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commit 02778bc4bcc408a0e90b81b75a980ca381bdfbcf Author: Michael R. Crusoe <[email protected]> Date: Mon May 2 22:52:33 2016 -0700 new upstream release --- debian/changelog | 19 ++ debian/control | 62 +++-- 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-examples.examples | 2 +- debian/mira-examples.lintian-overrides | 2 +- debian/mira-rfam-12s-rrna.install | 3 + debian/mira-rfam-12s-rrna.lintian-overrides | 2 + debian/mira-rfam-12s-rrna.postinst | 10 + debian/mira-rfam-12s-rrna.postrm | 7 + debian/patches/fix_strange_link_issue.patch | 16 -- debian/patches/gcc-6.patch | 16 -- debian/patches/make-reproducible | 19 -- debian/patches/man-directory | 9 + debian/patches/series | 5 +- debian/patches/sls-rrna-fix | 19 ++ debian/patches/spelling.patch | 390 +--------------------------- debian/rules | 78 ++---- 30 files changed, 130 insertions(+), 1810 deletions(-) diff --git a/debian/changelog b/debian/changelog index dccb5f6..24f9afd 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,3 +1,22 @@ +mira (4.9.6-1) unstable; urgency=medium + + * New upstream release. + * dropped all patches except for one spelling fix, as they were incorporated + upstream + * dropped the -examples package for now, as the minidemo is missing from + upstream in this release. + * our manpages have been adopted and adapted upstream, so they have been + removed + * added architecture independent package for rfam 12s rRNA database + * enable building docs & rfam packages separately + * Standards-Version bump to 3.9.8 + * Updated package descriptions to remove tools that upstream no longer + provides + * minidemo is missing from 4.9.6, commented out -examples package for now + * cleaned out unnecessary stanzas from debian/rules + + -- Michael R. Crusoe <[email protected]> Wed, 04 May 2016 11:18:26 -0700 + mira (4.9.5-6) unstable; urgency=medium * Fix build issue with gcc-6 diff --git a/debian/control b/debian/control index 7f57ee3..0c72d87 100644 --- a/debian/control +++ b/debian/control @@ -5,14 +5,12 @@ Uploaders: Charles Plessy <[email protected]>, Tim Booth <[email protected]>, Andreas Tille <[email protected]>, Thorsten Alteholz <[email protected]>, - Michael R. Crusoe <[email protected]> + Michael R. Crusoe <[email protected]> Section: science Priority: optional Build-Depends: debhelper (>= 9), - dblatex, dh-autoreconf, autoconf-archive, - docbook-xsl, libbz2-dev, libexpat1-dev, libgoogle-perftools-dev [i386 amd64], @@ -25,7 +23,9 @@ Build-Depends: debhelper (>= 9), libboost-filesystem-dev, libboost-system-dev, libboost-iostreams-dev -Standards-Version: 3.9.6 +Build-Depends-Indep: docbook-xsl, + dblatex +Standards-Version: 3.9.8 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/mira.git Vcs-Git: https://anonscm.debian.org/git/debian-med/mira.git Homepage: http://chevreux.org/projects_mira.html @@ -34,8 +34,9 @@ Package: mira-assembler Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} -Suggests: mira-examples, - mira-doc +Recommends: mira-rfam-12s-rrna +Suggests: mira-doc, +# mira-examples, 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 @@ -52,39 +53,36 @@ Description: Whole Genome Shotgun and EST Sequence Assembler 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 - 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 - 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 - 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. + * miramem: estimating memory needed to assemble projects. + * mirabait: a "grep" like tool to select reads with kmers up to 256 bases. + * miraconvert: is a tool to convert, extract and sometimes recalculate all + kinds of data related to sequence assembly files. + +#Package: mira-examples +#Architecture: all +#Depends: ${misc:Depends} +#Suggests: mira-assembler, +# mira-doc +#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. -Package: mira-examples +Package: mira-rfam-12s-rrna Architecture: all Depends: ${misc:Depends} -Suggests: mira-assembler, - mira-doc -Description: files to experiment with the mira assembler +Pre-Depends: mira-assembler +Suggests: mira-doc +Description: extract of RFAM 12 rRNA database 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. + This package contains data to enable MIRA and MIRABAIT to search for rRNA and + rDNA. This data set contains an excerpt of the RFAM database. Package: mira-doc Architecture: all diff --git a/debian/mans/convert_project.1 b/debian/mans/convert_project.1 deleted file mode 100644 index 028746c..0000000 --- a/debian/mans/convert_project.1 +++ /dev/null @@ -1,302 +0,0 @@ -.TH CONVERT_PROJECT "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -convert_project \- convert assembly and sequencing file types -.SH DESCRIPTION -This program is part of the MIRA assembler package. It is used to convert -project file types into other types. Please check out the -documentation below for more detailed information about convert_project. -.SH SYNOPSIS -.IP convert_project -[\-f <fromtype>] [\-t <totype> [\-t <totype> ...]] -[\-aChimMsuZ] -[\-AcflnNoqrtvxXyz {...}] -{infile} {outfile} [<totype> <totype> ...] -.SH OPTIONS -.TP -\fB\-f\fR <fromtype> -load this type of project files, where fromtype is: -.TP -caf -a complete assembly or single sequences from CAF -.TP -maf -a complete assembly or single sequences from CAF -.TP -fasta -sequences from a FASTA file -.TP -fastq -sequences from a FASTQ file -.TP -gbf -sequences from a GBF file -.TP -phd -sequences from a PHD file -.TP -fofnexp -sequences in EXP files from file of filenames -.TP -\fB\-t\fR <totype> -write the sequences/assembly to this type (multiple -mentions of \fB\-t\fR are allowed): -.TP -ace -sequences or complete assembly to ACE -.TP -caf -sequences or complete assembly to CAF -.TP -maf -sequences or complete assembly to MAF -.TP -sam -complete assembly to SAM -.TP -samnbb -like above, but leaving out reference (backbones) in mapping assemblies -.TP -gbf -sequences or consensus to GBF -.TP -gff3 -consensus to GFF3 -.TP -wig -assembly coverage info to wiggle file -.TP -gcwig -assembly gc content info to wiggle file -.TP -fasta -sequences or consensus to FASTA file (qualities to -.IP -\&.qual) -.TP -fastq -sequences or consensus to FASTQ file -.TP -exp -sequences or complete assembly to EXP files in -.IP -directories. Complete assemblies are suited for gap4 -import as directed assembly. -Note: using caf2gap to import into gap4 is recommended though -.TP -text -complete assembly to text alignment (only when \fB\-f\fR is -.IP -caf, maf or gbf) -.TP -html -complete assembly to HTML (only when \fB\-f\fR is caf, maf or -.IP -gbf) -.TP -tcs -complete assembly to tcs -.TP -hsnp -surrounding of SNP tags (SROc, SAOc, SIOc) to HTML -(only when \fB\-f\fR is caf, maf or gbf) -.TP -asnp -analysis of SNP tags -(only when \fB\-f\fR is caf, maf or gbf) -.TP -cstats -contig statistics file like from MIRA -(only when source contains contigs) -.TP -crlist -contig read list file like from MIRA -(only when source contains contigs) -.TP -maskedfasta -reads where sequencing vector is masked out -(with X) to FASTA file (qualities to .qual) -.TP -scaf -sequences or complete assembly to single sequences CAF -.TP -\fB\-a\fR -Append to target files instead of rewriting -.TP -\fB\-A\fR <string> -String with MIRA parameters to be parsed -Useful when setting parameters affecting consensus -calling like \fB\-CO\fR:mrpg etc. -E.g.: \fB\-a\fR "454_SETTINGS \fB\-CO\fR:mrpg=3" -.TP -\fB\-b\fR -Blind data -Replaces all bases in reads/contigs with a 'c' -.TP -\fB\-C\fR -Perform hard clip to reads -When reading formats which define clipping points, will -.IP -save only the unclipped part into the result file. -.IP -Applies only to files/formats which do not contain -.IP -contigs. -.TP -\fB\-d\fR -Delete gap only columns -When