[med-svn] [kmer-tools] 01/01: Draft packaging for ATAC and ESTMapper

[Afif Elghraoui]

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afif-guest pushed a commit to branch topic/atac-and-est
in repository kmer-tools.

commit 5ae2c5fd941a83112d7ae02076d4ce555789544a
Author: Afif Elghraoui <afif at ghraoui.name>
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 <debian-med-packaging at lists.alioth.debian.
 Uploaders: Afif Elghraoui <afif at ghraoui.name>
 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 <afif at ghraoui.name>
+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

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