[med-svn] [Git][med-team/genomethreader][master] 4 commits: do not install gthunit
Sascha Steinbiss
gitlab at salsa.debian.org
Fri Jan 10 15:58:19 GMT 2020
Sascha Steinbiss pushed to branch master at Debian Med / genomethreader
Commits:
af89066a by Sascha Steinbiss at 2020-01-10T16:57:37+01:00
do not install gthunit
- - - - -
8f924200 by Sascha Steinbiss at 2020-01-10T16:57:53+01:00
finish patches
- - - - -
077c0c86 by Sascha Steinbiss at 2020-01-10T16:58:00+01:00
add patch
- - - - -
59926519 by Sascha Steinbiss at 2020-01-10T16:58:09+01:00
add more manpages
- - - - -
14 changed files:
- debian/genomethreader.install
- + debian/man_src/gthbssmfileinfo.1.adoc
- + debian/man_src/gthbssmprint.1.adoc
- + debian/man_src/gthbssmrmsd.1.adoc
- + debian/man_src/gthbssmtrain.1.adoc
- + debian/man_src/gthconsensus.1.adoc
- + debian/man_src/gthfilestat.1.adoc
- + debian/man_src/gthgetseq.1.adoc
- + debian/man_src/gthmkbssmfiles.1.adoc
- + debian/man_src/gthsplit.1.adoc
- debian/patches/debian-gt-libs.patch
- debian/patches/gt-path-fix.patch
- + debian/patches/hardening.patch
- debian/patches/series
Changes:
=====================================
debian/genomethreader.install
=====================================
@@ -1,3 +1,14 @@
-bin/* usr/bin
+bin/align_dna usr/bin
+bin/gth usr/bin
+bin/gthbssmfileinfo usr/bin
+bin/gthbssmrmsd usr/bin
+bin/gthconsensus usr/bin
+bin/gthgetseq usr/bin
+bin/gthsplit usr/bin
+bin/gthbssmbuild usr/bin
+bin/gthbssmprint usr/bin
+bin/gthbssmtrain usr/bin
+bin/gthfilestat usr/bin
+bin/gthmkbssmfiles usr/bin
debian/bssm usr/lib/genomethreader
debian/gthdata usr/share/genomethreader
=====================================
debian/man_src/gthbssmfileinfo.1.adoc
=====================================
@@ -0,0 +1,21 @@
+# gthbssmfileinfo(1)
+
+## NAME
+
+gthbssmfileinfo - show info about splice site model
+
+## SYNOPSIS
+
+*gthbssmfileinfo* [option ...] bssm_file
+
+## DESCRIPTION
+
+Show information about the specified BSSM file.
+
+## OPTIONS
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gthbssmprint.1.adoc
=====================================
@@ -0,0 +1,21 @@
+# gthbssmprint(1)
+
+## NAME
+
+gthbssmprint - print splice site model
+
+## SYNOPSIS
+
+*gthbssmprint* [option ...] bssm_file
+
+## DESCRIPTION
+
+Print BSSM file bssm_file to stdout.
+
+## OPTIONS
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gthbssmrmsd.1.adoc
=====================================
@@ -0,0 +1,21 @@
+# gthbssmrmsd(1)
+
+## NAME
+
+gthbssmrmsd - calculate distance between splice site models
+
+## SYNOPSIS
+
+*gthbssmrmsd* [option ...] BSSM_file_1 BSSM_file_2
+
+## DESCRIPTION
+
+Show RMSDs between given BSSM files.
+
+## OPTIONS
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gthbssmtrain.1.adoc
=====================================
@@ -0,0 +1,107 @@
+# gthbssmtrain(1)
+
+## NAME
+
+gthbssmtrain - train splice site model
+
+## SYNOPSIS
+
+*gthbssmtrain* [option ...] GFF3_file
+
+## DESCRIPTION
+
+Create BSSM training data from annotation given in GFF3_file.
+
+## OPTIONS
+
+*-outdir*::
+ set name of output directory to which the training files are
+ written
+ default: training_data
+
+*-gcdonor*::
+ extract training data for GC donor sites
+ default: yes
+
+*-filtertype*::
+ set type of features to used for filtering (usually 'exon' or
+ 'CDS')
+ default: exon
+
+*-goodexoncount*::
+ set the minimum number of good exons a feature must have to be
+ included into the training data
+ default: 1
+
+*-cutoff*::
+ set the minimum score an exon must have to count towards the
+ ``good exon count'' (exons without a score count as good)
+ default: 1.00
+
+*-extracttype*::
+ set type of features to be extracted as exons (usually 'exon' or
+ 'CDS')
+ default: CDS
+
+*-seqfile*::
+ set the sequence file from which to take the sequences
+ default: undefined
+
+*-encseq*::
+ set the encoded sequence indexname from which to take the
+ sequences
+ default: undefined
+
+*-seqfiles*::
+ set the sequence files from which to extract the features
+ use '--' to terminate the list of sequence files
+
+*-matchdesc*::
+ search the sequence descriptions from the input files for the
+ desired sequence IDs (in GFF3), reporting the first match
+ default: no
+
+*-matchdescstart*::
+ exactly match the sequence descriptions from the input files for
+ the desired sequence IDs (in GFF3) from the beginning to the
+ first whitespace
+ default: no
+
+*-usedesc*::
+ use sequence descriptions to map the sequence IDs (in GFF3) to
+ actual sequence entries.
