[med-svn] [kmer] 01/07: new binary package: atac
Afif Elghraoui
afif at moszumanska.debian.org
Sun Dec 4 05:37:27 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a commit to branch master
in repository kmer.
commit f70dc58d0d47c9264221f4d9638006f31ca44673
Author: Afif Elghraoui <afif at debian.org>
Date: Sat Dec 3 16:27:07 2016 -0800
new binary package: atac
---
debian/atac.docs | 1 +
debian/atac.install | 62 +++++++++++++++++++++++++++
debian/atac.manpages | 1 +
debian/control | 37 +++++++++++++++-
debian/man/atac/atac.1 | 33 ++++++++++++++
debian/patches/atac-helper-script-paths.patch | 42 ++++++++++++++++++
debian/patches/atac-readme.patch | 22 ++++++++++
debian/patches/series | 2 +
debian/rules | 3 +-
9 files changed, 200 insertions(+), 3 deletions(-)
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..fa3a712
--- /dev/null
+++ b/debian/atac.install
@@ -0,0 +1,62 @@
+# atac-driver
+installdir/bin/atac /usr/bin
+installdir/bin/makeplot.pl /usr/lib/atac/bin
+
+# atac-driver/alignOverlap
+installdir/bin/overlap /usr/lib/atac/bin
+
+# atac-driver/chimera
+installdir/bin/happy-clones-span-clumps /usr/lib/atac/bin
+
+# atac-driver/gapShifter
+installdir/bin/gapShifter /usr/lib/atac/bin
+installdir/bin/extractSequence /usr/lib/atac/bin
+installdir/bin/extractUnmapped /usr/lib/atac/bin
+installdir/bin/coalesceMatches /usr/lib/atac/bin
+installdir/bin/correctGaps /usr/lib/atac/bin
+installdir/bin/testAtac /usr/lib/atac/bin
+installdir/bin/cleanAtac /usr/lib/atac/bin
+installdir/bin/projectFeatures /usr/lib/atac/bin
+
+
+installdir/bin/lengthFilter /usr/lib/atac/bin
+
+
+installdir/bin/matchExtender /usr/lib/atac/bin
+
+
+installdir/bin/mismatchCounter /usr/lib/atac/bin
+
+
+installdir/bin/statsGenerator /usr/lib/atac/bin
+
+
+installdir/bin/uniqueFilter /usr/lib/atac/bin
+
+
+installdir/bin/clumpMaker /usr/lib/atac/bin
+
+
+# atac-driver/chainer
+installdir/bin/AtacDriver.py /usr/lib/atac/bin
+installdir/lib/AtacDriver.py /usr/lib/atac/lib
+installdir/lib/AtacFile.py /usr/lib/atac/lib
+installdir/lib/DNA.py /usr/lib/atac/lib
+installdir/lib/IdxStore.py /usr/lib/atac/lib
+installdir/lib/MatchRecord.py /usr/lib/atac/lib
+installdir/lib/MyFile.py /usr/lib/atac/lib
+installdir/lib/PerfectRuns.py /usr/lib/atac/lib
+installdir/lib/TrimMatchOverlaps.py /usr/lib/atac/lib
+installdir/lib/UniqueFilter.py /usr/lib/atac/lib
+installdir/lib/dedashMatches.py /usr/lib/atac/lib
+installdir/lib/fillIntraRunGaps.py /usr/lib/atac/lib
+installdir/lib/mkstats.py /usr/lib/atac/lib
+installdir/lib/squeezeIntraRunGaps.py /usr/lib/atac/lib
+installdir/lib/halignmodule.so /usr/lib/atac/lib
+installdir/lib/localAlignerInterfacemodule.so /usr/lib/atac/lib
+
+# seatac
+installdir/bin/seatac /usr/lib/atac/bin
+installdir/bin/heavychains /usr/lib/atac/bin
+installdir/lib/filter-heavychains.so /usr/lib/atac/lib
+installdir/lib/filter-nop.so /usr/lib/atac/lib
diff --git a/debian/atac.manpages b/debian/atac.manpages
new file mode 100644
index 0000000..48c2466
--- /dev/null
+++ b/debian/atac.manpages
@@ -0,0 +1 @@
+debian/man/atac/*.1
diff --git a/debian/control b/debian/control
index 5338572..f71040c 100644
--- a/debian/control
+++ b/debian/control
@@ -3,7 +3,11 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Afif Elghraoui <afif at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 10)
+Build-Depends:
+ debhelper (>= 10),
+# For ATAC
+ dh-python,
+ python-all-dev,
Standards-Version: 3.9.8
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/kmer.git
Vcs-Git: https://anonscm.debian.org/git/debian-med/kmer.git
@@ -15,7 +19,8 @@ Section: metapackages
Depends: ${misc:Depends},
meryl,
leaff,
- sim4db
+ sim4db,
+ atac,
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);
@@ -109,3 +114,31 @@ 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: atac
+Architecture: any
+Depends:
+ ${shlibs:Depends},
+ ${misc:Depends},
+ ${python:Depends},
+ ${perl:Depends},
+ libfile-which-perl,
+ 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/man/atac/atac.1 b/debian/man/atac/atac.1
new file mode 100644
index 0000000..04ecab1
--- /dev/null
+++ b/debian/man/atac/atac.1
@@ -0,0 +1,33 @@
+.TH ATAC 1 "November 2016"
+.SH NAME
+atac \- comparative mapping between genome sequences
+.SH SYNOPSIS
+.B atac
+.BI -meryldir \0alignment_cache_dir
+.BI -dir \0result_dir
+.BI -id1 \0seqid1
+.BI -seq1 \0seqfile1.fasta
+.BI -id2 \0seqid2
+.BI -seq2 \0seqfile2.fasta
+.SH DESCRIPTION
+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.