output is contigs: delete columns that are -.IP -entirely gaps (like after having deleted reads during -editing in gap4 or similar) -.IP -When output is reads: delete gaps in reads -.TP -\fB\-F\fR -Filter to read groups -Special use case, do not use yet. -.TP -\fB\-m\fR -Make contigs (only for \fB\-t\fR = caf or maf) -Encase single reads as contig singlets into the CAF/MAF -file. -.TP -\fB\-n\fR <filename> -when given, selects only reads or contigs given by -name in that file. -.TP -\fB\-i\fR -when \fB\-n\fR is used, inverts the selection -.TP -\fB\-o\fR -fastq quality Offset (only for \fB\-f\fR = 'fastq') -Offset of quality values in FASTQ file. Default of 0 -tries to automatically recognise. -.TP -\fB\-Q\fR <quality> -Set default quality for bases in file types without quality values -Furthermore, do not stop if expected quality files are missing (e.g. '.fasta') -.TP -\fB\-R\fR <name> -Rename contigs/singlets/reads with given name string -to which a counter is appended. -Known bug: will create duplicate names if input -.IP -contains contigs/singlets as well as free reads, i.e. -reads not in contigs nor singlets. -.TP -\fB\-S\fR <name> -(name)Scheme for renaming reads, important for paired\-ends -Only 'solexa' is currently supported. -.SS The following switches work only when input (CAF or MAF) contains contigs. -Beware: CAF and MAf can also contain just reads. -.TP -\fB\-M\fR -Do not extract contigs (or their consensus), but the -sequence of the reads they are composed of. -.TP -\fB\-N\fR <filename> -like \fB\-n\fR, but sorts output according to order given -in file. -.TP -\fB\-r\fR [cCqf] -Recalculate consensus and / or consensus quality values -and / or SNP feature tags. -\&'c' recalc cons & cons qualities (with IUPAC) -\&'C' recalc cons & cons qualities (forcing non\-IUPAC) -\&'q' recalc consensus qualities only -\&'f' recalc SNP features -Note: only the last of cCq is relevant, f works as a -.IP -switch and can be combined with cQq (e.g. "\-r C \fB\-r\fR f") -.IP -Note: if the CAF/MAF contains multiple strains, -recalculation of cons & cons qualities is forced, you -.IP -can just influence whether IUPACs are used or not. -.TP -\fB\-s\fR -split output into multiple files instead of creating a -single file -.TP -\fB\-u\fR -\&'fillUp strain genomes' -Fill holes in the genome of one strain (N or @) -with sequence from a consensus of other strains -Takes effect only with \fB\-r\fR and \fB\-t\fR gbf or fasta/q -in FASTA/Q: bases filled up are in lower case -in GBF: bases filled up are in upper case -.TP -\fB\-q\fR <integer> -Defines minimum quality a consensus base of a strain -must have, consensus bases below this will be 'N' -Default: 0 -Only used with \fB\-r\fR, and \fB\-f\fR is caf/maf and \fB\-t\fR is (fasta -.IP -or gbf) -.TP -\fB\-v\fR -Print version number and exit -.TP -\fB\-x\fR <integer> -Minimum contig or read length -When loading, discard all contigs / reads with a -length less than this value. Default: 0 (=switched off) -Note: not applied to reads in contigs! -.TP -\fB\-X\fR <integer> -Similar to \fB\-x\fR but applies only to reads and -then to the clipped length. -.TP -\fB\-y\fR <integer> -Minimum average contig coverage -When loading, discard all contigs with an -average coverage less than this value. -Default: 1 -.TP -\fB\-z\fR <integer> -Minimum number of reads in contig -When loading, discard all contigs with a -number of reads less than this value. -Default: 0 (=switched off) -.TP -\fB\-l\fR <integer> -when output as text or HTML: number of bases shown in -one alignment line. Default: 60. -.TP -\fB\-c\fR <character> -when output as text or HTML: character used to pad -endgaps. Default: ' ' (blank) -.PP -Aliases: -caf2html, exp2fasta, ... etc. Any combination of "<validfromtype>2<validtotype>" -can be used as program name (also using links) so as that convert_project -automatically sets \fB\-f\fR and \fB\-t\fR accordingly. -.SH EXAMPLES -.IP -convert_project source.maf dest.sam -.IP -convert_project source.caf dest.fasta wig ace -.IP -convert_project \-x 2000 \-y 10 source.caf dest.caf -.IP -caf2html \-l 100 \-c . source.caf dest -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/fasta2frag.1 b/debian/mans/fasta2frag.1 deleted file mode 100644 index cb978c7..0000000 --- a/debian/mans/fasta2frag.1 +++ /dev/null @@ -1,95 +0,0 @@ -.TH FASTA2FRAG "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -.B fasta2frag \- splits a single fasta sequence into several overlapping fragments. -.SH DESCRIPTION -This program is part of the MIRA assembler package. The purpose of fasta2frag -is to fragment sequences into smaller, overlapping -subsequences. It can be used for simulating shotgun sequences. It can create -subsequences in both directions (/default) and also paired-end sequences. -Please check out the -documentation below for more detailed information about fasta2frag. -.SH SYNOPSIS -fasta2frag -\fI<options> infile outfile\fR -.SH OPTIONS -\fB\-l\fR -int Length of fragments (default=3000) -.TP -\fB\-i\fR -int Increment of fragment start site (default=2500) -.TP -\fB\-p\fR -int Paired end (default=0 is off, 1 is on) -.TP -\fB\-P\fR -int In paired\-end mode, reverse one of the reads -(0 is off, default=1 is on) -.TP -\fB\-s\fR -int Strobe sequencing (default=0 is off, 1 is on) -.TP -\fB\-q\fR -int Default quality when no quality data present (default=30) -.TP -\fB\-r\fR -int Reverse every nth fragment (default=2) -.TP -\fB\-c\fR -int Circularise fragments so that they form a ring -.IP -(default=0 is is off, 1 would be on) -.TP -\fB\-qualdivisor\fR -int Divide quality values by this (default=1) -.TP -\fB\-minqual\fR -int But give it at least this qual (default=0) -.TP -\fB\-insert_size\fR -int paired\-end: insert size (default=3000) -.TP -\fB\-insert_stdev\fR int -paired\-end: standard dev (default=900) -this is not working at the moment -.TP -\fB\-pairednaming\fR string -naming scheme for paired\-end: -sanger, 454 (default) or solexa -.TP -\fB\-minmut\fR -int min. number of mutations/seq. errors (def=0) -.TP -\fB\-maxmut\fR -int max. number of mutations/seq. errors (def=0) -.TP -\fB\-strobeon\fR -int number of bases read during strobe on -.TP -\fB\-strobeoff\fR -int number of bases during strobe off -.TP -\fB\-startoffset\fR -int start at offset position -.TP -\fB\-namesuffix\fR -string suffix name with string -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/fastaselect.1 b/debian/mans/fastaselect.1 deleted file mode 100644 index 1a133a8..0000000 --- a/debian/mans/fastaselect.1 +++ /dev/null @@ -1,47 +0,0 @@ -.TH FASTASELECT "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -.B fastaselect \- select fasta sequences in a file -.SH DESCRIPTION -This script selects fasta sequences in a file according to names given -in a name file. 