+ If a description contains a sequence range (e.g.,
+ III:1000001..2000000), the first part is used as sequence ID
+ ('III') and the first range position as offset ('1000001')
+ default: no
+
+*-regionmapping*::
+ set file containing sequence-region to sequence file mapping
+ default: undefined
+
+*-seed*::
+ set seed for random number generator manually
+ 0 generates a seed from the current time and the process id
+ default: 0
+
+*-v*::
+ be verbose
+ default: no
+
+*-gzip*::
+ write gzip compressed output files
+ default: no
+
+*-bzip2*::
+ write bzip2 compressed output files
+ default: no
+
+*-force*::
+ force writing to output files
+ default: no
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gthconsensus.1.adoc
=====================================
@@ -0,0 +1,92 @@
+# gthconsensus(1)
+
+## NAME
+
+gthconsensus - build consensus spliced alignments
+
+## SYNOPSIS
+
+*gthconsensus* [option ...] [file ...]
+
+## DESCRIPTION
+
+Show GenomeThreader output files containing intermediate results and assemble
+the contained spliced alignments to consensus spliced alignments.
+
+## OPTIONS
+
+*-translationtable*::
+ set the codon translation table used for codon translation in
+ matching, DP, and output
+ default: 1
+
+*-v*::
+ be verbose
+ default: no
+
+*-xmlout*::
+ show output in XML format
+ default: no
+
+*-gff3out*::
+ show output in GFF3 format
+ default: no
+
+*-md5ids*::
+ show MD5 fingerprints as sequence IDs
+ default: no
+
+*-o*::
+ redirect output to specified file
+ default: undefined
+
+*-gzip*::
+ write gzip compressed output file
+ default: no
+
+*-bzip2*::
+ write bzip2 compressed output file
+ default: no
+
+*-force*::
+ force writing to output file
+ default: no
+
+*-gs2out*::
+ output in old GeneSeqer2 format
+ default: no
+
+*-minalignmentscore*::
+ set the minimum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxalignmentscore*::
+ set the maximum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 1.00
+
+*-mincoverage*::
+ set the minimum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxcoverage*::
+ set the maximum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 9999.99
+
+*-intermediate*::
+ stop after calculation of spliced alignments and output
+ results in reusable XML format. Do not process this output
+ yourself, use the ``normal'' XML output instead!
+ default: no
+
+*-help*::
+ display help for basic options and exit
+
+*-help+*::
+ display help for all options and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gthfilestat.1.adoc
=====================================
@@ -0,0 +1,46 @@
+# gthfilestat(1)
+
+## NAME
+
+gthfilestat - show statistics about consensus spliced alignments
+
+## SYNOPSIS
+
+*gthfilestat* [option ...] [file ...]
+
+## DESCRIPTION
+
+Show statistics about spliced alignments in GenomeThreader output files
+containing intermediate results.
+
+## OPTIONS
+
+*-minalignmentscore*::
+ set the minimum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxalignmentscore*::
+ set the maximum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 1.00
+
+*-mincoverage*::
+ set the minimum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxcoverage*::
+ set the maximum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 9999.99
+
+*-v*::
+ be verbose
+ default: no
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gthgetseq.1.adoc
=====================================
@@ -0,0 +1,74 @@
+# gthgetseq(1)
+
+## NAME
+
+gthgetseq - get FASTA sequences from GenomeThreader files
+
+## SYNOPSIS
+
+*gthgetseq* -getcdna | -getprotein | -getgenomic [option ...] [file ...]
+
+## DESCRIPTION
+
+Get FASTA sequences from GenomeThreader files containing intermediate results.
+The sequences are shown on stdout.