+.SH OPTIONS
+Run with no options for a list of parameters.
+.SH SEE ALSO
+.BR leaff (1),
+.br
+/usr/share/doc/atac/README.atac
+.br
+http://kmer.sourceforge.net/wiki/index.php/Getting_Started_with_ATAC
diff --git a/debian/patches/atac-helper-script-paths.patch b/debian/patches/atac-helper-script-paths.patch
new file mode 100644
index 0000000..966ca13
--- /dev/null
+++ b/debian/patches/atac-helper-script-paths.patch
@@ -0,0 +1,42 @@
+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 debian.org>
+Forwarded: not-needed
+Last-Update: 2016-11-30
+--- kmer-tools.orig/atac-driver/atac.pl
++++ kmer-tools/atac-driver/atac.pl
+@@ -20,6 +20,7 @@
+
+ use strict;
+ use FindBin;
++use File::Which;
+
+ my $id1 = undef;
+ my $seq1 = undef;
+@@ -30,8 +31,8 @@
+ my $GENOMEdir = "default"; # Location of genome assemblies
+ my $MERYLdir = "default"; # Location of genome mercount databases
+
+-my $BINdir = "$FindBin::Bin";
+-my $LIBdir = "$FindBin::Bin/../lib";
++my $BINdir = "$FindBin::Bin/../lib/atac/bin";
++my $LIBdir = "$FindBin::Bin/../lib/atac/lib";
+
+ my $mersize = 20; # the mer size
+ my $minfill = 20; # the mimimum fill for a reported match.
+@@ -56,9 +57,9 @@
+
+ # Check that we have everything we need to run
+ #
+-my $leaff = "$BINdir/leaff";
+-my $meryl = "$BINdir/meryl";
+-my $existDB = "$BINdir/existDB";
++my $leaff = which("leaff");
++my $meryl = which("meryl");
++my $existDB = which("existDB");
+ my $seatac = "$BINdir/seatac";
+ my $chainer = "$BINdir/AtacDriver.py";
+ my $correctgaps = "$BINdir/correctGaps";
diff --git a/debian/patches/atac-readme.patch b/debian/patches/atac-readme.patch
new file mode 100644
index 0000000..1d1d4aa
--- /dev/null
+++ b/debian/patches/atac-readme.patch
@@ -0,0 +1,22 @@
+Description: Fix typo and adjust script name
+ The debian package uses the executable "atac" rather than "atac.pl".
+Author: Afif Elghraoui <afif at debian.org>
+Forwarded: no
+Last-Update: 2016-11-03
+--- kmer-tools.orig/README.atac
++++ kmer-tools/README.atac
+@@ -1,4 +1,4 @@
+-atac - assembly-to-assembly comparasion, comparative mapping between
++atac - assembly-to-assembly comparison, comparative mapping between
+ two genome assemblies (same species), or between two different
+ genomes (cross species).
+
+@@ -44,7 +44,7 @@
+
+ A simple invocation:
+
+-atac.pl \
++atac \
+ -dir ecoli-k-vs-o \
+ -meryldir atac-sequences \
+ -id1 K -seq2 /data/references/ecolik12.fasta \
diff --git a/debian/patches/series b/debian/patches/series
index afabe74..a717064 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1 +1,3 @@
allow-freebsd-build.patch
+atac-helper-script-paths.patch
+atac-readme.patch
diff --git a/debian/rules b/debian/rules
index 4f0bed0..a7af23d 100755
--- a/debian/rules
+++ b/debian/rules
@@ -18,7 +18,7 @@ unusable:= tapper/ trie/
# Note: Parallel build is not reliable
%:
- dh $@
+ dh $@ --with python2
override_dh_auto_build:
# The Makefile apparently doesn't use regular LDFLAGS.
@@ -28,6 +28,7 @@ override_dh_auto_build:
CLDFLAGS="$(LDFLAGS)" \
CXXLDFLAGS="$(LDFLAGS)"
# WITHOUT="$(unusable)"
+ mv installdir/bin/atac.pl installdir/bin/atac
override_dh_auto_clean:
$(MAKE) real-clean
--
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