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. -.PP -If fasta quality file is present (same basename, but with .qual appended), -then also selects sequences from there. -.PP -Please check out the documentation below for more detailed information. -.SH SYNOPSIS -fastaselect \fI<options>\fR -.SH OPTIONS -.TP -\fB\-infile\fR -name filename containing all fasta sequences -.TP -\fB\-name\fR -name filename containing all names of sequences to select -.TP -\fB\-outfile\fR name -filename where to write selcted sequences to -.SH "SEE ALSO" -fastqselect(1) -.PP -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/fastatool.1 b/debian/mans/fastatool.1 deleted file mode 100644 index cd3a917..0000000 --- a/debian/mans/fastatool.1 +++ /dev/null @@ -1,49 +0,0 @@ -.TH FASTATOOL "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -.B fastatool \- Provides a set of tools useful when working with FASTA files. -.SH DESCRIPTION -This program is part of the MIRA assembler package. -Fastatool provides a set of tools useful when working with FASTA trace files. -.PP -Please check out the documentation below for more detailed information. -.SH SYNOPSIS" -fastatool \fI<toolname>\fR \fI<tool parameters>\fR -.SH OPTIONS -.TP -clip -Clips bases on the left and right of a FASTA sequence, writes result to STDOUT. -.IP -Usage: -.TP - clipFASTA \-l leftclip \-r rightclip fastainfile -.TP -sanitize -Deletes sequences with non-IUPAC bases or empty sequences from a FASTA file, -writes the 'surviving' sequences to a new file. -If a quality file is given, a cleaned version of that is also written. -The sequences in the quality files (if given) MUST be in the same order than -in the fasta file. -.IP -Usage: -.TP - sanitizeFASTA fastainfile fastaoutfile [fastaqualin fastaqualoutfile] -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/fastqselect.1 b/debian/mans/fastqselect.1 deleted file mode 100644 index dea7157..0000000 --- a/debian/mans/fastqselect.1 +++ /dev/null @@ -1,47 +0,0 @@ -.TH FASTQSELECT "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -.B fastqselect \- select fastq sequences in a file -.SH DESCRIPTION -This script selects fastq sequences in a file according to names given -in a name file. Given a FASTQ file (and possibly a FASTQ quality file) and -a file with names of reads, select the sequences from the input FASTQ (and -quality file) and writes them to an output FASTQ. -.PP -If fastq quality file is present (same basename, but with .qual appended), -then also selects sequences from there. -.PP -Please check out the documentation below for more detailed information. -.SH SYNOPSIS -fastqselect \fI<options>\fR -.SH OPTIONS -.TP -\fB\-infile\fR -name filename containing all fastq sequences -.TP -\fB\-name\fR -name filename containing all names of sequences to select -.TP -\fB\-outfile\fR name -filename where to write selcted sequences to -.SH "SEE ALSO" -fastaselect(1) -.PP -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/fixACE4consed.1 b/debian/mans/fixACE4consed.1 deleted file mode 100644 index b81fa43..0000000 --- a/debian/mans/fixACE4consed.1 +++ /dev/null @@ -1,32 +0,0 @@ -.TH fixACE4consed "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -fixACE4consed \- workaround to allow consed loading the ACE generated by MIRA -.SH DESCRIPTION -The ACE output of MIRA is conforming to the file specification given in the -consed documentation. However, due to a bug in consed, consed cannot correctly -load tags set by MIRA. -.PP -The script fixACE4consed implements a workaround to allow consed loading the -ACE generated by MIRA. -.SH SYNOPSIS -fixACE4consed infile.ace >outfile.ace -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/mira.1 b/debian/mans/mira.1 deleted file mode 100644 index 2fa7874..0000000 --- a/debian/mans/mira.1 +++ /dev/null @@ -1,53 +0,0 @@ -.TH 3.9.17 "1" "June 2013" "User Commands" -.SH NAME -mira \- The Genome and EST Sequence Assembly System -.SH DESCRIPTION -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. -.PP -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. -.PP -The purpose of the \fBmira\fR executable is to assemble sequencing data. -.SH SYNOPSIS -mira -[\fIOPTION\fR] manifest_file [\fImanifest_file\fR] ... -.SH OPTIONS -.TP -\fB\-c\fR / \fB\-\-cwd=\fRdirectory -Change working directory -.TP -\fB\-r\fR / \fB\-\-resume\fR -Resume an interrupted assembly -.TP -\fB\-h\fR / \fB\-\-help\fR -Print short help and exit -.TP -\fB\-v\fR / \fB\-\-version\fR -Print version and exit -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/miraSearchESTSNPs.1 b/debian/mans/miraSearchESTSNPs.1 deleted file mode 100644 index 0e7cebd..0000000 --- a/debian/mans/miraSearchESTSNPs.1 +++ /dev/null @@ -1,43 +0,0 @@ -.TH miraSearchESTSNPs "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -miraSearchESTSNPs \- Pipeline to discover SNPs in ESTs from different strains -.SH DESCRIPTION -The program miraSearchESTSNPs can be used for assembly of EST data from -different strains (or organisms) and SNP detection within this assembly. -This is the former miraEST program which was renamed as many people got -confused regarding whether to use MIRA in est mode or miraEST. -.PP -miraSearchESTSNPs is a pipeline that reconstructs the pristine mRNA -transcript sequences gathered in EST sequencing projects of more than -one strain, which can be a reliable basis for subsequent analysis steps -like clustering or exon analysis. This means that even genes that -contain only one transcribed SNP on different alleles are first treated -as different transcripts. The optional last step of the assembly process -can be configured as a simple clusterer that can assemble transcripts -containing the same exon sequence -- but only differ in SNP positions -- -into one consensus sequence. Such SNPs can then be analysed, classified -and reliably assigned to their corresponding mRNA transcriptome -sequence. However, it is important to note that miraSearchESTSNPs is an -assembler and not a full blown clustering tool. -.SH SYNOPSIS -In version 3.9.17 this functionality is deactivated. -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/mirabait.1 b/debian/mans/mirabait.1 deleted file mode 100644 index 14a66b5..0000000 --- a/debian/mans/mirabait.1 +++ /dev/null @@ -1,131 +0,0 @@ -.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.43.3. -.TH MIRABAIT: "1" "August 2013" "MIRALIB version 3.9.18" "User Commands" -.SH NAME -mirabait \- select reads from a read collection -.SH SYNOPSIS -.B mirabait -[\fI\-f <fromtype>\fR] [\fI\-t <totype> [\-t <totype> ...]\fR] [\fI\-iklor\fR] baitfile infile <basename_for_outfile(s)> -.SH DESCRIPTION -\fBmirabait\fR selects reads from a read collection which -are partly similar or equal to sequences defined as target -baits. Similarity is defined by finding a user-adjustable number of -common k-mers (sequences of k consecutive bases) which are the same in -the bait sequences and the screened sequences to be selected, either in forward -or reverse complement direction. -.SH OPTIONS -.TP -\fB\-f\fR <fromtype> -load this type of project files, where fromtype is: -.TP -caf -sequences from CAF -.TP -maf -sequences from MAF -.TP -phd -sequences from a PHD -.TP -gbf -sequences from a GBF -.TP -fasta -sequences from a FASTA -.TP -fastq -sequences from a FASTQ -.TP -\fB\-t\fR <totype> -write the sequences to this type (multiple mentions -of \fB\-t\fR are allowed): -.TP -fasta -sequences to FASTA -.TP -fastq -sequences to FASTQ -.TP -caf -sequences to CAF -.TP -maf -sequences to MAF -.TP -txt -sequence names to text file -.TP -\fB\-k\fR -k\-mer, length of bait in bases (<32, default=31) -.TP -\fB\-n\fR -Min. number of k\-mer baits needed (default=1) -.TP -\fB\-i\fR -Inverse hit: writes only sequences that do not hit bait -.TP -\fB\-r\fR -No checking of reverse complement direction -.TP -\fB\-o\fR -fastq quality Offset (only for \fB\-f\fR = 'fastq') -Offset of quality values in FASTQ file. Default: 33 -A value of 0 tries to automatically recognise. -.TP -\fB\-f\fR <fromtype> -load this type of project files, where fromtype is: -.TP -caf -sequences from CAF -.TP -maf -sequences from MAF -.TP -phd -sequences from a PHD -.TP -gbf -sequences from a GBF -.TP -fasta -sequences from a FASTA -.TP -fastq -sequences from a FASTQ -.TP -\fB\-t\fR <totype> -write the sequences to this type (multiple mentions -of \fB\-t\fR are allowed): -.TP -fasta -sequences to FASTA -.TP -fastq -sequences to FASTQ -.TP -caf -sequences to CAF -.TP -maf -sequences to MAF -.TP -txt -sequence names to text file -.TP -\fB\-k\fR -k\-mer, length of bait in bases (<32, default=31) -.TP -\fB\-n\fR -Min. number of k\-mer baits needed (default=1) -.TP -\fB\-i\fR -Inverse hit: writes only sequences that do not hit bait -.TP -\fB\-r\fR -No checking of reverse complement direction -.TP -\fB\-o\fR -fastq quality Offset (only for \fB\-f\fR = 'fastq') -Offset of quality values in FASTQ file. Default: 33 -A value of 0 tries to automatically recognise. -.SH AUTHOR -Bastien Chevreux ([email protected]) diff --git a/debian/mans/miraconvert.1 b/debian/mans/miraconvert.1 deleted file mode 100644 index 671499b..0000000 --- a/debian/mans/miraconvert.1 +++ /dev/null @@ -1,327 +0,0 @@ -.TH MIRACONVERT "1" "December 2015" "miraconvert 4.9.5" "User Commands" -.SH NAME -miraconvert \- convert assembly and sequencing file types -.SH SYNOPSIS -.B miraconvert -[\-f <fromtype>] [\-t <totype> [\-t <totype> ...]] [\-aAChimMsuZ] [\-cflnNoPqrtvxXyYz {...