+
+## OPTIONS
+
+*-getcdna*::
+ get cDNA/EST sequences
+ default: no
+
+*-getcdnacomp*::
+ get complement of cDNA/EST sequences
+ default: no
+
+*-getprotein*::
+ get protein sequences
+ default: no
+
+*-getproteincomp*::
+ get complement of protein sequences
+ default: no
+
+*-getgenomic*::
+ get genomic sequences
+ default: no
+
+*-getgenomiccomp*::
+ get complement of genomic sequences
+ default: no
+
+*-minalignmentscore*::
+ set the minimum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxalignmentscore*::
+ set the maximum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 1.00
+
+*-mincoverage*::
+ set the minimum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxcoverage*::
+ set the maximum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 9999.99
+
+*-gzip*::
+ gzip compressed input file(s)
+ default: no
+
+*-bzip2*::
+ bzip2 compressed input file(s)
+ default: no
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
=====================================
debian/man_src/gthmkbssmfiles.1.adoc
=====================================
@@ -0,0 +1,22 @@
+# gthmkbssmfiles(1)
+
+## NAME
+
+gthmkbssmfiles - rite hard coded BSSM files
+
+## SYNOPSIS
+
+*gthmkbssmfiles* output_path
+
+## DESCRIPTION
+
+Write hard coded BSSM files to output_path.
+
+## OPTIONS
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
+
=====================================
debian/man_src/gthsplit.1.adoc
=====================================
@@ -0,0 +1,70 @@
+# gthsplit(1)
+
+## NAME
+
+gthsplit - split GenomeThreader output files
+
+## SYNOPSIS
+
+*gthsplit* -alignmentscore | -coverage [option ...] [file ...]
+
+## DESCRIPTION
+
+Split GenomeThreader output files containing intermediate results.
+
+## OPTIONS
+
+*-alignmentscore*::
+ split according to the overall alignment score (scr)
+ default: no
+
+*-coverage*::
+ split according to coverage (cov)
+ default: no
+
+*-range*::
+ set the percentage range used to create the sets
+ default: 5
+
+*-minalignmentscore*::
+ set the minimum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxalignmentscore*::
+ set the maximum alignment score for spliced alignments to be
+ included into the set of spliced alignments
+ default: 1.00
+
+*-mincoverage*::
+ set the minimum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 0.00
+
+*-maxcoverage*::
+ set the maximum coverage for spliced alignments to be
+ included into the set of spliced alignments
+ default: 9999.99
+
+*-v*::
+ be verbose
+ default: no
+
+*-gzip*::
+ write gzip compressed output file(s)
+ default: no
+
+*-bzip2*::
+ write bzip2 compressed output file(s)
+ default: no
+
+*-force*::
+ force writing to split files
+ default: no
+
+*-help*::
+ display help and exit
+
+*-version*::
+ display version information and exit
+
=====================================
debian/patches/debian-gt-libs.patch
=====================================
@@ -1,3 +1,5 @@
+Description: use Debian's GenomeTools
+Author: Sascha Steinbiss <satta at debian.org>
--- a/Makefile
+++ b/Makefile
@@ -15,19 +15,17 @@
=====================================
debian/patches/gt-path-fix.patch
=====================================
@@ -1,3 +1,5 @@
+Description: use Debian's gt path
+Author: Sascha Steinbiss <satta at debian.org>
--- a/testsuite/gthbssmtrain_include.rb
+++ b/testsuite/gthbssmtrain_include.rb
@@ -37,7 +37,7 @@
=====================================
debian/patches/hardening.patch
=====================================
@@ -0,0 +1,22 @@
+Description: Enable full hardening
+Author: Sascha Steinbiss <satta at debian.org>
+--- a/Makefile
++++ b/Makefile
+@@ -229,7 +229,7 @@
+ $(1): $(2)
+ @echo "[link $$(@F)]"
+ @test -d $$(@D) || mkdir -p $$(@D)
+- $$(CC) $$(LDFLAGS) $$(GTH_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \
++ $$(CC) $$(CPPFLAGS) $$(LDFLAGS) $$(GTH_LDFLAGS) $$(filter-out $$(OVERRIDELIBS),$$^) \
+ $$(filter-out $$(patsubst lib%.a,-l%,$$(notdir $$(OVERRIDELIBS))),\
+ $$(EXP_LDLIBS)) $$(OVERRIDELIBS) -o $$@
+ endef
+@@ -319,7 +319,7 @@
+ $(1): $(2)
+ @echo "[compile $$(@F)]"
+ @test -d $$(@D) || mkdir -p $$(@D)
+- $$(CC) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) $$(EXP_CFLAGS) \
++ $$(CC) $$(CPPFLAGS) -c $$< -o $$@ $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) $$(EXP_CFLAGS) \
+ $$(GTH_CFLAGS) $(3)
+ $$(CC) -c $$< -o $$(@:.o=.d) $$(EXP_CPPFLAGS) $$(GTH_CPPFLAGS) \
+ $(3) -MM -MP -MT $$@
=====================================
debian/patches/series
=====================================
@@ -1,2 +1,3 @@
debian-gt-libs.patch
gt-path-fix.patch
+hardening.patch
View it on GitLab: https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f
--
View it on GitLab: https://salsa.debian.org/med-team/genomethreader/compare/0445cb851591fe89bce32cc0e862179470ca869d...5992651908887879d83f52128d75cf4a0947ac4f
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