This is an automated email from the git hooks/post-receive script. afif-guest pushed a commit to branch topic/atac-and-est in repository kmer-tools.
commit 5ae2c5fd941a83112d7ae02076d4ce555789544a Author: Afif Elghraoui <[email protected]> Date: Fri Jan 1 23:28:02 2016 -0800 Draft packaging for ATAC and ESTMapper --- debian/atac.docs | 1 + debian/atac.install | 16 ++++++++++ debian/control | 42 +++++++++++++++++++++++++++ debian/estmapper.install | 3 ++ debian/patches/atac-helper-script-paths.patch | 30 +++++++++++++++++++ debian/patches/series | 1 + 6 files changed, 93 insertions(+) diff --git a/debian/atac.docs b/debian/atac.docs new file mode 100644 index 0000000..b030bf2 --- /dev/null +++ b/debian/atac.docs @@ -0,0 +1 @@ +README.atac diff --git a/debian/atac.install b/debian/atac.install new file mode 100644 index 0000000..6ffa59e --- /dev/null +++ b/debian/atac.install @@ -0,0 +1,16 @@ +installdir/bin/atac.pl usr/bin +installdir/bin/AtacDriver.py usr/bin +installdir/bin/cleanAtac usr/bin +installdir/bin/clumpMaker usr/bin + +installdir/bin/correctGaps usr/lib/atac +installdir/bin/statsGenerator usr/lib/atac +installdir/bin/makeplot.pl usr/lib/atac + +# From seatac subdir +installdir/bin/seatac usr/bin +installdir/bin/heavychains usr/bin + +# +installdir/lib/filter-heavychains.so usr/lib/atac + diff --git a/debian/control b/debian/control index d4611b5..ae6dfc6 100644 --- a/debian/control +++ b/debian/control @@ -5,6 +5,8 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Afif Elghraoui <[email protected]> Build-Depends: debhelper (>= 9), +# For ATAC + python-all-dev, Standards-Version: 3.9.6 Homepage: http://kmer.sourceforge.net Vcs-Git: git://anonscm.debian.org/debian-med/kmer-tools.git @@ -114,3 +116,43 @@ Description: batch spliced alignment of cDNA sequences to a target genome presented either as custom sim4db alignments or as GFF3 gene features. . This package is part of the Kmer suite. + +Package: estmapper +Architecture: any +Depends: + ${shlibs:Depends}, + ${misc:Depends}, +Description: biological sequence library utilities and applications + ESTmapper is a software package for the high-throughput alignment of large + cDNA (EST, mRNA) sequence sets to a large eukaryotic genome of the same + species. It can also be used to map relatively short DNA segments, such as + sequencing reads or SNP flanking sequences, to the genome. + . + This package is part of the Kmer suite. + +Package: atac +Architecture: any +Depends: + ${shlibs:Depends}, + ${misc:Depends}, + ${perl:Depends}, + ${python:Depends}, + leaff, + meryl, + gnuplot, +Description: genome assembly-to-assembly comparison + atac computes a one-to-one pairwise alignment of large DNA sequences. It first + finds the unique k-mers in each sequence, chains them to larger blocks, and + fills in spaces between blocks. It was written primarily to transfer + annotations between different assemblies of the human genome. + . + The output is a set of ungapped 'matches', and a set of gapped 'runs' formed + from the matches. Each match or run associates one sequence with the other + sequence. The association is 'unique', in that there is no other (sizeable) + associations for either sequence. Thus, large repeats and duplications are not + present in the output - they appear as unmapped regions. + . + Though the output is always pairwise, atac can cache intermediate results to + speed a comparisons of multiple sequences. + . + This package is part of the Kmer suite. diff --git a/debian/estmapper.install b/debian/estmapper.install new file mode 100644 index 0000000..fc3f8fd --- /dev/null +++ b/debian/estmapper.install @@ -0,0 +1,3 @@ +installdir/bin/ESTmapper.pl usr/bin +# From seagen/ +installdir/bin/seagen usr/bin diff --git a/debian/patches/atac-helper-script-paths.patch b/debian/patches/atac-helper-script-paths.patch new file mode 100644 index 0000000..797bade --- /dev/null +++ b/debian/patches/atac-helper-script-paths.patch @@ -0,0 +1,30 @@ +Description: Adjust paths for helper scripts to be found + ATAC uses some generically named scripts (like "makeplots") that + can't sensibly be placed in /usr/bin. We put them instead in + /usr/lib/atac and adjust the driver script to be able to find them + there. +Author: Afif Elghraoui <[email protected]> +Forwarded: not-needed +Last-Update: 2016-01-01 +--- kmer-tools.orig/atac-driver/atac.pl ++++ kmer-tools/atac-driver/atac.pl +@@ -31,7 +31,7 @@ + my $MERYLdir = "default"; # Location of genome mercount databases + + my $BINdir = "$FindBin::Bin"; +-my $LIBdir = "$FindBin::Bin/../lib"; ++my $LIBdir = "$FindBin::Bin/../lib/atac"; + + my $mersize = 20; # the mer size + my $minfill = 20; # the mimimum fill for a reported match. +@@ -62,8 +62,8 @@ + my $seatac = "$BINdir/seatac"; + my $chainer = "$BINdir/AtacDriver.py"; + my $correctgaps = "$BINdir/correctGaps"; +-my $statsgenerator = "$BINdir/statsGenerator"; +-my $makeplot = "perl $BINdir/makeplot.pl"; ++my $statsgenerator = "$LIBdir/statsGenerator"; ++my $makeplot = "perl $LIBdir/makeplot.pl"; + + die "Can't run $leaff\n" if (! -x $leaff); + die "Can't run $meryl\n" if (! -x $meryl); diff --git a/debian/patches/series b/debian/patches/series new file mode 100644 index 0000000..d49f297 --- /dev/null +++ b/debian/patches/series @@ -0,0 +1 @@ +atac-helper-script-paths.patch -- 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