}] {infile} {outfile} [<totype> <totype> ...] -.SH OPTIONS -.TP -\fB\-f\fR \fI<fromtype>\fR -load this type of project files, where fromtype is: -.IP -\fIcaf\fR -a complete assembly or single sequences from CAF -.IP -\fImaf\fR -a complete assembly or single sequences from CAF -.IP -\fIfasta\fR -sequences from a FASTA file -.IP -\fIfastq\fR -sequences from a FASTQ file -.IP -\fIgb[f|k|ff]\fR -sequences from a GenBank file -.IP -\fIphd\fR -sequences from a PHD file -.IP -\fIfofnexp\fR -sequences in EXP files from file of filenames -.TP -\fB\-t\fR \fI<totype>\fR -write the sequences/assembly to this type (multiple -mentions of \fB\-t\fR are allowed): -.IP -\fIace\fR -sequences or complete assembly to ACE -.IP -\fIcaf\fR -sequences or complete assembly to CAF -.IP -\fImaf\fR -sequences or complete assembly to MAF -.IP -\fIsam\fR -complete assembly to SAM -.IP -\fIsamnbb\fR -like above, but leaving out reference (backbones) in mapping assemblies -.IP -\fIgb[f|k|ff]\fR -sequences or consensus to GenBank -.IP -\fIgff3\fR -consensus to GFF3 -.IP -\fIwig\fR -assembly coverage info to wiggle file -.IP -\fIgcwig\fR -assembly gc content info to wiggle file -.IP -\fIfasta\fR -sequences or consensus to FASTA file (qualities to \&.qual) -.IP -\fIfastq\fR -sequences or consensus to FASTQ file -.IP -\fIexp\fR -sequences or complete assembly to EXP files in -directories. Complete assemblies are suited for gap4 -import as directed assembly. -Note: using caf2gap to import into gap4 is recommended -though -.IP -\fItext\fR -complete assembly to text alignment (only when \fB\-f\fR is -\fIcaf\fR, \fImaf\fR or \fIgbf\fR) -.IP -\fIhtml\fR -complete assembly to HTML (only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR) -.IP -\fItcs\fR -complete assembly to tcs -.IP -\fIhsnp\fR -surrounding of SNP tags (SROc, SAOc, SIOc) to HTML -(only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR) -.IP -\fIasnp\fR -analysis of SNP tags -(only when \fB\-f\fR is \fIcaf\fR, \fImaf\fR or \fIgbf\fR) -.IP -\fIcstats\fR -contig statistics file like from MIRA -(only when source contains contigs) -.IP -\fIcrlist\fR -contig read list file like from MIRA -(only when source contains contigs) -.IP -\fImaskedfasta\fR -reads where sequencing vector is masked out -(with X) to FASTA file (qualities to .qual) -.IP -\fIscaf\fR -sequences or complete assembly to single sequences CAF -.TP -\fB\-a\fR -Append to target files instead of rewriting -.TP -\fB\-A\fR -Do not Adjust sequence case -.IP -When reading formats which define clipping points, -and saving to formats which do not have clipping -information, miraconvert normally adjusts the case of -read sequences: lower case for clipped parts, upper -case for unclipped parts of reads. -Use \fB\-A\fR if you do not want this. See also \fB\-C\fR. -.IP -Applies only to files/formats which do not contain -contigs. -.TP -\fB\-b\fR -Blind data -.IP -Replaces all bases in reads/contigs with a 'c' -.TP -\fB\-C\fR -Perform hard clip to reads -.IP -When reading formats which define clipping points, will -save only the unclipped part into the result file. -.IP -Applies only to files/formats which do not contain -contigs. -.TP -\fB\-d\fR -Delete gap only columns -.IP -When output is contigs: delete columns that are -entirely gaps (like after having deleted reads during -editing in gap4 or similar) -.IP -When output is reads: delete gaps in reads -.TP -\fB\-F\fR -Filter read groups to different files -.IP -Works only for input files with readgroups (CAF/MAF) -3 (or 4) files generated: one or two for paired, one -for unpaired and one for debris reads. -.IP -Reads in paired file are interlaced by default, use \fB\-F\fR -twice to create separate files. -.TP -\fB\-m\fR -Make contigs (only for \fB\-t\fR = \fIcaf\fR or \fImaf\fR) -.IP -Encase single reads as contig singlets into the CAF/MAF -file. -.TP -\fB\-n\fR <filename> -when given, selects only reads or contigs given by -name in that file. -.TP -\fB\-N\fR <filename> -like \fB\-n\fR, but sorts output according to order given -in file. -.TP -\fB\-i\fR -when \fB\-n\fR is used, inverts the selection -.TP -\fB\-o\fR <quality>t -FASTQ quality Offset (only for \fB\-f\fR = 'fastq') -.IP -Offset of quality values in FASTQ file. Default of 33 -loads Sanger/Phred style files, using 0 tries to -automatically recognise. -.TP -\fB\-P\fR <string> -String with MIRA parameters to be parsed -.IP -Useful when setting parameters affecting consensus -calling like \fB\-CO\fR:mrpg etc. -.IP -E.g.: \fB\-P\fR "454_SETTINGS \fB\-CO\fR:mrpg=3" -.TP -\fB\-q\fR <quality> -Set default quality for bases in file types without -quality values. Furthermore, do not stop if expected -quality files are missing (e.g. '.fasta') -.TP -\fB\-R\fR <name> -Rename contigs/singlets/reads with given name string -to which a counter is appended. -.IP -Known bug: will create duplicate names if input -contains contigs/singlets as well as free reads, i.e. -reads not in contigs nor singlets. -.TP -\fB\-S\fR <name> -(name)Scheme for renaming reads, important for -paired\-ends. Only 'solexa' is currently supported. -.TP -\fB\-T\fR -When converting single reads, trim/clip away stretches -of N and X and ends of reads. Note: remember to use \fB\-C\fR to -also perform a hard clip (e.g. with FASTA as output). -.TP -\fB\-v\fR -Print version number and exit -.TP -\fB\-Y\fR <integer> -Yield. Max (clipped/padded) bases to convert. -.IP -When used on reads: output will contain first reads of -file where length of clipped bases totals at least \fB\-Y\fR. -When used on contigs: output will contain first contigs -of file where length of padded contigs totals at least -\fB\-Y\fR. -.P -The following switches work only when input (CAF or MAF) -contains contigs. Beware: CAF and MAf can also contain -just reads. -.TP -\fB\-M\fR -Do not extract contigs (or their consensus), but the -sequence of the reads they are composed of. -.TP -\fB\-r\fR [\fIcCqf\fR] -Recalculate consensus and / or consensus quality values -and / or SNP feature tags. -.IP -\&'\fIc\fR' recalc cons & cons qualities (with IUPAC) -.IP -\&'\fIC\fR' recalc cons & cons qualities (forcing non\-IUPAC) -.IP -\&'\fIq\fR' recalc consensus qualities only -.IP -\&'\fIf\fR' recalc SNP features -.IP -Note: only the last of \fIcCq\fR is relevant, \fIf\fR works as a -switch and can be combined with \fIcQq\fR (e.g. "\fB\-r\fR \fIC\fR \fB\-r\fR \fIf\fR") -.IP -Note: if the CAF/MAF contains multiple strains, -recalculation of cons & cons qualities is forced, you -can just influence whether IUPACs are used or not. -.TP -\fB\-s\fR -split output into multiple files instead of creating a -single file -.TP -\fB\-u\fR -\&'fillUp strain genomes' -.IP -Fill holes in the genome of one strain (N or @) -with sequence from a consensus of other strains -.IP -Takes effect only with \fB\-r\fR and \fB\-t\fR gbf or fasta/q -in FASTA/Q: bases filled up are in lower case -in GBF: bases filled up are in upper case -.TP -\fB\-Q\fR <integer> -Defines minimum quality a consensus base of a strain -must have, consensus bases below this will be 'N' -Default: 0 -.IP -Only used with \fB\-r\fR, and \fB\-f\fR is caf/maf and \fB\-t\fR is (fasta -or gbf) -.TP -\fB\-V\fR <integer> -Defines