; \
- fi
-
+override_dh_auto_test:
+ make check
+
+#Make the docs
+override_dh_auto_build:
- # some *.cc files are created by old flex version which breaks the build
- # see bug #812681
- find -name '*.ll' | sed -e 's/[.]ll$$/.cc/' | xargs rm
- dh_auto_build --parallel
++ dh_auto_build
+ifneq (,$(findstring mira-doc, $(shell dh_listpackages)))
- dh_auto_build --sourcedir=doc --parallel
++ dh_auto_build --sourcedir=doc
+endif
+
+#Remove unneeded .tcl extensions from scripts
+override_dh_install:
+ dh_install
- if [ -d debian/$(pkg) ] ; then \
- for f in $$(ls debian/$(pkg)/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \
++ if [ -d debian/mira-assembler ] ; then \
++ for f in $$(ls debian/mira-assembler/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \
+ fi
- # In version 3.9.17 executing miraSearchESTSNPs just leads to "De-activated atm, sorry."
- # If this is the case, it should not be installed
- for deactivated in miraSearchESTSNPs miraclip ; do \
- if [ -e debian/$(pkg)/usr/bin/$${deactivated} ] ; then \
- if [ "`debian/$(pkg)/usr/bin/$${deactivated} 2>&1 | tee`" = "De-activated atm, sorry." ] ; then rm -f debian/$(pkg)/usr/bin/$${deactivated} ; fi \
- else \
- echo "debian/$(pkg)/usr/bin/$${deactivated} does not exist" ; \
- fi ; \
- done
+
- #Must clean up the docs before cleaning out config.status
- #Then scrub some junk not picked up by 'make clean'
- override_dh_auto_clean:
- ( cd doc ; make clean ) || true
- dh_auto_clean
- find * -name Makefile -exec rm '{}' ';'
- find * -name '*.xxd.H' -exec rm '{}' ';'
- find * -name '*.par.H' -exec rm '{}' ';'
- find * -name 'compileinfo.*' -exec rm '{}' ';'
++#Hacky thing to allow building against tcmalloc without installing
++#troublesome libbgoogle-perftools-dev, see README.Debian
++export LDFLAGS=-L$(CURDIR)/lib
+
+override_dh_clean:
+ dh_clean
+ rm -rf lib
+
+override_dh_auto_configure :
+ mkdir lib
- ln -s /usr/lib/libtcmalloc_minimal.so.4 lib/libtcmalloc_minimal.so
- #dh_auto_configure
- dh_auto_configure -- --with-boost-libdir=/usr/lib/$(DEB_HOST_MULTIARCH)
-
- override_dh_builddeb:
- dh_builddeb -- -Z xz
-
- get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --destdir=../tarballs
++ ln -s /usr/lib/libtcmalloc_minimal.so.0 lib/libtcmalloc_minimal.so
++ dh_auto_configure
+
diff --cc debian/stamp-autotools-files
index 0000000,0000000..e69de29
new file mode 100644
--- /dev/null
+++ b/debian/stamp-autotools-files
diff --cc debian/stamp-makefile-build
index 0000000,0000000..e69de29
new file mode 100644
--- /dev/null
+++ b/debian/stamp-makefile-build
diff --cc debian/stamp-makefile-check
index 0000000,0000000..e69de29
new file mode 100644
--- /dev/null
+++ b/debian/stamp-makefile-check
diff --cc debian/upstream-metadata.yaml
index 0000000,0000000..6a76082
new file mode 100644
--- /dev/null
+++ b/debian/upstream-metadata.yaml
@@@ -1,0 -1,0 +1,18 @@@
++Bugs: http://sourceforge.net/apps/trac/mira-assembler/newticket
++DOI: 10.1101/gr.1917404
++Homepage: http://www.chevreux.org/projects_mira.html
++Homepage: http://sourceforge.net/apps/trac/mira-assembler
++PubMed: 15140833
++Reference: |
++ @article{BastienChevreux062004,
++ author = {Chevreux, Bastien and Pfisterer, Thomas and Drescher, Bernd and Driesel, Albert J. and Müller, Werner E.G. and Wetter, Thomas and Suhai, Sándor},
++ title={{Using the miraEST Assembler for Reliable and Automated mRNA Transcript Assembly and SNP Detection in Sequenced ESTs}},
++ journal = {Genome Research},
++ volume = {14},
++ number = {6},
++ pages = {1147-1159},
++ doi = {10.1101/gr.1917404},
++ year = {2004},
++ URL = {http://genome.cshlp.org/content/14/6/1147.abstract},
++ eprint = {http://genome.cshlp.org/content/14/6/1147.full.pdf+html}
++ }
diff --cc debian/watch
index 2775ae7,0000000..acc9210
mode 100644,000000..100644
--- a/debian/watch
+++ b/debian/watch
@@@ -1,2 -1,0 +1,2 @@@
+version=3
- http://sf.net/mira-assembler/mira-([\d.]+)\.tar\.bz2
++opts="uversionmangle=s/rc/~rc/" http://sf.net/mira-assembler/mira-(.*).tar.bz2
--
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