This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch master in repository kmer-tools.
commit 85bd00e2a7016168f5418b6037ef0daa99fe5126 Author: Afif Elghraoui <[email protected]> Date: Fri Jan 1 22:21:30 2016 -0800 Add leaff and sim4db binary packages --- debian/control | 45 ++++++++++++++++++++++++++++++++++++++++++++- debian/leaff.docs | 1 + debian/leaff.install | 1 + debian/rules | 13 ++++++++----- debian/sim4db.docs | 1 + debian/sim4db.install | 27 +++++++++++++++++++++++++++ 6 files changed, 82 insertions(+), 6 deletions(-) diff --git a/debian/control b/debian/control index 8424146..05a9d43 100644 --- a/debian/control +++ b/debian/control @@ -14,7 +14,9 @@ Package: kmer Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, - meryl + meryl, + leaff, + sim4db, Description: suite of tools for DNA sequence analysis The kmer package is a suite of tools for DNA sequence analysis. It provides tools for searching (ESTs, mRNAs, sequencing reads); @@ -52,6 +54,8 @@ Description: in- and out-of-core kmer counting and utilities report the histogram of counts, the list of kmers and their counts, or can perform mathematical and set operations on the processed data files. + . + This package is part of the Kmer suite. Package: libmeryl-dev Architecture: any @@ -70,3 +74,42 @@ Description: in- and out-of-core kmer counting and utilities (development lib) on the processed data files. . This package contains the static libraries and header files. + +Package: leaff +Architecture: any +Depends: + ${shlibs:Depends}, + ${misc:Depends}, +Description: biological sequence library utilities and applications + LEAFF (Let's Extract Anything From Fasta) is a utility program for + working with multi-fasta files. In addition to providing random access + to the base level, it includes several analysis functions. + . + This package is part of the Kmer suite. + +Package: sim4db +Architecture: any +Depends: + ${shlibs:Depends}, + ${misc:Depends}, +Recommends: + leaff, +Description: biological sequence library utilities and applications + Sim4db performs fast batch alignment of large cDNA (EST, mRNA) sequence + sets to a set of eukaryotic genomic regions. It uses the sim4 and sim4cc + algorithms to determine the alignments, but incorporates a fast sequence + indexing and retrieval mechanism, implemented in the sister package + 'leaff', to speedily process large volumes of sequences. + . + While sim4db produces alignments in the same way as sim4 or sim4cc, it + has additional features to make it more amenable for use with whole-genome + annotation pipelines. A script file can be used to group pairings between + cDNAs and their corresponding genomic regions, to be aligned as one run + and using the same set of parameters. Sim4db also optionally reports more + than one alignment for the same cDNA within a genomic region, as long + as they meet user-defined criteria such as minimum length, percentage + sequence identity or coverage. This feature is instrumental in finding + all alignments of a gene family at one locus. Lastly, the output is + presented either as custom sim4db alignments or as GFF3 gene features. + . + This package is part of the Kmer suite. diff --git a/debian/leaff.docs b/debian/leaff.docs new file mode 100644 index 0000000..e50f353 --- /dev/null +++ b/debian/leaff.docs @@ -0,0 +1 @@ +README.leaff diff --git a/debian/leaff.install b/debian/leaff.install new file mode 100644 index 0000000..341d21a --- /dev/null +++ b/debian/leaff.install @@ -0,0 +1 @@ +installdir/bin/leaff usr/bin diff --git a/debian/rules b/debian/rules index 63d2482..d168a9d 100755 --- a/debian/rules +++ b/debian/rules @@ -9,7 +9,10 @@ CXXFLAGS:=$(CPPFLAGS) $(CXXFLAGS) # The trailing slashes are very important to the build system subdirectories:= $(filter-out debian/, $(shell ls -d */)) -meryl:= libbio/ libkmer/ libmeryl/ libseq/ libutil/ meryl/ + +# Reference for unusable modules: +# https://lists.debian.org/debian-med/2015/05/msg00075.html +unusable:= tapper/ trie/ %: dh $@ @@ -18,10 +21,10 @@ override_dh_auto_build: # The Makefile apparently doesn't use regular LDFLAGS. # It defines CLDFLAGS and CXXLDFLAGS as empty strings, so let's # use them here. - $(MAKE) \ - CLDFLAGS="$(LDFLAGS)" \ - CXXLDFLAGS="$(LDFLAGS)" \ - WITHOUT="$(filter-out $(meryl), $(subdirectories))" install + $(MAKE) install \ + CLDFLAGS="$(LDFLAGS)" \ + CXXLDFLAGS="$(LDFLAGS)" +# WITHOUT="$(unusable)" ln -sf $(shell uname)-* installdir override_dh_auto_clean: diff --git a/debian/sim4db.docs b/debian/sim4db.docs new file mode 100644 index 0000000..2d7c735 --- /dev/null +++ b/debian/sim4db.docs @@ -0,0 +1 @@ +README.sim4db diff --git a/debian/sim4db.install b/debian/sim4db.install new file mode 100644 index 0000000..d9b3961 --- /dev/null +++ b/debian/sim4db.install @@ -0,0 +1,27 @@ +installdir/bin/sim4db usr/bin +# sim4dbutils +installdir/bin/filterPolishes usr/bin +installdir/bin/headPolishes usr/bin +installdir/bin/mappedCoverage usr/bin +installdir/bin/mergePolishes usr/bin +installdir/bin/sortPolishes usr/bin +installdir/bin/pickBestPolish usr/bin +installdir/bin/pickBestPair usr/bin +installdir/bin/pickUniquePolish usr/bin +installdir/bin/cleanPolishes usr/bin +installdir/bin/fixPolishesIID usr/bin +installdir/bin/plotCoverageVsIdentity usr/bin +installdir/bin/parseSNP usr/bin +installdir/bin/comparePolishes usr/bin +installdir/bin/convertToAtac usr/bin +installdir/bin/convertToExtent usr/bin +installdir/bin/convertPolishes usr/bin +installdir/bin/depthOfPolishes usr/bin +installdir/bin/detectChimera usr/bin +installdir/bin/uniqPolishes usr/bin +installdir/bin/summarizePolishes usr/bin +installdir/bin/removeDuplicate usr/bin +installdir/bin/vennPolishes usr/bin +installdir/bin/realignPolishes usr/bin +installdir/bin/removeRedundant usr/bin +installdir/bin/reportAlignmentDifferences usr/bin -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/kmer-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