minimum coverage a consensus base of a strain -must have, bases with coverage below this will be 'N' -Default: 0 -.IP -Only used with \fB\-r\fR, and \fB\-t\fR is (fasta -or gbf) -.TP -\fB\-x\fR <integer> -Minimum contig or unclipped read length -.IP -When loading, discard all contigs / reads with a -length less than this value. Default: 0 (=switched off) -.IP -Note: not applied to reads in contigs! -.TP -\fB\-X\fR <integer> -Similar to \fB\-x\fR but applies only to reads and -then to the clipped length. -.TP -\fB\-y\fR <integer> -Minimum average contig coverage -When loading, discard all contigs with an -average coverage less than this value. -Default: 1 -.TP -\fB\-z\fR <integer> -Minimum number of reads in contig -When loading, discard all contigs with a -number of reads less than this value. -Default: 0 (=switched off) -.TP -\fB\-l\fR <integer> -when output as text or HTML: number of bases shown in -one alignment line. Default: 60. -.TP -\fB\-c\fR <character> -when output as text or HTML: character used to pad -endgaps. Default: ' ' (blank) -.SH EXAMPLES -.IP -miraconvert source.maf dest.sam -.IP -miraconvert source.caf dest.fasta wig ace -.IP -miraconvert \-x 2000 \-y 10 source.caf dest.caf -.IP -miraconvert \-x 40 \-C \-F \-F source.maf .fastq -.IP -miraconvert: Missing infile and out\-basename as arguments! -.SH AUTHOR -The program \fBmiraconvert\fR was written by Bastien Chevreux <[email protected]>. -.P -This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. diff --git a/debian/mans/miradiff.1 b/debian/mans/miradiff.1 deleted file mode 100644 index 7085ede..0000000 --- a/debian/mans/miradiff.1 +++ /dev/null @@ -1,36 +0,0 @@ -.TH MIRADIFF "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -miradiff \- diff two data sets of mira(1) -.SH DESCRIPTION -This program is part of the MIRA assembler package. Please check out the -documentation below for more detailed information about miradiff. -.SH SYNOPSIS -miradiff -[\fIOPTION\fR] -.SH OPTIONS -.TP -\fB\-h\fR / \fB\-\-help\fR -Print short help and exit -.TP -\fB\-v\fR / \fB\-\-version\fR -Print version and exit -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/miramem.1 b/debian/mans/miramem.1 deleted file mode 100644 index edf907d..0000000 --- a/debian/mans/miramem.1 +++ /dev/null @@ -1,33 +0,0 @@ -.TH MIRAMEM "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -miramem \- estimating needed memory for a MIRA assembly project -.SH DESCRIPTION -When called from the command line, it will ask a number of questions and -then print out an estimate of the amount of RAM needed to assemble the -project. Take this estimate with a grain of salt, depending on the -sequences properties, variations in the estimate can be +/- 30% for -bacteria and 'simple' eukaryotes. The higher the number of repeats is, -the more likely you will need to restrict memory usage in some way or -another. -.SH SYNOPSIS -miramem -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/miramer.1 b/debian/mans/miramer.1 deleted file mode 100644 index bf12ac2..0000000 --- a/debian/mans/miramer.1 +++ /dev/null @@ -1,36 +0,0 @@ -.TH MIRAMER "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -miramer \- handle k-mer statistics of a data set -.SH DESCRIPTION -This program is part of the MIRA assembler package. Please check out the -documentation below for more detailed information about miramer. -.SH SYNOPSIS -miramer -[\fIOPTION\fR] -.SH OPTIONS -.TP -\fB\-h\fR / \fB\-\-help\fR -Print short help and exit -.TP -\fB\-v\fR / \fB\-\-version\fR -Print version and exit -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mans/scftool.1 b/debian/mans/scftool.1 deleted file mode 100644 index bb6f431..0000000 --- a/debian/mans/scftool.1 +++ /dev/null @@ -1,50 +0,0 @@ -.TH SCFTOOL "1" "June 2013" "3.9.17" "User Commands" -.SH NAME -scftool \- provides a set of tools useful when working with SCF trace files. -.SH SYNOPSIS -.IP -scftool -<\fBtoolname\fR> <\fBtool parameters\fR> -.SH OPTIONS -Available tools: -.IP convert -Cuts the given range out of an SCF file and makes a new SCF out of it. -.IP -To get help more specific help please type \fIscftool convert\fR -.IP cut -Cuts a given range of a SCF file into a new SCF file. -.IP remix -Combines trace information of a SCF file with new bases, qualities and peak -values (either in FASTA or PHD format) into a new SCF file. -.SH EXAMPLES -Example for cut: -.IP -scftool cut infile lower_base_bound upper_base_bound outfile -.PP -Usage of remix (when using PHD files as input for bases, quals and peaks): -.IP -scftool remix scf_infile phd_infile scf_outfile -.PP -Usage of remix (when using FASTA files as input for bases, quals and peaks): -.IP -scftool remix scf_infile bases_infile quals_infile peaks_infile scf_outfile -.SH "SEE ALSO" -A more extensive documentation is provided in the mira-doc package and can be found at -/usr/share/doc/mira-assembler/DefinitiveGuideToMIRA.html. -.PP -You can also subscribe one of the MIRA mailing lists at -.IP -http://www.chevreux.org/mira_mailinglists.html -.PP -After subscribing, mail general questions to the MIRA talk mailing list: -.IP [email protected] -.SH BUGS -To report bugs or ask for features, please use the new ticketing system at: -.IP -http://sourceforge.net/apps/trac/mira\-assembler/ -.SH AUTHOR -The author of the mira code is Bastien Chevreux <[email protected]> -.PP -This manual page was written by Andreas Tille <[email protected]> but can be freely used for any other -distribution. diff --git a/debian/mira-examples.examples b/debian/mira-examples.examples index 85d39e6..4a32932 100644 --- a/debian/mira-examples.examples +++ b/debian/mira-examples.examples @@ -1 +1 @@ -minidemo +#minidemo diff --git a/debian/mira-examples.lintian-overrides b/debian/mira-examples.lintian-overrides index 98bc551..e9bde92 100644 --- a/debian/mira-examples.lintian-overrides +++ b/debian/mira-examples.lintian-overrides @@ -1,3 +1,3 @@ # Exclude false positives that are verbose copies from upstream tarball -mira-examples: package-contains-timestamped-gzip usr/share/doc/mira-examples/examples/minidemo/data/scf/*.scf.gz +#mira-examples: package-contains-timestamped-gzip usr/share/doc/mira-examples/examples/minidemo/data/scf/*.scf.gz diff --git a/debian/mira-rfam-12s-rrna.install b/debian/mira-rfam-12s-rrna.install new file mode 100644 index 0000000..e542a95 --- /dev/null +++ b/debian/mira-rfam-12s-rrna.install @@ -0,0 +1,3 @@ +src/other/sls/rfam_rrna-21-12.sls.gz usr/share/mira/ +src/other/sls/mira-install-sls-rrna.sh usr/share/mira/ + diff --git a/debian/mira-rfam-12s-rrna.lintian-overrides b/debian/mira-rfam-12s-rrna.lintian-overrides new file mode 100644 index 0000000..a13e808 --- /dev/null +++ b/debian/mira-rfam-12s-rrna.lintian-overrides @@ -0,0 +1,2 @@ +# tarball is from upstream +mira-rfam-12s-rrna: package-contains-timestamped-gzip usr/share/mira/rfam_rrna-21-12.sls.gz diff --git a/debian/mira-rfam-12s-rrna.postinst b/debian/mira-rfam-12s-rrna.postinst new file mode 100755 index 0000000..8534dc9 --- /dev/null +++ b/debian/mira-rfam-12s-rrna.postinst @@ -0,0 +1,10 @@ +#!/bin/bash + +set -e + +mkdir -p /usr/share/mira/mhs +/usr/share/mira/mira-install-sls-rrna.sh /usr/share/mira/rfam_rrna-21-12.sls.gz +cd /usr/share/mira/mhs +ln -s -f rfam_rrna-21-12.mhs.gz filter_default_rrna.mhs.gz + +#DEBHELPER# diff --git a/debian/mira-rfam-12s-rrna.postrm b/debian/mira-rfam-12s-rrna.postrm new file mode 100755 index 0000000..0f5df46 --- /dev/null +++ b/debian/mira-rfam-12s-rrna.postrm @@ -0,0 +1,7 @@ +#!/bin/bash + +set -e + +#DEBHELPER# + +rm -Rf /usr/share/mira/mhs diff --git a/debian/patches/fix_strange_link_issue.patch b/debian/patches/fix_strange_link_issue.patch deleted file mode 100644 index 308e6cb..0000000 --- a/debian/patches/fix_strange_link_issue.patch +++ /dev/null @@ -1,16 +0,0 @@ -Author: Andreas Tille <[email protected]> -Last-Update: Wed, 01 Jul 2015 22:00:48 +0200 -Description: The missing '&&' in the statement leads to a strange - "No such directory miramer" error - ---- mira.orig/src/progs/Makefile.am -+++ mira/src/progs/Makefile.am -@@ -51,7 +51,7 @@ - rm -f mirabait$(EXEEXT) && \ - $(LN_S) mira$(EXEEXT) mirabait$(EXEEXT) &&\ - rm -f miraconvert$(EXEEXT) && \ -- $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) \ -+ $(LN_S) mira$(EXEEXT) miraconvert$(EXEEXT) && \ - rm -f miramer$(EXEEXT) && \ - $(LN_S) mira$(EXEEXT) miramer$(EXEEXT) - diff --git a/debian/patches/gcc-6.patch b/debian/patches/gcc-6.patch deleted file mode 100644 index 1580bc9..0000000 --- a/debian/patches/gcc-6.patch +++ /dev/null @@ -1,16 +0,0 @@ -Description: Fix build issue with gcc-6 -Bug-Debian: http://bugs.debian.org/822474 -Author: Andreas Tille <[email protected]> -Last-Update: Mon, 25 Apr 2016 23:46:32 +0200 - ---- a/src/mira/contig_consensus.C -+++ b/src/mira/contig_consensus.C -@@ -30,7 +30,7 @@ - #include "util/timer.H" - - #include <boost/lexical_cast.hpp> -- -+#include <numeric> - - using namespace std; - diff --git a/debian/patches/make-reproducible b/debian/patches/make-reproducible deleted file mode 100644 index 6e05ff1..0000000 --- a/debian/patches/make-reproducible +++ /dev/null @@ -1,19 +0,0 @@ -Author: Michael R. Crusoe <[email protected]> -Description: Make reproducible -Fixes a FTBFS when the locale uses non-ASCII characters when printing the date. -Also makes the build more reproducible ---- mira.orig/src/progs/Makefile.am -+++ mira/src/progs/Makefile.am -@@ -16,10 +16,8 @@ - - compileinfo.itxt: - @/bin/echo -n "Compiled by: " >compileinfo.itxt.xxd -- @whoami >>compileinfo.itxt.xxd -- @date >>compileinfo.itxt.xxd -- @/bin/echo -n "On: " >>compileinfo.itxt.xxd -- @uname -a >>compileinfo.itxt.xxd -+ @$$DEBIAN_MAINTAINER >>compileinfo.itxt.xxd -+ @echo $$SOURCE_DATE_EPOCH >>compileinfo.itxt.xxd - @echo "Making .H out of .xxd" $@ - @$(SHELL) -ec 'grep -v "^#" compileinfo.itxt.xxd | xxd -i >compileinfo.itxt.xxd.H' - @rm compileinfo.itxt.xxd diff --git a/debian/patches/man-directory b/debian/patches/man-directory new file mode 100644 index 0000000..48f1e82 --- /dev/null +++ b/debian/patches/man-directory @@ -0,0 +1,9 @@ +Author: Michael R. Crusoe +Description: Follow the FHS +--- mira.orig/man/Makefile.am ++++ mira/man/Makefile.am +@@ -1,3 +1,3 @@ + + dist_pkgdata_DATA = mirabait.1 miradiff.1 miramer.1 mira.1 miraconvert.1 miramem.1 +-pkgdatadir=$(prefix)/man/man1 ++pkgdatadir=$(prefix)/share/man/man1 diff --git a/debian/patches/series b/debian/patches/series index 13aa111..6bc6dc6 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -1,4 +1,3 @@ -make-reproducible -fix_strange_link_issue.patch spelling.patch -gcc-6.patch +sls-rrna-fix +man-directory diff --git a/debian/patches/sls-rrna-fix b/debian/patches/sls-rrna-fix new file mode 100644 index 0000000..06b1e32 --- /dev/null +++ b/debian/patches/sls-rrna-fix @@ -0,0 +1,19 @@ +Author: Michael R. Crusoe <[email protected]> +Description: ship the rfam database, don't run unpacker yet + +--- mira.orig/src/other/sls/Makefile.am ++++ mira/src/other/sls/Makefile.am +@@ -6,13 +6,6 @@ + mira-createsls + + +-install-exec-hook: +- cp mira-install-sls-rrna.sh $(DESTDIR)$(bindir) && \ +- mkdir -p $(prefix)/share/mira/mhs && \ +- ./mira-install-sls-rrna.sh rfam_rrna-21-12.sls.gz && \ +- cd $(prefix)/share/mira/mhs && \ +- $(LN_S) -f rfam_rrna-21-12.mhs.gz filter_default_rrna.mhs.gz +- + uninstall-hook: + rm $(DESTDIR)$(bindir)/mira-install-sls-rrna.sh && \ + rm -f $(prefix)/share diff --git a/debian/patches/spelling.patch b/debian/patches/spelling.patch index 4163069..309b684 100644 --- a/debian/patches/spelling.patch +++ b/debian/patches/spelling.patch @@ -4,393 +4,25 @@ Description: Fix spelling Remark: Lintian found another issue ressize -> resize but I can not find this inside the code ---- mira.orig/src/util/fileanddisk.C -+++ mira/src/util/fileanddisk.C -@@ -866,7 +866,7 @@ - getCanonicalFileAndZipType(tmptype,dummypathto,dummystem,overridetype,ziptype); - if(overridetype.empty()){ - tmptype=tmptype.substr(1,999); -- MIRANOTIFY(Notify::FATAL,"You tried to explicitely define a file type via " << tmptype << "::" << dn << ", however the type '" << tmptype << "' is not known to MIRA."); -+ MIRANOTIFY(Notify::FATAL,"You tried to explicitly define a file type via " << tmptype << "::" << dn << ", however the type '" << tmptype << "' is not known to MIRA."); - } - //cout << "###" << overridetype << "###\n"; - } ---- mira.orig/configure.ac -+++ mira/configure.ac -@@ -1751,7 +1751,7 @@ - echo "problems in compilation/linking. Please give it a try and report success" - echo "or failure." - echo -- echo "Type 'make' to make the binaries and if no error occured," -+ echo "Type 'make' to make the binaries and if no error occurred," - echo "then 'make install' to install them." - echo - echo "In case of failure, please help to fix if you can." ---- mira.orig/doc/docbook/chap_bonus_part.xml -+++ mira/doc/docbook/chap_bonus_part.xml -@@ -61,7 +61,7 @@ - </para> - <para> - Today was a day where I had - the first time ever - ups and downs -- occuring absolutely simultaneously. Something which is physically -+ occurring absolutely simultaneously. Something which is physically - impossible, I know, but don't tell any physicist or astronomist about - that or else they'll embark you on a lengthy discussion on how - isochronicity is a myth by telling you stories on lightning, thunder and -@@ -259,7 +259,7 @@ - <itemizedlist> - <listitem> - an artefact was very sporadically observed during MIRA runs where sequences -- (containing lot's of 'A') suddenly contained at least one '@'. This occured -+ (containing lot's of 'A') suddenly contained at least one '@'. This occurred - after several passes, i.e., not on loading. - </listitem> - <listitem> -@@ -276,7 +276,7 @@ - </listitem> - <listitem> - MIRA loaded the data twice flawlessly before the artefact in the filesystem -- occured. -+ occurred. - </listitem> - </itemizedlist> - <para> -@@ -339,7 +339,7 @@ - </listitem> - <listitem> - the disk controllers and UDMA controller are innocent! Some of the glitches observed in -- previous weeks occured during runs of MIRA, inside the MIRA address space, -+ previous weeks occurred during runs of MIRA, inside the MIRA address space, - long after initial loading, when UDMA had already finished their job. - </listitem> - </itemizedlist> ---- mira.orig/minidemo/demo1/runme.sh -+++ mira/minidemo/demo1/runme.sh -@@ -29,7 +29,7 @@ - echo - echo "If all went well, the results are in '*_results' directory." - echo " also have a look at files in '*_info', e.g. at the contigstats file.." --echo "Consult log_assmbly.txt and/or stderr if errors occured." -+echo "Consult log_assmbly.txt and/or stderr if errors occurred." - echo - echo "(and please read the comments on top of the 'runme.sh' script)" - ---- mira.orig/minidemo/demo2/runme.sh -+++ mira/minidemo/demo2/runme.sh -@@ -17,7 +17,7 @@ - echo - echo "If all went well, the results are in 'demo2_results' directory." - echo " also have a look at files in 'demo2_info', e.g. at the contigstats file.." --echo "Consult log_assmbly.txt and/or stderr if errors occured." -+echo "Consult log_assmbly.txt and/or stderr if errors occurred." - echo - echo "(and please read the comments on top of the 'runme.sh' script)" - ---- mira.orig/minidemo/demo3/runme.sh -+++ mira/minidemo/demo3/runme.sh -@@ -9,7 +9,7 @@ - mira --params=demo3.par | tee log_assmbly.txt - echo - echo "If all went well, the results are in 'demo3_out*' files/directories." --echo "Consult log_assmbly.txt and/or stderr if errors occured." -+echo "Consult log_assmbly.txt and/or stderr if errors occurred." - echo - echo "(and please read the comments on top of the 'runme.sh' script)" - ---- mira.orig/minidemo/demo4/runme.sh -+++ mira/minidemo/demo4/runme.sh -@@ -16,7 +16,7 @@ - mira -job=denovo,genome,normal,sanger -lowqualitydata --fasta=../data/fasta_set1/U13small_m.fasta -DIRECTORY:scf=../data/scf SANGER_SETTINGS -CLIPPING:qc=yes -LR:mxti=no | tee log_assembly.txt - echo - echo "If all went well, the results are in 'mira_out*' files/directories." --echo "Consult log_assmbly.txt and/or stderr if errors occured." -+echo "Consult log_assmbly.txt and/or stderr if errors occurred." - echo - echo "(and please read the comments on top of the 'runme.sh' script)" - ---- mira.orig/minidemo/demo5/runme.sh -+++ mira/minidemo/demo5/runme.sh -@@ -16,7 +16,7 @@ - mira --project=nmpvc -job=denovo,genome,normal,sanger -lowqualitydata --fasta=../data/fasta_set1/U13small_nm.fasta -DIRECTORY:scf=../data/scf SANGER_SETTINGS -CLIPPING:qc=yes -LR:mxti=no > run_nmpvc.log - echo - echo "If all went well, the results are in 'nmpvc_results' directory." --echo "Consult run_nmpvc.log and/or stderr if errors occured." -+echo "Consult run_nmpvc.log and/or stderr if errors occurred." - - echo - echo -@@ -25,7 +25,7 @@ - mira --project=nmqconly --job=denovo,genome,normal,sanger -lowqualitydata --fasta=../data/fasta_set1/U13small_nm.fasta -DIRECTORY:scf=../data/scf SANGER_SETTINGS -CLIPPING:pvlc=no:qc=yes:emlc=no -LR:mxti=no > run_nmqconly.log - echo - echo "If all went well, the results are in 'nmqconly_results' directory." --echo "Consult run_nmqconly.log and/or stderr if errors occured." -+echo "Consult run_nmqconly.log and/or stderr if errors occurred." - - echo - echo -@@ -34,6 +34,6 @@ - mira --project=nmnocl --job=denovo,genome,normal,sanger -lowqualitydata --noclipping --fasta=../data/fasta_set1/U13small_nm.fasta -DIRECTORY:scf=../data/scf -LR:mxti=no > run_nmnocl.log - echo - echo "If all went well, the results are in 'nmnocl_results' directory." --echo "Consult run_nmnocl.log and/or stderr if errors occured." -+echo "Consult run_nmnocl.log and/or stderr if errors occurred." - echo - echo "(and please read the comments on top of the 'runme.sh' script)" ---- mira.orig/minidemo/estdemo1/runme.sh -+++ mira/minidemo/estdemo1/runme.sh -@@ -18,4 +18,4 @@ - miraSearchESTSNPs --fasta | tee run.log - echo "Done." - echo "If all went well, the results are in 'step3_results' directory." --echo "Consult run.log and/or stderr if errors occured." -+echo "Consult run.log and/or stderr if errors occurred." ---- mira.orig/src/io/so.obo -+++ mira/src/io/so.obo -@@ -7212,7 +7212,7 @@ - [Term] - id: SO:0000858 - name: orthologous --def: "An attribute describing a kind of homology where divergence occured after a speciation event." [SO:ke] -+def: "An attribute describing a kind of homology where divergence occurred after a speciation event." [SO:ke] - is_a: SO:0000857 ! homologous - - [Term] -@@ -9696,7 +9696,7 @@ - id: SO:0001146 - name: polypeptide_variation_site - alt_id: BS:00336 --def: "A site of sequence variation (alteration). Alternative sequence due to naturally occuring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke] -+def: "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and altermatve splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke] - comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations. - subset: biosapiens - synonym: "sequence_variations" EXACT [] ---- mira.orig/src/memorc/memorc.C -+++ mira/src/memorc/memorc.C -@@ -24,7 +24,7 @@ - - uint32 MemORC::MOC_innewcount=0; - --bool MemORC::MOC_mostfatalerroroccured=false; -+bool MemORC::MOC_mostfatalerroroccurred=false; - bool MemORC::MOC_allhot=false; - - bool MemORC::MOC_fillondelete=false; -@@ -170,14 +170,14 @@ - - void * MemORC::internalMAlloc(size_t n) - { -- if(MOC_mostfatalerroroccured){ -+ if(MOC_mostfatalerroroccurred){ - abort(); - } - void * newmem=malloc(n); - // Most significant bit set? Come on ... not on x86_64! Must be a magic number - // for invalid mem - if(reinterpret_cast<uint64>(newmem)&0x8000000000000000ull){ -- MOC_mostfatalerroroccured=true; -+ MOC_mostfatalerroroccurred=true; - printf("Houston, we have a malloc pointer problem: %p\n",newmem); - statistics(); - MemORC::checkAllMemBlocks(); ---- mira.orig/src/memorc/memorc.H -+++ mira/src/memorc/memorc.H -@@ -18,7 +18,7 @@ - - static uint32 MOC_innewcount; - -- static bool MOC_mostfatalerroroccured; -+ static bool MOC_mostfatalerroroccurred; - static bool MOC_newallocsgetthisnocheckflag; - static bool MOC_allhot; - static bool MOC_fillondelete; // unused atm ---- mira.orig/src/mira/assembly_io.C -+++ mira/src/mira/assembly_io.C -@@ -270,7 +270,7 @@ +--- mira.orig/src/mira/contig_consensus.C ++++ mira/src/mira/contig_consensus.C +@@ -2578,7 +2578,7 @@ } - - if(hassomeerror){ -- MIRANOTIFY(Notify::FATAL,"While looking at or loading ancillary files named in the manifest, some errors occured. Please check the log."); -+ MIRANOTIFY(Notify::FATAL,"While looking at or loading ancillary files named in the manifest, some errors occurred. Please check the log."); + default : { + cout << "seqtype: " << seqtype << endl; +- MIRANOTIFY(Notify::INTERNAL, "Uknown seqtype to rate?"); ++ MIRANOTIFY(Notify::INTERNAL, "Unknown seqtype to rate?"); } - - // delayed creation of backbone contigs from single reads -@@ -516,7 +516,7 @@ } - if(hassomeerror){ -- MIRANOTIFY(Notify::FATAL,"While looking at or loading data files named in the manifest, some errors occured. Please check the log."); -+ MIRANOTIFY(Notify::FATAL,"While looking at or loading data files named in the manifest, some errors occurred. Please check the log."); - } - } - ---- mira.orig/src/mira/assembly_pbcorrect.C -+++ mira/src/mira/assembly_pbcorrect.C -@@ -986,7 +986,7 @@ - if(isupper(oread.getBaseInSequence(posor)) - && (oread.getQualities())[posor]>0){ - // adjustment vector must match!!! {pos-1, pos, pos+1} -- // if deletion occured next to it, don't take. E.g. {pos-1, pos, pos+2} -+ // if deletion occurred next to it, don't take. E.g. {pos-1, pos, pos+2} - // - // Rationale: e.g. xATAAAAx -> xATAx (RLE: 114) -> xAx (RLE: 1) -> ouch! - // xAAAAAAx -> xA**x (RLE: 5--) -> xAx (RLE: 5) -> OK -@@ -1870,7 +1870,7 @@ - BUGIFTHROW(AS_naclipl.size()!=AS_readpool.size(),"AS_naclipl.size() " << AS_naclipl.size() << " != AS_readpool.size() " << AS_readpool.size()); - BUGIFTHROW(AS_naclipr.size()!=AS_readpool.size(),"AS_naclipr.size() " << AS_naclipr.size() << " != AS_readpool.size() " << AS_readpool.size()); - -- // *sigh* through indels occuring in the generatePBEdits() call prior to the call to this function, -+ // *sigh* through indels occurring in the generatePBEdits() call prior to the call to this function, - // things may be slightly out of sync - // just make sure this is called late in the whole correction proces, ideally (next to) last pass - ---- mira.orig/src/mira/assembly_swalign.C -+++ mira/src/mira/assembly_swalign.C -@@ -663,7 +663,7 @@ - - void Assembly::makeAlignments(bool (* checkfunction)(Assembly & as,int32,int32), bool takefullskimfilenames, const bool trans100percent, int32 version, const string prefix, const string postfix, const string tmpfname) - { -- //pr�fen, ob AS_posfmatch und ...cmatch nach alignments gel�scht werden k�nnen -+ //pr?fen, ob AS_posfmatch und ...cmatch nach alignments gel?scht werden k?nnen - - FUNCSTART("void Assembly::makeAlignments()"); - -@@ -1600,7 +1600,7 @@ - - /************************************************************************* - * -- * Checks an ADS for mismatches occuring at RepeatMarkerBase positions -+ * Checks an ADS for mismatches occurring at RepeatMarkerBase positions - * - * Function does not care about quality, those tags are set by the contig - * and are therefore not to be questioned -@@ -1715,7 +1715,7 @@ - int32 r2newctagfrom=-1; - int32 r2newctagto=-1; - -- bool problemoccured=false; -+ bool problemoccurred=false; - - // keep count in this loop forward, is used further downward! - for(uint32 count=0; count<ads.getOverlapLen(); ++count, ++cons, r1index+=r1delta, r2index+=r2delta, ++alseq1, ++alseq2){ -@@ -1729,21 +1729,21 @@ - - if(r1index<0) { - cout << "Megaproblem: r1index<0" << endl; -- problemoccured=true; -+ problemoccurred=true; - } - if(r1index >= static_cast<int32>(AS_readpool.getRead(id1).getLenSeq())){ - cout << "Megaproblem: r1index >= AS_readpool.getRead(id1).getLenSeq()" << endl; -- problemoccured=true; -+ problemoccurred=true; - } - if(r2index<0) { - cout << "Megaproblem: r2index<0" << endl; -- problemoccured=true; -+ problemoccurred=true; - } - if(r2index >= static_cast<int32>(AS_readpool.getRead(id2).getLenSeq())){ - cout << "Megaproblem: r2index >= AS_readpool.getRead(id2).getLenSeq()" << endl; -- problemoccured=true; -+ problemoccurred=true; - } -- if(problemoccured){ -+ if(problemoccurred){ - cout << "ADSfrm: (" << id1 << ") " << AS_readpool.getRead(id1).getName() << " (" << id2 << ") " << AS_readpool.getRead(id2).getName() << endl << endl; - - Read::setCoutType(Read::AS_CAF); ---- mira.orig/src/mira/read.C -+++ mira/src/mira/read.C -@@ -774,7 +774,7 @@ - * Initial version tried to preserve the adjustments of the original reads, - * but the PacBio corrector routines depend on continuous adjustment values - * (0,1,2,3,...) to find out where during correction insertions or deletions -- * occured. -+ * occurred. - * As I am not sure what the original adjustments could be used for and - * I do not want to keep two vectors, I'm switching to continuous for - * the moment. -@@ -2486,7 +2486,7 @@ - /************************************************************************* - * - * starting from the actual quality clips, clip more from the ends while -- * the characters occuring are X, N, *. That is, results will differ -+ * the characters occurring are X, N, *. That is, results will differ - * whether or not a previous quality clipping might have happened or not - * - * stretches with other bases will be merged while being <= 'gapsize', --- mira.orig/src/progs/mira.C +++ mira/src/progs/mira.C -@@ -239,7 +239,7 @@ +@@ -245,7 +245,7 @@ } - catch (exception& e) - { -- cout << "A 'standard' exception occured (that's NOT normal):\n" << e.what() << "\n\nIf the cause is not immediatly obvious, please contact: [email protected]\n\n"; + catch (std::exception& e) { + cout.flush(); cerr.flush(); +- cout << "A 'standard' exception occurred (that's NOT normal):\n" << e.what() << "\n\nIf the cause is not immediatly obvious, please contact: [email protected]\n\n"; + cout << "A 'standard' exception occurred (that's NOT normal):\n" << e.what() << "\n\nIf the cause is not immediately obvious, please contact: [email protected]\n\n"; doAbort(); } catch(...){ ---- mira.orig/src/mira/contig_consensus.C -+++ mira/src/mira/contig_consensus.C -@@ -2563,7 +2563,7 @@ - } - default : { - cout << "seqtype: " << seqtype << endl; -- MIRANOTIFY(Notify::INTERNAL, "Uknown seqtype to rate?"); -+ MIRANOTIFY(Notify::INTERNAL, "Unknown seqtype to rate?"); - } - } - ---- mira.orig/THANKS -+++ mira/THANKS -@@ -31,8 +31,8 @@ - sequences and thoroughly testing the 454 assemblies - Gerrit Schramm from Roche in helping me out to understand some of the less - well known things regarding the 454 sequencing system --Hern�ndez Alvarez -- Alfredo Jos� providing patches to have MIRA compile again on Solaris -+Hern?ndez Alvarez -+ Alfredo Jos? providing patches to have MIRA compile again on Solaris - Lionel Guy implementing bug fixes in sff_extract and making available - data sets to hunt down some ugly bugs in MIRA - Sven Klages for insightful feedback and providing a fix for the ACE -@@ -52,7 +52,7 @@ - Jorge Duarte from BIOGEMMA for making available test sets to track down - memory corruption bugs - Dag Ahren making available a test set to track down a rather nasty -- problem occuring during clipping -+ problem occurring during clipping - Jan van Haarst Running benchmarks over NFS to find poorly performing - input/output routines - Peter Cock Invaluable feedback for implementing SAM format and ---- mira.orig/doc/docbook/chap_seqtechdesc_part.xml -+++ mira/doc/docbook/chap_seqtechdesc_part.xml -@@ -246,7 +246,7 @@ - <para> - Note that projects using reads ≤ 100 bp assembled fine with MIRA - 4.9.3 and before as the default algorithms for proposed-end-clip -- (<arg>-CL:pec</arg>) implicitly caught chimeras occuring near the -+ (<arg>-CL:pec</arg>) implicitly caught chimeras occurring near the - read ends and the remaining chimeras were caught by the algorithms - for low level chimeras. - </para> ---- mira.orig/src/mira/contig_analysis.C -+++ mira/src/mira/contig_analysis.C -@@ -342,7 +342,7 @@ - /************************************************************************* - * - * Checks a (newly entered at call time, but might be used for other means) -- * read whether it has mismatches occuring at SRMB or WRMB position -+ * read whether it has mismatches occurring at SRMB or WRMB position - * - * Gives back 'true' if a certain level of danger is attained - * -@@ -4061,7 +4061,7 @@ - CEBUG("readswithgaps: " << readswithgaps << "\treadswithnogaps: " << readswithnogaps << '\n'); - CEBUG("hasgapsforward: " << hasgapsforward << "\thasgapsreverse: " << hasgapsreverse << '\n'); - CEBUG("maxgaprunlen: " << maxgaprunlen << '\n'); -- CEBUG("most frequent gap size: " << mostfrequentgapsize << "\toccuring: " << gapruns[mostfrequentgapsize]<<'\n'); -+ CEBUG("most frequent gap size: " << mostfrequentgapsize << "\toccurring: " << gapruns[mostfrequentgapsize]<<'\n'); - - if(readswithgaps<mingroupsize) continue; - if(needbothstrands && !(hasgapsforward && hasgapsreverse)) continue; diff --git a/debian/rules b/debian/rules index 5c0cd78..7c29b1f 100755 --- a/debian/rules +++ b/debian/rules @@ -2,10 +2,8 @@ # 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 export DEBIAN_MAINTAINER=$(dpkg-parsechangelog -SMaintainer) +export DEB_BUILD_MAINT_OPTIONS=hardening=+all pkg=mira-assembler exampledir=usr/share/doc/mira-examples/examples/minidemo/data/bbdataset1/ @@ -13,88 +11,44 @@ exampledir=usr/share/doc/mira-examples/examples/minidemo/data/bbdataset1/ include /usr/share/dpkg/default.mk %: - dh $@ --with autoreconf + dh $@ --with autoreconf --parallel -override_dh_auto_install : +override_dh_auto_install-arch: make install DESTDIR=$(CURDIR)/debian/$(pkg) + +override_dh_auto_install-indep: #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 \ 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: +override_dh_auto_test-arch: make check -#Make the docs -override_dh_auto_build: +override_dh_auto_test-indep: + +override_dh_auto_build-arch: # some *.cc files are created by old flex version which breaks the build # see bug #812681 find -name '*.ll' | sed -e 's/[.]ll$$/.cc/' | xargs rm - dh_auto_build --parallel -ifneq (,$(findstring mira-doc, $(shell dh_listpackages))) - dh_auto_build --sourcedir=doc --parallel -endif + dh_auto_build -#Remove unneeded .tcl extensions from scripts -override_dh_install: - dh_install - if [ -d debian/$(pkg) ] ; then \ - for f in $$(ls debian/$(pkg)/usr/bin/*.tcl) ; do mv "$$f" "$${f%.tcl}"; done \ - 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 +override_dh_auto_build-indep: + dh_auto_build --sourcedir=doc + +override_dh_installchangelogs: + dh_installchangelogs src/mira/CHANGES.txt #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 + dh_auto_clean || true find * -name Makefile -exec rm '{}' ';' find * -name '*.xxd.H' -exec rm '{}' ';' find * -name '*.par.H' -exec rm '{}' ';' find * -name 'compileinfo.*' -exec rm '{}' ';' -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 -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/mira.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
